The third variable (V3) domain has been implicated in determining the human immunodeficiency virus (HIV) phenotype, including fusion capacity and monocytotropism. In a large set of primary H1V type 1 (HIV-1) isolates, V3 sequence analysis revealed that fast-replicating, syncytium-inducing isolates contained V3 sequences with a significantly higher positive charge than those of slow-replicating, non-syncytium-inducing monocytotropic isolates. It appeared that these differences in charge could be attributed to highly variable amino acid residues located on either side of the V3 loop, midway between the cysteine residues and the central GPG motif. In non-syncytium-inducing monocytotropic isolates, these residues were negatively charged or uncharged, whereas in syncytium-inducing nonmonocytotropic isolates, either one or both were positively charged. The substitutions at these positions result in changes in the predicted secondary structure of the V3 loop. Our data suggest that two amino acid residues in the highly variable V3 domain are responsible for phenotype differences and point to conformational differences in V3 loops from phenotypically distinct HIV-1 isolates.

bioRxiv preprint SARS-CoV-2, a coronavirus that newly emerged in China in late 2019 1,2 and spread rapidly 12 worldwide, caused the first witnessed pandemic sparked by a coronavirus. As the pandemic 13 progresses, information about the modes of transmission of SARS-CoV-2 among humans is critical 14 to apply appropriate infection control measures and to slow its spread. Here we show that SARS-15 CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or 16 aerosols) between ferrets. Intranasal inoculation of donor ferrets resulted in a productive upper 17 respiratory tract infection and long-term shedding, up to 11 to 19 days post-inoculation. SARS-18 CoV-2 transmitted to four out of four direct contact ferrets between 1 and 3 days after exposure 19 and via the air to three out of four independent indirect recipient ferrets between 3 and 7 days 20 after exposure. The pattern of virus shedding in the direct contact and indirect recipient ferrets 21 was similar to that of the inoculated ferrets and infectious virus was isolated from all positive 22 animals, showing that ferrets were productively infected via either route. This study provides 23 experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the 24 implementation of community-level social distancing measures currently applied in many 25 countries in the world and informing decisions on infection control measures in healthcare 26 settings 3 . In late December 2019, clusters of patients in China presenting with pneumonia of unknown etiology 29 were reported to the World Health Organization (WHO) 1 . The causative agent was rapidly identified 30 as being a virus from the Coronaviridae family, closely related to the severe acute respiratory 31 syndrome coronavirus (SARS-CoV) 2,4,5 . The SARS-CoV epidemic affected 26 countries and resulted in 32 more than 8000 cases in 2003. The newly emerging coronavirus, named SARS-CoV-2 6 , rapidly spread 33 worldwide and was declared pandemic by the WHO on March 11, 2020 7 . The first evidence 34 suggesting human-to-human transmission came from the descriptions of clusters among the early 35 cases 8,9 . Based on epidemiological data from China before measures were taken to control the 36 spread of the virus, the reproductive number R0 (the number of secondary cases directly generated 37 from each case) was estimated to be between 2 and 3 10-12 . In order to apply appropriate infection 38 control measures to reduce the R0, the modes of transmission of SARS-CoV-2 need to be elucidated.39 Respiratory viruses can be transmitted via direct and indirect contact (via fomites), and through the 40 air via respiratory droplets and/or aerosols. Transmission via respiratory droplets (> 5 μm) is 41 mediated by expelled particles that have a propensity to settle quickly and is therefore reliant on 42 close proximity between infected and susceptible individuals, usually within 1 m of the site of 43 expulsion. Transmission via aerosols (< 5 μm) is mediated by expelled parti...

The recently raised awareness of the threat of a new influenza pandemic has stimulated interest in the detection of influenza A viruses in human as well as animal secretions. Virus isolation alone is unsatisfactory for this purpose because of its inherent limited sensitivity and the lack of host cells that are universally permissive to all influenza A viruses. Previously described PCR methods are more sensitive but are targeted predominantly at virus strains currently circulating in humans, since the sequences of the primer sets display considerable numbers of mismatches to the sequences of animal influenza A viruses. Therefore, a new set of primers, based on highly conserved regions of the matrix gene, was designed for single-tube reverse transcription-PCR for the detection of influenza A viruses from multiple species. This PCR proved to be fully reactive with a panel of 25 genetically diverse virus isolates that were obtained from birds, humans, pigs, horses, and seals and that included all known subtypes of influenza A virus. It was not reactive with the 11 other RNA viruses tested. Comparative tests with throat swab samples from humans and fecal and cloacal swab samples from birds confirmed that the new PCR is faster and up to 100-fold more sensitive than classical virus isolation procedures.

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. Our analysis of wild bird migration suggested that these viruses may have been carried across the Atlantic via Iceland, Greenland/Arctic or pelagic routes. The here documented incursion of HPAI GsGd viruses into North America raises concern for further virus spread across the Americas by wild bird migration.

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks—in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996—have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.