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Since the emergence of the Highly Pathogenic Avian Influenza H5N1 goose/Guangdong (Gs/GD) lineage in China in 1996, these viruses have spread globally. This includes the recent introduction of the Gs/GD lineage 2.3.4.4b in the Americas in 2021, which has affected both wild and domestic bird populations causing high mortality. Since November 2022, reports of mortality in wild birds in numerous South American countries along the Pacific Migratory Flyway have been attributed to this lineage. Through an ongoing longitudinal avian influenza virus (AIV) surveillance, we determined that AIV prevalence remained below 1% in the Lluta river wetland from August through October 2022. However, there was a significant increase in prevalence to 2.6% and 11.7% in November and December respectively, coinciding with the arrival of migratory birds from the Northern Hemisphere. Of the AIV RT-qPCR positive environmental feces samples 7 were identified as A/H5. Sequencing of the COI gene demonstrated that the H5 positive samples were obtained from Peruvian pelican (n=1), Franklin’s gull (n=1), Gray gull (n=1), Elegant tern (n=2) and Black skimmer (n=2). Full genomes were obtained from 3 samples and the putative cleavage site composition of the HA was polybasic REKRRKR/GLF for all. Phylogenetic analysis of the samples revealed them to belong to the H5 2.3.4.4b clade, closely related to isolates obtained in Peru in late November. The emergence of H5 clade 2.3.4.4b in South America has an immediate impact on public health, animal production and wildlife, hence increased active surveillance is warranted.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and has since caused a global pandemic resulting in millions of cases and deaths1-4. Diagnostic tools and serological assays are critical for controlling the outbreak5-7, especially assays designed to quantitate neutralizing antibody levels, considered the best correlate of protection8-11. As vaccines become increasingly available12, it is important to identify reliable methods for measuring neutralizing antibody responses that correlate with authentic virus neutralization but can be performed outside of biosafety level 3 (BSL3) laboratories. While many neutralizing assays using pseudotyped virus have been developed, there have been few studies comparing the different assays to each other as surrogates for authentic virus neutralization9,10,13,14. Here we characterized three enzyme-linked immunosorbent assays (ELISAs) and three pseudotyped VSV virus neutralization assays and assessed their concordance with authentic virus neutralization. The most accurate assays for predicting authentic virus neutralization were luciferase and secreted embryonic alkaline phosphatase (SEAP) expressing pseudotyped virus neutralizations, followed by GFP expressing pseudotyped virus neutralization, and then the ELISAs.

The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses. IMPORTANCE Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.