Scientific publications

Trends in Salmonella Dublin over time in Denmark from food and animal related isolates
Leekitcharoenphon et al. 2023

Salmonella enterica serovar Dublin is highly adapted to cattle and a relatively rare cause of human infections. In Denmark S. Dublin has been endemic in the cattle population for many years. A national surveillance program in the cattle population was established at herd-level to reduce the occurrence of S. Dublin. In this study, we analyzed 421 S. Dublin genomes from cattle and food in order to determine the trend of S. Dublin's population size over time in Denmark and the impact of intervention in the cattle industry on the bacterial population size. A phylogenetic tree based on SNPs exhibited two major clades and one small cluster.

DOI: https://doi.org/10.1016/j.meegid.2023.105475 07 July 2023

Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants
Mäkelä et al. 2023

The emergence of increasingly immunoevasive SARS-CoV-2 variants emphasizes the need for prophylactic strategies to complement vaccination in fighting the COVID-19 pandemic. Intranasal administration of neutralizing antibodies has shown encouraging protective potential but there remains a need for SARS-CoV-2 blocking agents that are less vulnerable to mutational viral variation and more economical to produce in large scale. Here we describe TriSb92, a highly manufacturable and stable trimeric antibody-mimetic sherpabody targeted against a conserved region of the viral spike glycoprotein.

DOI: https://doi.org/10.1038/s41467-023-37290-6 22 March 2023

SARS-CoV-2 and type 1 diabetes in children in Finland: an observational study
Knip et al. 2023

Some epidemiological studies have suggested an increase in incidence of type 1 diabetes during the COVID-19 pandemic, however the mechanism(s) behind such an increase have yet to be identified. In this study we aimed to evaluate the possible role of the SARS-CoV-2 virus in the reported increase in the rate of type 1 diabetes.

DOI: https://doi.org/10.1016/S2213-8587(23)00041-4 21 March 2023

Dynamics of social media behavior before and after SARS-CoV-2 infection
Durazzi et al. 2023

Online social media have been both a field of research and a source of data for research since the beginning of the COVID-19 pandemic. In this study, we aimed to determine how and whether the content of tweets by Twitter users reporting SARS-CoV-2 infections changed over time.

DOI: https://doi.org/10.3389/fpubh.2022.1069931 23 February 2023

Timeliness of online COVID-19 reports from official sources
Espinoza et al. 2023

Making epidemiological indicators for COVID-19 publicly available through websites and social media can support public health experts in the near-real-time monitoring of the situation worldwide, and in the establishment of rapid response and public health measures to reduce the consequences of the pandemic. Little is known, however, about the timeliness of such sources. Here, we assess the timeliness of official public COVID-19 sources for the WHO regions of Europe and Africa.

DOI: https://doi.org/10.3389/fpubh.2022.1027812 23 January 2023

West Nile Virus in Culex Mosquitoes in Central Macedonia, Greece, 2022
Tsioka et al. 2023

In 2022, Greece was the second most seriously affected European country in terms of the West Nile virus (WNV), after Italy. Specifically, Central Macedonia was the region with the most reported human cases (81.5%). In the present study, 30,816 female Culex pipiens sensu lato mosquitoes were collected from May to September 2022 in the seven regional units of Central Macedonia; they were then grouped into 690 pools and tested for WNV, while next-generation sequencing was applied to the samples, which showed a cycle threshold of Ct < 30 in a real-time RT-PCR test.

DOI: https://doi.org/10.3390/v15010224 13 January 2023

Normalisation of SARS-CoV-2 concentrations in wastewater: The use of flow, electrical conductivity and crAssphage
Langeveld et al. 2022

Over the course of the Corona Virus Disease-19 (COVID-19) pandemic in 2020–2022, monitoring of the severe acute respiratory syndrome coronavirus 2 ribonucleic acid (SARS-CoV-2 RNA) in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic.

DOI: https://doi.org/10.1016/j.scitotenv.2022.161196 26 December 2022

Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
Munk et al. 2022

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation.

DOI: https://doi.org/10.1038/s41467-022-34312-7 01 December 2022

Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining
Clausen 2022

The neighbor-joining (NJ) algorithm is a widely used method to perform iterative clustering and forms the basis for phylogenetic reconstruction in several bioinformatic pipelines. Although NJ is considered to be a computationally efficient algorithm, it does not scale well for datasets exceeding several thousand taxa (>100 000). Optimizations to the canonical NJ algorithm have been proposed; these optimizations are, however, achieved through approximations or extensive memory usage, which is not feasible for large datasets. In this article, two new algorithms, dynamic neighbor joining (DNJ) and heuristic neighbor joining (HNJ), are presented, which optimize the canonical NJ method to scale to millions of taxa without increasing the memory requirements. Both DNJ and HNJ outperform the current gold standard methods to construct NJ trees, while DNJ is guaranteed to produce exact NJ trees.

DOI: https://doi.org/10.1093/bioinformatics/btac774 01 December 2022

Modeling the impact of surveillance activities combined with physical distancing interventions on COVID-19 epidemics at a local level
Chen et al. 2022

Physical distancing and contact tracing are two key components in controlling the COVID-19 epidemics. Understanding their interaction at local level is important for policymakers. We propose a flexible modeling framework to assess the effect of combining contact tracing with different physical distancing strategies. Using scenario tree analyses, we compute the probability of COVID-19 detection using passive surveillance, with and without contact tracing, in metropolitan Barcelona.

DOI: https://doi.org/10.1016/j.idm.2022.11.001 17 November 2022

Prevalence, Infectious Characteristics and Genetic Diversity of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus (MRSA) in Two Raw-Meat Processing Establishments in Northern Greece
Komodromos et al. 2022

In the present study, we investigated the isolation frequency, the genetic diversity, and the infectious characteristics of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) from the incoming meat and the meat products, the environment, and the workers’ nasal cavities, in two meat-processing establishments in northern Greece. The isolated S. aureus strains were examined for their resistance to antimicrobials, carriage of the mecA and mecC genes, carriage of genes encoding for the production of nine staphylococcal enterotoxins, carriage of the Panton–Valentine Leukocidin and Toxic Shock Syndrome genes, and the ability to form biofilm.

DOI: https://doi.org/10.3390/pathogens11111370 17 November 2022

Evaluation of the use of alternative sample types for mosquito-borne flavivirus surveillance: Using Usutu virus as a model
Atama et al. 2022

Wild birds are reservoirs of several zoonotic arboviruses including West Nile virus (WNV) and Usutu virus (USUV), and are often monitored as indicators for virus introduction and spread. To optimize the bird surveillance for arboviruses in the Netherlands and to explore the possibilities for citizen science in surveillance, we investigated the suitability of using alternative sample types from live and dead birds.

DOI: https://doi.org/10.1016/j.onehlt.2022.100456 13 November 2022

West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers
Lu et al. 2022

Spread and emergence of West Nile virus (WNV) in Europe have been very different from those observed in North America. Here, we describe key drivers by combining viral genome sequences with epidemiological data and possible factors of spread into phylodynamic models. WNV in Europe has greater lineage diversity than other regions of the world, suggesting repeated introductions and local amplification.

DOI: https://doi.org/10.1101/2022.11.10.515886 12 November 2022

Rapid spread of a new West Nile virus lineage 1 associated with increased risk of neuroinvasive disease during a large outbreak in Italy in 2022
Barzon et al. 2022

A new strain of West Nile virus lineage 1 (WNV-1) emerged in the Veneto Region, northern Italy, in 2021, 8 years after the last WNV-1 outbreak in Italy. The virus, which co-circulates with West Nile virus lineage 2 (WNV-2), has become endemic in the region, where, in 2022, most human cases of neuroinvasive disease (WNND) reported in Europe have occurred.

DOI: https://doi.org/10.1093/jtm/taac125 04 November 2022

Canine Saliva as a Possible Source of Antimicrobial Resistance Genes
Tóth et al. 2022

While the One Health issues of intensive animal farming are commonly discussed, keeping companion animals is less associated with the interspecies headway of antimicrobial resistance. With the constant advance in veterinary standards, antibiotics are regularly applied in companion animal medicine. Due to the close coexistence of dogs and humans, dog bites and other casual encounters with dog saliva (e.g., licking the owner) are common. According to our metagenome study, based on 26 new generation sequencing canine saliva datasets from 2020 and 2021 reposited in NCBI SRA by The 10,000 Dog Genome Consortium and the Broad Institute within Darwin’s Ark project, canine saliva is rich in bacteria with predictably transferable antimicrobial resistance genes (ARGs).

DOI: https://doi.org/10.3390/antibiotics11111490 27 October 2022

Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America
Günther et al. 2022

Highly pathogenic avian influenza viruses (HPAIVs) of hemagglutinin type H5 and clade 2.3.4.4b have widely spread within the northern hemisphere since 2020 and threaten wild bird populations, as well as poultry production. We present phylogeographic evidence that Iceland has been used as a stepping stone for HPAIV translocation from northern Europe to North America by infected but mobile wild birds. At least 2 independent incursions of HPAIV H5N1 clade 2.3.4.4b assigned to 2 hemagglutinin clusters, B1 and B2, are documented for summer‒autumn 2021 and spring 2022. Spread of HPAIV H5N1 to and among colony-breeding pelagic avian species in Iceland is ongoing.

DOI: https://doi.org/10.3201/eid2812.221086 19 October 2022

An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany
Santos et al. 2022

West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual, inconsistent, and the use of names for different levels of the hierarchical levels is unstructured.

DOI: https://doi.org/10.1101/2022.10.05.509209 Posted 07 October 2022

Nanobody engineering for SARS-CoV-2 neutralization and detection
Hannula et al. 2022

In response to the ongoing SARS-CoV-2 pandemic, the quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, ‘nanobodies’. Here, we explore the potential of nanobody engineering in the development of antivirals and diagnostic tools. Through fusion of nanobody domains that target distinct binding sites, we engineered multimodular nanobody constructs that neutralize wild-type SARS-CoV-2 and the Alpha and Delta variants with high potency, with IC50 values up to 50 pM. However, we observed a limitation in the efficacy of multimodular nanobodies against the Beta (B.1.351) and Omicron variants (B.1.1.529), underlining the importance of accounting for viral evolution in the design of biologics.

DOI: https://doi.org/10.1101/2022.09.14.507920 Posted 05 October 2022

Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states
Papp et al. 2022

As pollinators and producers of numerous human-consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their body’s functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. Regarding bacteriome composition, a significant difference was found between the samples from March and May. The samples’ bacteriome from March showed a significant composition difference between cooler and warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriomes in honey bees varies depending on the climatic and seasonal conditions.

DOI: https://doi.org/10.1371/journal.pone.0273844 09 September 2022

Image-based & machine learning-guided multiplexed serology test for SARS-CoV-2
Pietiäinen et al. 2022

Here, we describe a scalable and automated, high-content microscopy -based mini-immunofluorescence assay (mini-IFA) for serological testing i.e., detection of antibodies. Unlike conventional IFA, which often relies on the use of cells infected with the target pathogen, our assay employs transfected cells expressing individual viral antigens.

DOI: https://doi.org/10.1101/2022.09.08.22279729 Posted 09 September 2022

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome
Martiny et al. 2022

The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data. We retrieved 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive (ENA) and aligned them using a uniform approach against ARGs and 16S/18S rRNA genes. Here, we present the results of this extensive computational analysis and share the counts of reads aligned.

DOI: https://doi.org/10.1371/journal.pbio.3001792 06 September 2022

Connect to Protect: Dynamics and Genetic Connections of Highly Pathogenic Avian Influenza Outbreaks in Poultry from 2016 to 2021 in Germany
King et al. 2022

During autumn/winter in 2016–2017 and 2020–2021, highly pathogenic avian influenza viruses (HPAIV) caused severe outbreaks in Germany and Europe. Multiple clade 2.3.4.4b H5 HPAI subtypes were responsible for increased mortality in wild birds and high mortality and massive losses in the poultry sector. To clarify putative entry sources and delineate interconnections between outbreaks in poultry holdings and wild birds, we applied whole-genome sequencing and phylodynamic analyses combined with the results of epidemiological outbreak investigations.

DOI: https://doi.org/10.3390/v14091849 23 August 2022

Risks of SARS-CoV-2 transmission between free-ranging animals and captive mink in the Netherlands
Sikkema et al. 2022

In the Netherlands, 69 of the 126 (55%) mink farms in total became infected with SARS-CoV-2 in 2020. Despite strict biosecurity measures and extensive epidemiological investigations, the main transmission route remained unclear. A better understanding of SARS-CoV-2 transmission between mink farms is of relevance for countries where mink farming is still common practice and can be used as a case study to improve future emerging disease preparedness. We assessed whether SARS-CoV-2 spilled over from mink to free-ranging animals, and whether free-ranging animals may have played a role in farm-to-farm transmission in the Netherlands.

DOI: https://doi.org/10.1111/tbed.14686 21 August 2022

Circulating microRNA signatures associated with disease severity and outcome in COVID-19 patients
Giannella et al. 2022

SARS-CoV-2 induces a spectrum of clinical conditions ranging from asymptomatic infection to life threatening severe disease. Host microRNAs have been involved in the cytokine storm driven by SARS-CoV-2 infection and proposed as candidate biomarkers for COVID-19.

DOI: https://doi.org/10.3389/fimmu.2022.968991 11 August 2022

Sindbis virus outbreak and evidence for geographical expansion in Finland, 2021
Suvanto et al. 2022

Sindbis virus (SINV) caused a large outbreak in Finland in 2021 with 566 laboratory-confirmed human cases and a notable geographical expansion. Compared with the last large outbreak in 2002, incidence was higher in several hospital districts but lower in traditionally endemic locations in eastern parts of the country.

DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.31.2200580 04 August 2022

Integrating Global Citizen Science Platforms to Enable Next-Generation Surveillance of Invasive and Vector Mosquitoes
Carney et al. 2022

Mosquito-borne diseases continue to ravage humankind with >700 million infections and nearly one million deaths every year. Yet only a small percentage of the >3500 mosquito species transmit diseases, necessitating both extensive surveillance and precise identification. Unfortunately, such efforts are costly, time-consuming, and require entomological expertise. As envisioned by the Global Mosquito Alert Consortium, citizen science can provide a scalable solution.

DOI: https://doi.org/10.3390/insects13080675 27 July 2022

Sotrovimab resistance and viral persistence after treatment of immunocompromised patients infected with the SARS-CoV-2 Omicron variant
Huygens et al. 2022

Viral evolution was evaluated in 47 immunocompromised patients treated with sotrovimab. Sequencing of SARS-CoV-2 following therapy was successful in 16. Mutations associated with sotrovimab resistance were documented in 6, viral replication continued after 30 days in 5. Combination antibody therapy may be required to avoid acquired resistance in immunocompromised patients.

DOI: https://doi.org/10.1093/cid/ciac601 22 July 2022

Early start of seasonal transmission and co-circulation of West Nile virus lineage 2 and a newly introduced lineage 1 strain, northern Italy, June 2022
Barzon et al. 2022

In 2022, the start of West Nile virus (WNV) activity in Europe was demonstrated as early as the beginning of June in the Veneto region, north-eastern Italy. We describe here WNV infections detected in mosquitoes, birds, and humans up to 8 July 2022 in the region, where a newly introduced WNV lineage 1 (WNV-1) strain co-circulated with WNV lineage 2. Phylogenetic analysis of full genome sequences of WNV-1 and WNV-2 detected in 2021 and 2022 is also reported.

DOI: https://doi.org/10.2807/1560-7917.ES.2022.27.29.2200548 21 July 2022

Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021
Caliendo et al. 2022

Highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage (GsGd), which threaten the health of poultry, wildlife and humans, are spreading across Asia, Europe, Africa and North America but are currently absent from South America and Oceania. In December 2021, H5N1 HPAI viruses were detected in poultry and a free-living gull in St. John’s, Newfoundland and Labrador, Canada. Our phylogenetic analysis showed that these viruses were most closely related to HPAI GsGd viruses circulating in northwestern Europe in spring 2021.

DOI: https://doi.org/10.1038/s41598-022-13447-z 11 July 2022

Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct
Myktyn et al. 2022

The emergence and rapid spread of SARS-CoV-2 variants may impact vaccine efficacy significantly. The Omicron variant termed BA.2, which differs substantially from BA.1 based on genetic sequence, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed. Here, we used antigenic cartography to quantify and visualize antigenic differences between early SARS-CoV-2 variants (614G, Alpha, Beta, Gamma, Zeta, Delta and Mu) using hamster antisera obtained after primary infection. We first verified that the choice of the cell line for the neutralization assay did not affect the topology of the map substantially. Antigenic maps generated using pseudotyped SARS-CoV-2 on the widely used VeroE6 cell line and the human airway cell line Calu-3 generated similar maps. Maps made using authentic SARS-CoV-2 on Calu-3 cells also closely resembled those generated with pseudotyped viruses. The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped based on mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers.

DOI: https://doi.org/10.1126/sciimmunol.abq4450 23 June 2022

Has Epizootic Become Enzootic? Evidence for a Fundamental Change in the Infection Dynamics of Highly Pathogenic Avian Influenza in Europe, 2021
Pohlmann et al. 2022

Phylogenetic evidence from the recent resurgence of high-pathogenicity avian influenza (HPAI) virus subtype H5N1, clade 2.3.4.4b, observed in European wild birds and poultry since October 2021, suggests at least two different and distinct reservoirs. We propose contrasting hypotheses for this emergence: (i) resident viruses have been maintained, presumably in wild birds, in northern Europe throughout the summer of 2021 to cause some of the outbreaks that are part of the most recent autumn/winter 2021 epizootic, or (ii) further virus variants were reintroduced by migratory birds, and these two sources of reintroduction have driven the HPAI resurgence.

DOI: https://doi.org/10.1128/mbio.00609-22 21 June 2022

One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings
Rebelo et al. 2022

Antimicrobial susceptibility testing (AST) should be fast and accurate, leading to proper interventions and therapeutic success. Clinical microbiology laboratories rely on phenotypic methods, but the continuous improvement and decrease in the cost of whole-genome sequencing (WGS) technologies make them an attractive alternative. Studies evaluating the performance of WGS-based prediction of antimicrobial resistance (AMR) for selected bacterial species have shown promising results. There are, however, significant gaps in the literature evaluating the applicability of WGS as a diagnostics method in real-life clinical settings against the range of bacterial pathogens experienced there. Thus, we compared standard phenotypic AST results with WGS-based predictions of AMR profiles in bacterial isolates without preselection of defined species, to evaluate the applicability of WGS as a diagnostics method in clinical settings.

DOI: https://doi.org/10.3389/fmicb.2022.804627 10 June 2022

Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history
Lavezzo et al. 2022

The continuous emergence of SARS-CoV-2 variants of concern (VOC) with immune escape properties, such as Delta (B.1.617.2) and Omicron (B.1.1.529), questions the extent of the antibody-mediated protection against the virus. Here we investigated the long-term antibody persistence in previously infected subjects and the extent of the antibody-mediated protection against B.1, B.1.617.2 and BA.1 variants in unvaccinated subjects previously infected, vaccinated naïve and vaccinated previously infected subjects.

DOI: https://doi.org/10.1186/s13073-022-01066-2 10 June 2022

The phylodynamics of SARS-CoV-2 during 2020 in Finland
Nguyen et al. 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus.

DOI: https://doi.org/10.1038/s43856-022-00130-7 10 June 2022

Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression
Ruggiero et al. 2022

The DNA secondary structures that deviate from the classic Watson and Crick base pairing are increasingly being reported to form transiently in the cell and regulate specific cellular mechanisms. Human viruses are cell parasites that have evolved mechanisms shared with the host cell to support their own replication and spreading. Contrary to human host cells, viruses display a diverse array of nucleic acid types, which include DNA or RNA in single-stranded or double-stranded conformations. This heterogeneity improves the possible occurrence of non-canonical nucleic acid structures.

DOI: https://doi.org/10.3389/fmicb.2022.915069 01 June 2022

Mosquito alert: leveraging citizen science to create a GBIF mosquito occurrence dataset
Južnič-Zonta et al. 2022

The Mosquito Alert dataset includes occurrence records of adult mosquitoes collected worldwide in 2014–2020 through Mosquito Alert, a citizen science system for investigating and managing disease-carrying mosquitoes. Records are linked to citizen science-submitted photographs and validated by entomologists to determine the presence of five targeted European mosquito vectors: Aedes albopictus, Ae. aegypti, Ae. japonicus, Ae. koreicus, and Culex pipiens.

DOI: https://doi.org/10.46471/gigabyte.54 30 May 2022

ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies
Plyusnin et al. 2022

SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in-depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance.

DOI: https://doi.org/10.1186/s12859-022-04709-8 28 May 2022

Experimental Infection of Mink with SARS-COV-2 Omicron Variant and Subsequent Clinical Disease
Virtanen et al. 2022

We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that mink remain positive for viral RNA for days, experience clinical signs and histopathologic changes, and transmit the virus to uninfected recipients. Preparedness is crucial to avoid spread among mink and spillover to human populations.

DOI: https://doi.org/10.3201/eid2806.220328 13 May 2022

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection
Gittelman et al. 2022

T cells play a prominent role in orchestrating the immune response to viral diseases, but their role in the clinical presentation and subsequent immunity to SARS-CoV-2 infection remains poorly understood. As part of a population-based survey of the municipality of Vo’, Italy, conducted after the initial SARS-CoV-2 outbreak, we sampled the T cell receptor (TCR) repertoires of the population 2 months after the initial PCR survey and followed up positive cases 9 and 15 months later. At 2 months, we found that 97.0% (98 of 101) of cases had elevated levels of TCRs associated with SARS-CoV-2. T cell frequency (depth) was increased in individuals with more severe disease.

DOI: https://doi.org/10.1172/jci.insight.151849 19 April 2022

Highly pathogenic avian influenza virus incursions of subtype H5N8, H5N5, H5N1, H5N4, and H5N3 in Germany during 2020-21
King et al. 2022

From October 2020 to July 2021, five different subtypes (H5N8, H5N5, H5N1, H5N4, and H5N3) and seven genotypes of highly pathogenic avian influenza viruses (HPAIV) belonging to clade 2.3.4.4b were detected in a broad array of avian hosts in Germany.

DOI: https://doi.org/10.1093/ve/veac035 13 April 2022

History and classification of Aigai virus (formerly Crimean–Congo haemorrhagic fever virus genotype VI)
Papa et al. 2022

Crimean–Congo haemorrhagic fever virus (CCHFV) is the medically most important member of the rapidly expanding bunyaviral family Nairoviridae. Traditionally, CCHFV isolates have been assigned to six distinct genotypes. Here, the International Committee on Taxonomy of Viruses (ICTV) Nairoviridae Study Group outlines the reasons for the recent decision to re-classify genogroup VI (aka Europe-2 or AP-92-like) as a distinct virus, Aigai virus (AIGV).

DOI: https://doi.org/10.1099/jgv.0.001734 full paper 12 April 2022

Introduction and Rapid Spread of SARS-CoV-2 Omicron Variant and Dynamics of BA.1 and BA.1.1 Sublineages, Finland, December 2021
Vauhkonen et al. 2022

Multiple introductions of SARS-COV-2 Omicron variant BA.1 and BA.1.1. lineages to Finland were detected in early December 2021. Within 3 weeks, Omicron overtook Delta as the most common variant in the capital region. Sequence analysis demonstrated the emergence and spread through community transmission of a large cluster of BA.1.1 virus.

DOI: https://doi.org/10.3201/eid2806.220515 04 April 2022

Antimicrobial resistance determinants in silage
Nagy et al. 2022

Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer’s body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have?

DOI: https://doi.org/10.1038/s41598-022-09296-5 28 March 2022

Changes in molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in the intensive care units of a Greek hospital, 2018–2021
Zarras et al. 2022

The spread of multi-drug resistant (MDR) Gram-negative bacteria, including Klebsiella pneumoniae, constitutes a global threat. The most frequent mechanism of acquired carbapenem resistance is the production of carbapenemases, especially KPC, NDM, VIM, IMP and OXA-48. We analyzed the epidemiological trend of carbapenem resistance genes of carbapenem-resistant K. pneumoniae (CRKP) strains isolated from critically ill patients in a Greek tertiary hospital.

DOI: https://doi.org/10.1556/030.2022.01715 17 March 2022

Detection and molecular characterization of West Nile virus in Culex pipiens mosquitoes in Central Macedonia, Greece, 2019–2021
Tsioka et al. 2022

Since 2010 when West Nile virus (WNV) emerged in Greece, it causes seasonal outbreaks of human infections almost every year. During May-October of 2019–2021 a total number of 51,504 Culex pipiens mosquitoes were trapped in all seven regional units of Central Macedonia in northern Greece. They were grouped into 1099 pools and tested for WNV. The virus was detected in 5% of the mosquito pools (1.5%, 3.6% and 9.6% pools in 2019, 2020, and 2021, respectively), with significant rate differences among the regional units and years.

DOI: https://doi.org/10.1016/j.actatropica.2022.106391 07 March 2022

Infections with highly pathogenic avian influenza A virus (HPAIV) H5N8 in harbor seals at the German North Sea coast, 2021
Postel et al. 2022

In brain tissue of three harbor seals of the German North Sea coast, high virus loads of highly pathogenic avian influenza virus (HPAIV) H5N8 were detected. Identification of different virus variants indicates high exposure to HPAIV circulating in wild birds, but there is no evidence for H5 specific antibodies in healthy seals.

DOI: https://doi.org/10.1080/22221751.2022.2043726 01 March 2022

Early initiation of the respiratory syncytial virus season in 2021–2022, Greece
Pappa et al. 2022

Respiratory syncytial virus (RSV) is the most common viral pathogen causing respiratory disease in the pediatric population. An unexpected sudden upsurge of RSV infections among children was observed in September 2021 in Greece. Forty-one rhinopharyngeal samples from children under the age of 2 years with confirmed RSV bronchiolitis were tested to identify the genotype(s) of the RSV strain(s).

DOI: https://doi.org/10.1002/jmv.27671 23 February 2022

Infections with highly pathogenic avian influenza A virus (HPAIV) H5N8 in harbor seals at the German North Sea coast, 2021
Postel et al. 2022

DOI: https://doi.org/10.6084/m9.figshare.19187785.v2 17 February 2022

Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes
Manuto et al. 2022

In February 2020, the municipality of Vo’, a small town near Padua (Italy) was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. To investigate the viral prevalence and clinical features, the entire population was swab tested in two sequential surveys. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo’ belongs to lineage B, carrying the mutations G11083T and G26144T. The viral sequences allowed us to investigate the viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo’. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptom severity or immune system deficiencies.

DOI: https://doi.org/10.3390/v14020399 15 February 2022

Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes
Manuto et al. 2022

DOI: https://doi.org/10.3390/v14020399 13 February 2022

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods
Rebelo et al. 2022

Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark.

DOI: https://doi.org/10.1371/journal.pone.0261999 11 February 2022

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
Florensa et al. 2022

Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the individual antimicrobial resistance genes (ARGs) is essential for understanding the evolution and emergence of AMR and to provide appropriate treatment. The rapid developments in next-generation sequencing technologies have made this technology available to researchers and microbiologists at routine laboratories around the world. However, tools available for those with limited experience with bioinformatics are lacking, especially to enable researchers and microbiologists in low- and middle-income countries (LMICs) to perform their own studies. The CGE-tools (Center for Genomic Epidemiology) including ResFinder (https://cge.cbs.dtu.dk/services/ResFinder/) was developed to provide freely available easy to use online bioinformatic tools allowing inexperienced researchers and microbiologists to perform simple bioinformatic analyses. The main purpose was and is to provide these solutions for people involved in frontline diagnosis especially in LMICs. Since its original publication in 2012, ResFinder has undergone a number of improvements including improvement of the code and databases, inclusion of point mutations for selected bacterial species and predictions of phenotypes also for selected species.

DOI: http://dx.doi.org/10.1099/mgen.0.000748 24 January 2022

Emergence of ST39 carbapenem-resistant Klebsiella pneumoniae producing VIM-1 and KPC-2
Karampatakis et al. 2021

Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes life-threatening hospital-acquired infections. KPC and VIM carbapenemase production is the main molecular mechanism for carbapenem resistance. The aim of the current study was the genetic characterization of four ST39 CRKP isolates simultaneously producing VIM-1 and KPC-2, obtained in a Greek tertiary hospital.

DOI: https://doi.org/10.1016/j.micpath.2021.105373 24 December 2021

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
Lu Lu, et al. 2021

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms. High number of farm infections (68/126) in minks and farm workers (>50% of farms) were detected, with limited community spread. Three of five initial introductions of SARS-CoV-2 led to subsequent spread between mink farms until November 2020. Viruses belonging to the largest cluster acquired an amino acid substitution in the receptor binding domain of the Spike protein (position 486), evolved faster and spread longer and more widely. Movement of people and distance between farms were statistically significant predictors of virus dispersal between farms. Our study provides novel insights into SARS-CoV-2 transmission between mink farms and highlights the importance of combining genetic information with epidemiological information when investigating outbreaks at the animal-human interface.

DOI: https://doi.org/10.1038/s41467-021-27096-9 23 November 2021

Detection of antimicrobial resistance genes in urban air
Becsei et al. 2021

To understand antibiotic resistance in pathogenic bacteria, we need to monitor environmental microbes as reservoirs of antimicrobial resistance genes (ARGs). These bacteria are present in the air and can be investigated with the whole metagenome shotgun sequencing approach. This study aimed to investigate the feasibility of a method for metagenomic analysis of microbial composition and ARGs in the outdoor air.

DOI: https://doi.org/10.1002/mbo3.1248 16 November 2021

Association between guilds of birds in the African-Western Palaearctic region and the tick species Hyalomma rufipes, one of the main vectors of Crimean-Congo hemorrhagic fever virus
Hoffman et al. 2021

The ecology of the vertebrate host contributes to the geographical range expansion of ticks. In this study, we investigated which tick taxa that infest and are dispersed by birds along African-Western Palaearctic flyways during northward migration, and whether bird ecology was associated with tick taxa.

DOI: https://doi.org/10.1016/j.onehlt.2021.100349 11 November 2021

Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant
Kant et al. 2021

Small animal models are of crucial importance for assessing COVID-19 countermeasures. Common laboratory mice would be well-suited for this purpose but are not susceptible to infection with wild-type SARS-CoV-2. However, the development of mouse-adapted virus strains has revealed key mutations in the SARS-CoV-2 spike protein that increase infectivity, and interestingly, many of these mutations are also present in naturally occurring SARS-CoV-2 variants of concern. This suggests that these variants might have the ability to infect common laboratory mice. Herein we show that the SARS-CoV-2 beta variant attains infectibility to BALB/c mice and causes pulmonary changes within 2–3 days post infection, consistent with results seen in other murine models of COVID-19, at a reasonable virus dose (2 × 105 PFU). The findings suggest that common laboratory mice can serve as the animal model of choice for testing the effectiveness of antiviral drugs and vaccines against SARS-CoV-2.

DOI: https://doi.org/10.3390/v13112263 11 November 2021

Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021
Kant et al. 2021

Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. We used phylogenetic clustering to identify sources of spreading. We found that outbreaks were mostly seeded by a few introductions, highlighting the importance of surveillance and prevention policies.

DOI: https://doi.org/10.3201/eid2712.211631 27 October 2021

Case Report: The Carotid Body in COVID-19: Histopathological and Virological Analyses of an Autopsy Case Series
Porzionato et al. 2021

Various authors have hypothesized carotid body (CB) involvement in Coronavirus Disease 2019 (COVID-19), through direct invasion or indirect effects by systemic stimuli (‘cytokine storm’, angiotensin-converting enzyme [ACE]1/ACE2 imbalance). However, empirical evidence is limited or partial. Here, we present an integrated histopathological and virological analysis of CBs sampled at autopsy from four subjects (2 males and 2 females; age: >70 years old) who died of COVID-19.

DOI: https://doi.org/10.3389/fimmu.2021.736529 26 October 2021

Mobile Antimicrobial Resistance Genes in Probiotics
Toth et al. 2021

Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

DOI: https://doi.org/10.3390/antibiotics10111287 21 October 2021

Detection of antimicrobial resistance genes in urban air
Becsei et al. 2021

DOI: https://doi.org/10.1002/mbo3.1248 20 October 2021

Synergistic Block of SARS-CoV-2 Infection by Combined Drug Inhibition of the Host Entry Factors PIKfyve Kinase and TMPRSS2 Protease
Kreutzberger et al. 2021

Repurposing FDA-approved inhibitors able to prevent infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could provide a rapid path to establish new therapeutic options to mitigate the effects of coronavirus disease 2019 (COVID-19). Proteolytic cleavages of the spike (S) protein of SARS-CoV-2, mediated by the host cell proteases cathepsin and TMPRSS2, alone or in combination, are key early activation steps required for efficient infection. The PIKfyve kinase inhibitor apilimod interferes with late endosomal viral traffic and through an ill-defined mechanism prevents in vitro infection through late endosomes mediated by cathepsin. Similarly, inhibition of TMPRSS2 protease activity by camostat mesylate or nafamostat mesylate prevents infection mediated by the TMPRSS2-dependent and cathepsin-independent pathway.

DOI: https://doi.org/10.1128/JVI.00975-21 13 October 2021

Pandemics– One Health preparedness for the next
Frank M. Aarestrup, Marc Bonten, Marion Koopmans

The majority of emerging infectious diseases originate in animals. Current routine surveillance is focused on known diseases and clinical syndromes, but the increasing likelihood of emerging disease outbreaks shows the critical importance of early detection of unusual illness or circulation of pathogens - prior to human disease manifestation. In this Viewpoint, we focus on one key pillar of preparedness—the need for early warning surveillance at the human, animal, environmental interface. The COVID-19 pandemic has revolutionized the scale of sequencing of pathogen genomes, and the current investments in global genomic surveillance offer great potential for a novel, truly integrated Disease X (with epidemic or pandemic potential) surveillance arm provided we do not make the mistake of developing them solely for the case at hand.

DOI: https://doi.org/10.1016/j.lanepe.2021.100210 07 October 2021

Mis-tweeting communication: a Vaccine Hesitancy analysis among twitter users in Italy
Gori et al. 2021

A previously unseen body of scientific knowledge of varying quality has been produced during the ongoing COVID-19 pandemic. It has proven extremely difficult to navigate for experts and laymen alike, originating a phenomenon described as “Infodemic”, a breeding ground for misinformation. This has a potential impact on vaccine hesitancy that must be considered in a situation where efficient vaccination campaigns are of the greatest importance. We aimed at describing the polarization and volumes of Italian language tweets in the months before and after the start of the vaccination campaign in Italy.

DOI: https://doi.org/10.23750/abm.v92iS6.12251 05 October 2021

Clusters of science and health related Twitter users become more isolated during the COVID-19 pandemic
Durazzi et al. 2021

COVID-19 represents the most severe global crisis to date whose public conversation can be studied in real time. To do so, we use a data set of over 350 million tweets and retweets posted by over 26 million English speaking Twitter users from January 13 to June 7, 2020. We characterize the retweet network to identify spontaneous clustering of users and the evolution of their interaction over time in relation to the pandemic’s emergence. We identify several stable clusters (super-communities), and are able to link them to international groups mainly involved in science and health topics, national elites, and political actors. The science- and health-related super-community received disproportionate attention early on during the pandemic, and was leading the discussion at the time.

DOI: https://doi.org/10.1038/s41598-021-99301-0 04 October 2021

The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
Oude Munnink et al. 2021

The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.

DOI: https://doi.org/10.1038/s41591-021-01472-w 09 September 2021

Seasonal coronavirus–specific B cells with limited SARS-CoV-2 cross-reactivity dominate the IgG response in severe COVID-19
Aguilar-Bretones et al. 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19). Little is known about the interplay between preexisting immunity to endemic seasonal coronaviruses and the development of a SARS-CoV-2–specific IgG response. We investigated the kinetics, breadth, magnitude, and level of cross-reactivity of IgG antibodies against SARS-CoV-2 and heterologous seasonal and epidemic coronaviruses at the clonal level in patients with mild or severe COVID-19 as well as in disease control patients. We assessed antibody reactivity to nucleocapsid and spike antigens and correlated this IgG response to SARS-CoV-2 neutralization. Patients with COVID-19 mounted a mostly type-specific SARS-CoV-2 response.

DOI: https://doi.org/10.1172/JCI150613 09 September 2021

Differential plasmacytoid dendritic cell phenotype and type I Interferon response in asymptomatic and severe COVID-19 infection
Severa et al. 2021

SARS-CoV-2 fine-tunes the interferon (IFN)-induced antiviral responses, which play a key role in preventing coronavirus disease 2019 (COVID-19) progression. Indeed, critically ill patients show an impaired type I IFN response accompanied by elevated inflammatory cytokine and chemokine levels, responsible for cell and tissue damage and associated multi-organ failure. Here, the early interaction between SARS-CoV-2 and immune cells was investigated by interrogating an in vitro human peripheral blood mononuclear cell (PBMC)-based experimental model. We found that, even in absence of a productive viral replication, the virus mediates a vigorous TLR7/8-dependent production of both type I and III IFNs and inflammatory cytokines and chemokines, known to contribute to the cytokine storm observed in COVID-19.

DOI: https://doi.org/10.1371/journal.ppat.1009878 02 September 2021

The central role of Italy in the spatial spread of USUTU virus in Europe
Zecchin et al. 2021

USUTU virus (USUV) is an arbovirus maintained in the environment through a bird–mosquito enzootic cycle. Previous surveillance plans highlighted the endemicity of USUV in North-eastern Italy. In this work, we sequenced 138 new USUV full genomes from mosquito pools (Culex pipiens) and wild birds collected in North-eastern Italy and we investigated the evolutionary processes (phylogenetic analysis, selection pressure and evolutionary time-scale analysis) and spatial spread of USUV strains circulating in the European context and in Italy, with a particular focus on North-eastern Italy. Our results confirmed the circulation of viruses belonging to four different lineages in Italy (EU1, EU2, EU3 and EU4), with the newly sequenced viruses from the North-eastern regions, Veneto and Friuli Venezia Giulia, belonging to the EU2 lineage and clustering into two different sub-lineages, EU2-A and EU2-B.

DOI: https://doi.org/10.1093/ve/veab048 31 August 2021

Wolbachia prevalence in the vector species Culex pipiens and Culex torrentium in a Sindbis virus-endemic region of Sweden
Alexander Bergman & Jenny C. Hesson

Wolbachia pipientis are endosymbiotic bacteria present in a large proportion of terrestrial arthropods. The species is known to sometimes affect the ability of its host to transmit vector-borne pathogens. Central Sweden is endemic for Sindbis virus (SINV), where it is mainly transmitted by the vector species Culex pipiens and Culex torrentium, with the latter established as the main vector. In this study we investigated the Wolbachia prevalence in these two vector species in a region highly endemic for SINV.

DOI: https://doi.org/10.1186/s13071-021-04937-6 26 August 2021

Autochthonous dengue outbreak in Italy 2020: Clinical, virological and entomological findings
Barzon et al. 2021

Background: In August 2020, in the context of COVID-19 pandemics, an autochthonous dengue outbreak was identified for the first time in Italy.
Methods: Following the reporting of the index case of autochthonous dengue, epidemiological investigation, vector control, and substances of human origin safety measures were immediately activated, according to the national arbovirus surveillance plan. Dengue cases were followed-up with weekly visits and laboratory tests until recovery and clearance of viral RNA from blood.

DOI: https://doi.org/10.1093/jtm/taab130 18 August 2021

Temporal Dynamics of Influenza A(H5N1) Subtype before and after the Emergence of H5N8
Amer et al. 2021

Highly pathogenic avian influenza (HPAI) viruses continue to circulate worldwide, causing numerous outbreaks among bird species and severe public health concerns. H5N1 and H5N8 are the two most fundamental HPAI subtypes detected in birds in the last two decades. The two viruses may compete with each other while sharing the same host population and, thus, suppress the spread of one of the viruses. In this study, we performed a statistical analysis to investigate the temporal correlation of the HPAI H5N1 and HPAI H5N8 subtypes using globally reported data in 2015–2020. This was joined with an in-depth analysis using data generated via our national surveillance program in Egypt. A total of 6412 outbreaks were reported worldwide during this period, with 39% (2529) as H5N1 and 61% (3883) as H5N8. In Egypt, 65% of positive cases were found in backyards, while only 12% were found in farms and 23% in live bird markets.

DOI: https://doi.org/10.3390/v13081565 07 August 2021

Genetic data in the fight against pandemics, 2021/ A genetikai adatok szerepe a járványok elleni küzdelemben
Becsei et al. 2021

Hungarian language article
A COVID–19-járvány alatt bizonyossá vált, hogy az adattudományok, az adatok gyors megosztása és a nemzetközi összefogás a hatékony járványkezelés kulcsfontosságú eszközei. A járvány előtt létrejött Újonnan Felbukkanó fertőző betegségek Obszervatóriuma (Versatile Emerging infectious disease Observatory, VEO) nevű nemzetközi konzorcium célja egy olyan monitorozó rendszer kiépítése, amely a potenciálisan veszélyes kórokozókat még az előtt azonosítja, mielőtt azok tömeges megbetegedéseket okoznának, lehetőséget adva ezzel a gyors reagálásra.

DOI: https://doi.org/10.1556/112.2021.00006 30 July 2021

At the tip of an iceberg: citizen science and active surveillance collaborating to broaden the known distribution of Aedes japonicus in Spain
Eritja et al. 2021

Active surveillance aimed at the early detection of invasive mosquito species is usually focused on seaports and airports as points of entry, and along road networks as dispersion paths. In a number of cases, however, the first detections of colonizing populations are made by citizens, either because the species has already moved beyond the implemented active surveillance sites or because there is no surveillance in place. This was the case of the first detection in 2018 of the Asian bush mosquito, Aedes japonicus, in Asturias (northern Spain) by the citizen science platform Mosquito Alert.

DOI: https://doi.org/10.1186/s13071-021-04874-4 26 July 2021

HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
Nguyen et al. 2021

SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately.

DOI: https://doi.org/10.1186/s12859-021-04294-2 17 July 2021

Hypopharyngeal Ulcers in COVID-19: Histopathological and Virological Analyses – A Case Report
Porzionato et al. 2021

In coronavirus disease 2019 (COVID-19), ulcerative lesions have been episodically reported in various segments of the gastrointestinal (GI) tract, including the oral cavity, oropharynx, esophagus, stomach and bowel. In this report, we describe an autopsy case of a COVID-19 patient who showed two undiagnosed ulcers at the level of the anterior and posterior walls of the hypopharynx. Molecular testing of viruses involved in pharyngeal ulcers demonstrated the presence of severe acute respiratory syndrome – coronavirus type 2 (SARS-CoV-2) RNA, together with herpes simplex virus 1 DNA.

DOI: https://doi.org/10.3389/fimmu.2021.676828 05 July 2021

Predicting Spatial Patterns of Sindbis Virus (SINV) Infection Risk in Finland Using Vector, Host and Environmental Data
Uusitalo et al. 2021

Pogosta disease is a mosquito-borne infection, caused by Sindbis virus (SINV), which causes epidemics of febrile rash and arthritis in Northern Europe and South Africa. Resident grouse and migratory birds play a significant role as amplifying hosts and various mosquito species, including Aedes cinereus, Culex pipiens, Cx. torrentium and Culiseta morsitans are documented vectors. As specific treatments are not available for SINV infections, and joint symptoms may persist, the public health burden is considerable in endemic areas. To predict the environmental suitability for SINV infections in Finland, we applied a suite of geospatial and statistical modeling techniques to disease occurrence data. Using an ensemble approach, we first produced environmental suitability maps for potential SINV vectors in Finland. These suitability maps were then combined with grouse densities and environmental data to identify the influential determinants for SINV infections and to predict the risk of Pogosta disease in Finnish municipalities. Our predictions suggest that both the environmental suitability for vectors and the high risk of Pogosta disease are focused in geographically restricted areas. This provides evidence that the presence of both SINV vector species and grouse densities can predict the occurrence of the disease. The results support material for public-health officials when determining area-specific recommendations and deliver information to health care personnel to raise awareness of the disease among physicians.

DOI: https://doi.org/10.3390/ijerph18137064 01 July 2021

West Nile fever upsurge in a Greek regional unit, 2020
Papa et al. 2021

During the 2020 West Nile virus (WNV) transmission season, Greece was the most affected EU Member State. More than one third of human cases occurred in Serres regional unit in northern Greece, which is characterized by the presence of a major wetland (Kerkini lake and Strimon river). A total of 2809 Culex pipiens mosquitoes collected in Serres were grouped into 70 pools and tested for WNV. Ten (14.3%) pools were found positive, and all WNV sequences belonged to the Central European subclade of WNV lineage 2. The first human case occurred in a village nearby the lake, and all following cases occurred across the connected river and its tributaries. Similar distribution presented the sites where WNV-positive mosquitoes were detected. The number of Culex spp. mosquitoes per trap per night was higher in 2020 than in previous years (2017-2019). The spatial and temporal distribution of human cases and WNV-positive mosquitoes in 2020 in Serres regional unit suggest that the upsurge of the virus circulation was probably related with factors that affected the ecosystem of the wetland.

DOI: https://doi.org/10.1016/j.actatropica.2021.106010 12 June 2021

SARS-CoV-2 Neutralizing Human Antibodies Protect Against Lower Respiratory Tract Disease in a Hamster Model
Haagmans et al. 2021

Effective clinical intervention strategies for coronavirus disease 2019 (COVID-19) are urgently needed. Although several clinical trials have evaluated use of convalescent plasma containing virus-neutralizing antibodies, levels of neutralizing antibodies are usually not assessed and the effectiveness has not been proven. We show that hamsters treated prophylactically with a 1:2560 titer of human convalescent plasma or a 1:5260 titer of monoclonal antibody were protected against weight loss, had a significant reduction of virus replication in the lungs, and showed reduced pneumonia. Interestingly, this protective effect was lost with a titer of 1:320 of convalescent plasma. These data highlight the importance of screening plasma donors for high levels of neutralizing antibodies. Our data show that prophylactic administration of high levels of neutralizing antibody, either monoclonal or from convalescent plasma, prevent severe SARS-CoV-2 pneumonia in a hamster model, and could be used as an alternative or complementary to other antiviral treatments for COVID-19.

DOI: https://doi.org/10.1093/infdis/jiab289 08 June 2021

SARS-CoV-2 in hospital indoor environments is predominantly non-infectious
Krambrich et al. 2021

The ongoing SARS-CoV-2 pandemic has spread rapidly worldwide and disease prevention is more important than ever. In the absence of a vaccine, knowledge of the transmission routes and risk areas of infection remain the most important existing tools to prevent further spread.

DOI: https://doi.org/10.1186/s12985-021-01556-6 02 June 2021

Evaluation of Production Lots of a Rapid Point-of-Care Lateral Flow Serological Test Intended for Identification of IgM and IgG against the N-Terminal Part of the Spike Protein (S1) of SARS-CoV-2
Hoffman et al. 2022

The potential of rapid point-of-care (POC) tests has been subject of doubt due to an eventual risk of production errors. The aim was therefore to evaluate the two separate production lots of a commercial POC lateral flow test, intended for the detection of IgM and IgG against the SARS-CoV-2 spike protein (S1). Control samples consisted of serum from individuals with confirmed SARS-CoV-2 infection and pre-COVID-19 negative sera gathered from a biobank.

DOI: https://doi.org/10.3390/v13061043 31 May 2021

Diagnostic Potential of a Luminex-Based Coronavirus Disease 2019 Suspension Immunoassay (COVID-19 SIA) for the Detection of Antibodies against SARS-CoV-2
Hoffman et al. 2021

Due to the current, rapidly increasing Coronavirus disease 2019 (COVID-19) pandemic, efficient and highly specific diagnostic methods are needed. The receptor-binding part of the spike (S) protein, S1, has been suggested to be highly virus-specific; it does not cross-react with antibodies against other coronaviruses.

DOI: https://doi.org/10.3390/v13060993 26 May 2021

Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays
Virtanen et al. 2021

Increasing evidence suggests that some newly emerged SARS-CoV-2 variants of concern (VoCs) resist neutralization by antibodies elicited by the early-pandemic wild-type virus. We applied neutralization tests to paired recoveree sera (n = 38) using clinical isolates representing the first wave (D614G), VoC1, and VoC2 lineages (B.1.1.7 and B 1.351).

DOI: https://doi.org/10.3390/v13060996 26 May 2021

MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads
Hallgren et al. 2021

For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from the Illumina sequencing platforms and long reads from Oxford Nanopore Technologies’ (ONT) platforms as input. MINTyper performs automated reference identification, alignment, alignment trimming, optional methylation masking, and pairwise distance calculations. With this approach, we could rapidly and accurately cluster a set of DNA sequenced isolates, with a known epidemiological relationship to confirm the clustering. Functions were built to allow for both high-accuracy methylation-aware base-called MinION reads (hac_m Q10) and fast generated lower-quality reads (fast Q8) to be used, also in combination with Illumina data. With fast Q8 reads a higher number of base pairs were excluded from the calculated distance matrix, compared with the high-accuracy methylation-aware Q10 base-calling of ONT data. Nonetheless, when using different qualities of ONT data with corresponding input parameters, the clustering of isolates were nearly identical.

DOI: https://doi.org/10.1093/biomethods/bpab008 21 April 2021

Targeting the NS2B-NS3 protease of tick-borne encephalitis virus with pan-flaviviral protease inhibitors
Akaberi et al. 2021

Tick-borne encephalitis (TBE) is a severe neurological disorder caused by tick-borne encephalitis virus (TBEV), a member of the Flavivirus genus. Currently, two vaccines are available in Europe against TBEV. However, TBE cases have been rising in Sweden for the past twenty years, and thousands of cases are reported in Europe, emphasizing the need for antiviral treatments against this virus.

DOI: https://doi.org/10.1016/j.antiviral.2021.105074 16 April 2021

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium
Izquierdo-Lara et al. 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a major global health problem, and public health surveillance is crucial to monitor and prevent virus spread. Wastewater-based epidemiology has been proposed as an addition to disease-based surveillance because virus is shed in the feces of ≈40% of infected persons. We used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium. Phylogenetic analysis revealed the presence of the most prevalent clades (19A, 20A, and 20B) and clustering of sewage samples with clinical samples from the same region. We distinguished multiple clades within a single sewage sample by using low-frequency variant analysis. In addition, several novel mutations in the SARS-CoV-2 genome were detected. Our results illustrate how wastewater can be used to investigate the diversity of SARS-CoV-2 viruses circulating in a community and identify new outbreaks.

DOI: https://doi.org/10.3201/eid2705.204410 31 March 2021

Sindbis virus neutralising antibodies detected in Swedish horses
Björnström et al. 2021

A number of viruses transmitted by mosquitoes are well known to cause disease in both humans and horses, ranging from mild fevers to mortal neurological disease. A recently discovered connection between the alphavirus Sindbis virus (SINV) and neurological disease in horses in South Africa initiated this serological study in northern Europe, where the same genotype of SINV (SINV-I) is also highly endemic.

DOI: https://doi.org/10.1016/j.onehlt.2021.100242 25 March 2021

Experimental SARS-CoV-2 Infection of Bank Voles
Ulrich et al. 2021

After experimental inoculation, severe acute respiratory syndrome coronavirus 2 infection was confirmed in bank voles by seroconversion within 8 days and detection of viral RNA in nasal tissue for up to 21 days. However, transmission to contact animals was not detected. Thus, bank voles are unlikely to establish effective transmission cycles in nature.

DOI: https://doi.org/10.3201/eid2704.204945 11 March 2021

Co-infections: Simultaneous detections of West Nile virus and Usutu virus in birds from Germany
Santos et al. 2021

The emergence of West Nile virus (WNV) and Usutu virus (USUV) in Europe resulted in significant outbreaks leading to avifauna mortality and human infections. Both viruses have overlapping geographical, host and vector ranges, and are often co-circulating in Europe. In Germany, a nationwide bird surveillance network was established to monitor these zoonotic arthropod-borne viruses in migratory and resident birds. In this framework, co-infections with WNV and USUV were detected in six dead birds collected in 2018 and 2019. Genomic sequencing and phylogenetic analyses classified the detected WNV strains as lineage 2 and the USUV strains as lineages Africa 2 (n = 2), Africa 3 (n = 3) and Europe 2 (n = 1). Preliminary attempts to co-propagate both viruses in vitro failed. However, we successfully cultivated WNV from two animals. Further evidence for WNV-USUV co-infection was obtained by sampling live birds in four zoological gardens with confirmed WNV cases. Three snowy owls had high neutralizing antibody titres against both WNV and USUV, of which two were also positive for USUV-RNA. In conclusion, further reports of co-infections in animals as well as in humans are expected in the future, particularly in areas where both viruses are present in the vector population.

DOI: https://doi.org/10.1111/tbed.14050 02 March 2021

SARS-CoV-2 Infection and Disease Modelling Using Stem Cell Technology and Organoids
Trevisan et al. 2021

In this Review, we briefly describe the basic virology and pathogenesis of SARS-CoV-2, highlighting how stem cell technology and organoids can contribute to the understanding of SARS-CoV-2 cell tropisms and the mechanism of disease in the human host, supporting and clarifying findings from clinical studies in infected individuals. We summarize here the results of studies, which used these technologies to investigate SARS-CoV-2 pathogenesis in different organs. Studies with in vitro models of lung epithelia showed that alveolar epithelial type II cells, but not differentiated lung alveolar epithelial type I cells, are key targets of SARS-CoV-2, which triggers cell apoptosis and inflammation, while impairing surfactant production. Experiments with human small intestinal organoids and colonic organoids showed that the gastrointestinal tract is another relevant target for SARS-CoV-2. The virus can infect and replicate in enterocytes and cholangiocytes, inducing cell damage and inflammation. Direct viral damage was also demonstrated in in vitro models of human cardiomyocytes and choroid plexus epithelial cells. At variance, endothelial cells and neurons are poorly susceptible to viral infection, thus supporting the hypothesis that neurological symptoms and vascular damage result from the indirect effects of systemic inflammatory and immunological hyper-responses to SARS-CoV-2 infection.

DOI: https://doi.org/10.3390/ijms22052356 26 February 2021

SARS-CoV-2 spike D614G change enhances replication and transmission
Zhou et al. 2021

During the evolution of SARS-CoV-2 in humans, a D614G substitution in the spike glycoprotein (S) has emerged; virus containing this substitution has become the predominant circulating variant in the COVID-19 pandemic1. However, whether the increasing prevalence of this variant reflects a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains unknown. Here we use isogenic SARS-CoV-2 variants to demonstrate that the variant that contains S(D614G) has enhanced binding to the human cell-surface receptor angiotensin-converting enzyme 2 (ACE2), increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a human ACE2 knock-in mouse model, and markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Our data show that the D614G substitution in S results in subtle increases in binding and replication in vitro, and provides a real competitive advantage in vivo—particularly during the transmission bottleneck. Our data therefore provide an explanation for the global predominance of the variant that contains S(D614G) among the SARS-CoV-2 viruses that are currently circulating.

DOI: https://doi.org/10.1038/s41586-021-03361-1 26 February 2021

Deep learning identification for citizen science surveillance of tiger mosquitoes
Pataki et al. 2021

Global monitoring of disease vectors is undoubtedly becoming an urgent need as the human population rises and becomes increasingly mobile, international commercial exchanges increase, and climate change expands the habitats of many vector species. Traditional surveillance of mosquitoes, vectors of many diseases, relies on catches, which requires regular manual inspection and reporting, and dedicated personnel, making large-scale monitoring difficult and expensive. New approaches are solving the problem of scalability by relying on smartphones and the Internet to enable novel community-based and digital observatories, where people can upload pictures of mosquitoes whenever they encounter them. An example is the Mosquito Alert citizen science system, which includes a dedicated mobile phone app through which geotagged images are collected. This system provides a viable option for monitoring the spread of various mosquito species across the globe, although it is partly limited by the quality of the citizen scientists’ photos. To make the system useful for public health agencies, and to give feedback to the volunteering citizens, the submitted images are inspected and labeled by entomology experts.

DOI: https://doi.org/10.1038/s41598-021-83657-4 25 February 2021

Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2
Wylezich et al. 2021

The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2.

DOI: https://doi.org/10.1186/s40168-020-00973-z 20 February 2021

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response
Lin et al. 2021

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.

DOI: https://doi.org/10.1016/j.chom.2021.01.015 29 January 2021

A 10-Minute “Mix and Read” Antibody Assay for SARS-CoV-2
Rusanen et al. 2021

Accurate and rapid diagnostic tools are needed for management of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Antibody tests enable detection of individuals past the initial phase of infection and help examine vaccine responses. The major targets of human antibody response in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the spike glycoprotein (SP) and nucleocapsid protein (NP).

DOI: https://doi.org/10.3390/v13020143 20 January 2021

Filling the gaps in the global prevalence map of clinical antimicrobial resistance
Oldenkamp et al. 2020

Surveillance is critical in containing globally increasing antimicrobial resistance (AMR). Affordable methodologies to prioritize AMR surveillance efforts are urgently needed, especially in low- and middle-income countries (LMICs), where resources are limited. While socioeconomic characteristics correlate with clinical AMR prevalence, this correlation has not yet been used to estimate AMR prevalence in countries lacking surveillance. We captured the statistical relationship between AMR prevalence and socioeconomic characteristics in a suite of beta-binomial principal component regression models for nine pathogens resistant to 19 (classes of) antibiotics. Prevalence data from ResistanceMap were combined with socioeconomic profiles constructed from 5,595 World Bank indicators. Cross-validated models were used to estimate clinical AMR prevalence and temporal trends for countries lacking data. Our approach provides robust estimates of clinical AMR prevalence in LMICs for most priority pathogens (cross-validated q2 > 0.78 for six out of nine pathogens).

DOI: https://doi.org/10.1073/PNAS.2013515118 05 January 2021

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt
Tóth et al. 2020

Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria.

DOI: https://doi.org/10.1038/s41598-020-80444-5 31 December 2020

Occurrence of Antibodies against SARS-CoV-2 in the Domestic Cat Population of Germany
Michelitsch et al. 2020

Domestic cats (Felis catus) are popular companion animals that live in close contact with their human owners. Therefore, the risk of a trans-species spreading event between domestic cats and humans is ever-present. Shortly after the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread around the world, the role of domestic cats in the transmission cycle was questioned. In the present study, the first large-scale survey of antibody occurrence in the domestic cat population in Germany was conducted, in order to assess the incidence of naturally occurring human to cat transmission of SARS-CoV-2. A total of 920 serum samples, which were collected from April to September of 2020, were screened by an indirect multispecies ELISA.

DOI: https://doi.org/10.3390/vaccines8040772 17 December 2020

Sindbis Virus Infection in Non-Blood-Fed Hibernating Culex pipiens Mosquitoes in Sweden
Bergman et al. 2020

A crucial, but unresolved question concerning mosquito-borne virus transmission is how these viruses can remain endemic in regions where the transmission is halted for long periods of time, due to mosquito inactivity in, e.g., winter. In northern Europe, Sindbis virus (SINV) (genus alphavirus, Togaviridae) is transmitted among birds by Culex mosquitoes during the summer, with occasional symptomatic infections occurring in humans.

DOI: https://doi.org/10.3390/v12121441 14 December 2020

SARS-CoV-2 infections among healthcare workers at Helsinki University Hospital, Finland, spring 2020: Serosurvey, symptoms and risk factors
Kantele et al. 2020

The rate of CoV(+) was 3.3% (36/1095) and seropositivity 3.0% (33/1095). CoV(+) was associated with contact with a known Covid-19 case, and working on a Covid-19-dedicated ward or one with cases among staff. The rate in the Covid-19-dedicated ICU was negligible. Smoking and age <55 years were associated with decreased risk. CoV(+) was strongly associated with ageusia, anosmia, myalgia, fatigue, fever, and chest pressure. Seropositivity was recorded for 89.3% of those with prior documented RT-PCR-positivity and 2.4% of those RT-PCR-negative. The rate of previously unidentified cases was 0.7% (8/1067) and asymptomatic ones 0% (0/36).

DOI: https://doi.org/10.1016/j.tmaid.2020.101949 13 December 2020

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types
Plyusnin et al. 2020

The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.

DOI: https://dx.doi.org/10.1093%2Fve%2Fveaa091 02 December 2020

Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection
Freuling et al. 2020

Raccoon dogs might have been intermediate hosts for severe acute respiratory syndrome–associated coronavirus in 2002–2004. We demonstrated susceptibility of raccoon dogs to severe acute respiratory syndrome coronavirus 2 infection and transmission to in-contact animals. Infected animals had no signs of illness. Virus replication and tissue lesions occurred in the nasal conchae.

DOI: 10.3201/eid2612.203733 18 November 2020

Multi‐species ELISA for the detection of antibodies against SARS‐CoV‐2 in animals
Wernike et al. 2020

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease – referred to as COVID‐19 – unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS‐CoV‐2 infections in animals once test systems are evaluated for use in different species. Here, we developed an indirect multi‐species ELISA based on the receptor‐binding domain (RBD) of SARS‐CoV‐2.

DOI: https://doi.org/10.1111/tbed.13926 15 November 2020

Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity
Cantuti-Castelvetri et al. 2020

The causative agent of coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For many viruses, tissue tropism is determined by the availability of virus receptors and entry cofactors on the surface of host cells. In this study, we found that neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, an effect blocked by a monoclonal blocking antibody against NRP1. A SARS-CoV-2 mutant with an altered furin cleavage site did not depend on NRP1 for infectivity. Pathological analysis of olfactory epithelium obtained from human COVID-19 autopsies revealed that SARS-CoV-2 infected NRP1-positive cells facing the nasal cavity. Our data provide insight into SARS-CoV-2 cell infectivity and define a potential target for antiviral intervention.

DOI: 10.1126/science.abd2985 13 November 2020

Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans
Oude Munnink et al. 2020

Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.

DOI: https://doi.org/10.1126/science.abe5901 10 November 2020

Phylogenetic Investigation of Norovirus Transmission between Humans and Animals
Villabruna et al. 2020

Norovirus infections are a leading cause of acute gastroenteritis worldwide, affecting people of all ages. There are 10 norovirus genogroups (GI-GX) that infect humans and animals in a host-specific manner. New variants and genotypes frequently emerge, and their origin is not well understood. One hypothesis is that new human infections may be seeded from an animal reservoir, as human noroviruses have occasionally been detected in animal species.

DOI: https://doi.org/10.3390/v12111287 10 November 2020

Automated download and clean-up of family-specific databases for kmer-based virus identification
Allesøe et al. 2020

Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. The default contamination entries include sequences from the UniVec database of plasmids, marker genes and sequencing adapters from NCBI, an E.coli genome, rRNA sequences, vectors and satellite sequences. Furthermore, duplicates are removed and the database is automatically screened for sequences from green fluorescent protein, luciferase and antibiotic resistance genes that might be present in some GenBank viral entries, and could lead to false positives in virus identification.

DOI: https://doi.org/10.1093/bioinformatics/btaa857 08 October 2020

Experimental Infection and Genetic Characterization of Two Different Capripox Virus Isolates in Small Ruminants
Wolff et al. 2020

Capripox viruses, with their members “lumpy skin disease virus (LSDV)”, “goatpox virus (GTPV)” and “sheeppox virus (SPPV)”, are described as the most serious pox diseases of production animals. A GTPV isolate and a SPPV isolate were sequenced in a combined approach using nanopore MinION sequencing to obtain long reads and Illumina high throughput sequencing for short precise reads to gain full-length high-quality genome sequences. Concomitantly, sheep and goats were inoculated with SPPV and GTPV strains, respectively. During the animal trial, varying infection routes were compared: a combined intravenous and subcutaneous infection, an only intranasal infection, and the contact infection between naïve and inoculated animals.

DOI: https://doi.org/10.3390/v12101098 28 September 2020

The genetics of highly pathogenic avian influenza viruses of subtype H5 in Germany, 2006–2020
King et al. 2020b

The H5 A/Goose/Guangdong/1/1996 (gs/GD) lineage emerged in China in 1996. Rooted in the respective gs/GD lineage, the hemagglutinin (HA) gene of highly pathogenic avian influenza viruses (HPAIV) has genetically diversified into a plethora of clades and subclades and evolved into an assortment of sub‐ and genotypes. Some caused substantial losses in the poultry industry and had a major impact on wild bird populations alongside public health implications due to a zoonotic potential of certain clades. After the primary introduction of the HPAI H5N1 gs/GD lineage into Europe in autumn 2005 and winter 2005/2006, Germany has seen recurring incursions of four varying H5Nx subtypes (H5N1, H5N8, H5N5, H5N6) carrying multiple distinct reassortants, all descendants of the gs/GD virus.

DOI: https://doi.org/10.1111/tbed.13843 22 September 2020

Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses
King et al. 2020a

Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR.

DOI: https://doi.org/10.1186/s12879-020-05367-y 03 September 2020

CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data
Yusibova et al. 2020

Resistance to clarithromycin in Helicobacter pylori (H pylori) is mediated by mutations in the domain V of the 23S rRNA gene (A2142G, A2143G, A2142C). Other polymorphisms in the 23S rRNA gene have been reported to cause low-level clarithromycin resistance but their importance is still under debate. In this study, we aimed to develop and evaluate the CRHP Finder webtool for detection of the most common mutations mediating clarithromycin resistance from whole-genome sequencing (WGS) data. Moreover, we included an analysis of 23 H pylori strains from Danish patients between January 2017 and September 2019 in Copenhagen, Denmark.

DOI: https://doi.org/10.1111/hel.12752 26 August 2020

Modelling West Nile Virus and Usutu Virus Pathogenicity in Human Neural Stem Cells
Riccetti et al. 2020

West Nile virus (WNV) and Usutu virus (USUV) are genetically related neurotropic mosquito-borne flaviviruses, which frequently co-circulate in nature. Despite USUV seeming to be less pathogenic for humans than WNV, the clinical manifestations induced by these two viruses often overlap and may evolve to produce severe neurological complications. The aim of this study was to investigate the effects of WNV and USUV infection on human induced pluripotent stem cell-derived neural stem cells (hNSCs), as a model of the neural progenitor cells in the developing fetal brain and in adult brain.

DOI: https://doi.org/10.3390/v12080882 12 August 2020

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands
Oude Munnink et al. 2020

In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands.

DOI: https://doi.org/10.1038/s41591-020-0997-y 16 July 2020

Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics
Petersen et al. 2020

The objective of this Personal View is to compare transmissibility, hospitalisation, and mortality rates for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with those of other epidemic coronaviruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and pandemic influenza viruses. The basic reproductive rate (R0) for SARS-CoV-2 is estimated to be 2·5 (range 1·8–3·6) compared with 2·0–3·0 for SARS-CoV and the 1918 influenza pandemic, 0·9 for MERS-CoV, and 1·5 for the 2009 influenza pandemic. SARS-CoV-2 causes mild or asymptomatic disease in most cases; however, severe to critical illness occurs in a small proportion of infected individuals, with the highest rate seen in people older than 70 years. The measured case fatality rate varies between countries, probably because of differences in testing strategies. Population-based mortality estimates vary widely across Europe, ranging from zero to high. Numbers from the first affected region in Italy, Lombardy, show an all age mortality rate of 154 per 100 000 population. Differences are most likely due to varying demographic structures, among other factors. However, this new virus has a focal dissemination; therefore, some areas have a higher disease burden and are affected more than others for reasons that are still not understood. Nevertheless, early introduction of strict physical distancing and hygiene measures have proven effective in sharply reducing R0 and associated mortality and could in part explain the geographical differences.

DOI: https://dx.doi.org/10.1016%2FS1473-3099(20)30484-9 03 July 2020

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study
Sikkema et al. 2020

10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers.

DOI: https://doi.org/10.1016/S1473-3099(20)30527-2 02 July 2020

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’
Lavezzo et al. 2020

On 21 February 2020, a resident of the municipality of Vo’, a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo’ at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1–3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8–1.8%). Notably, 42.5% (95% CI: 31.5–54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9–9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon–Mann–Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.

DOI: https://doi.org/10.1038/s41586-020-2488-1 30 June 2020

Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model
Rockx et al. 2020

The current pandemic coronavirus, severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2), was recently identified in patients with an acute respiratory syndrome, coronavirus disease 2019 (COVID-19). To compare its pathogenesis with that of previously emerging coronaviruses, we inoculated cynomolgus macaques with SARS-CoV-2 or Middle East respiratory syndrome (MERS)–CoV and compared the pathology and virology with historical reports of SARS-CoV infections. In SARS-CoV-2–infected macaques, virus was excreted from nose and throat in the absence of clinical signs and detected in type I and II pneumocytes in foci of diffuse alveolar damage and in ciliated epithelial cells of nasal, bronchial, and bronchiolar mucosae.

DOI: https://doi.org/10.1126/science.abb7314 29 May 2020

Human West Nile Virus Lineage 2 Infection: Epidemiological, Clinical, and Virological Findings
Pacenti et al. 2020

West Nile virus (WNV) lineage 2 is expanding and causing large outbreaks in Europe. In this study, we analyzed the epidemiological, clinical, and virological features of WNV lineage 2 infection during the large outbreak that occurred in northern Italy in 2018. The study population included 86 patients with neuroinvasive disease (WNND), 307 with fever (WNF), and 34 blood donors. Phylogenetic analysis of WNV full genome sequences from patients’ samples showed that the virus belonged to the widespread central/southern European clade of WNV lineage 2 and was circulating in the area at least since 2014. The incidence of WNND and WNF progressively increased with age and was higher in males than in females. Among WNND patients, the case fatality rate was 22%. About 70% of blood donors reported symptoms during follow-up. Within the first week after symptom onset, WNV RNA was detectable in the blood or urine of 80% of patients, while 20% and 40% of WNND and WNF patients, respectively, were WNV IgM-seronegative. In CSF samples of WNND patients, WNV RNA was typically detectable when WNV IgM antibodies were absent. Blunted or no WNV IgM response and high WNV IgG levels were observed in seven patients with previous flavivirus immunity.

DOI: https://doi.org/10.3390/v12040458 18 April 2020

Novel HPAIV H5N8 Reassortant (Clade 2.3.4.4b) Detected in Germany
King et al. 2020

A novel H5N8 highly pathogenic avian influenza virus (HPAIV) was detected in a greater white-fronted goose in January 2020 in Brandenburg, Germany, and, in February 2020, in domestic chickens belonging to a smallholding in Baden-Wuerttemberg, Germany. Full-genome sequencing was conducted on the MinION platform, enabling further phylogenetic analyses. The virus of clade 2.3.4.4b holds six segments from a Eurasian/Asian/African HPAIV H5N8 reassortant and two segments from low pathogenic avian influenza H3N8 subtype viruses recently detected in wild birds in Central Russia. These new entries continue to show the reassortment potential of the clade 2.3.4.4 H5Nx viruses, underlining the necessity for full-genome sequencing and continuous surveillance.

DOI: https://doi.org/10.3390/v12030281 04 March 2020

Updated by Jeffrey Edward Skiby on 10 July 2023