Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022

Jimenez-Bluhm, P.; Siegers, J. Y.; Tan, S.; Sharp, B.; Freiden, P.; Johow, M.; Orozco, K.; Ruiz, S.; Baumberger, C.; Galdames, P.; Gonzalez, M. A.; Rojas, C.; Karlsson, E. A.; Hamilton-West, C. N.; Schultz-Cherry, S.

doi:10.1101/2023.02.01.526205

bioRxiv · 10.1101/2023.02.01.526205

Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022

Jimenez-Bluhm, P.·Siegers, J. Y.·Tan, S.·Sharp, B.·Freiden, P.·Johow, M.·Orozco, K.·Ruiz, S.·Baumberger, C.·Galdames, P.·Gonzalez, M. A.·Rojas, C.·Karlsson, E. A.·Hamilton-West, C. N.·Schultz-Cherry, S.

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Abstract

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), Franklins 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.

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Jimenez-Bluhm, P., Siegers, J. Y., Tan, S., Sharp, B., Freiden, P., Johow, M., Orozco, K., Ruiz, S., Baumberger, C., Galdames, P., Gonzalez, M. A., Rojas, C., Karlsson, E. A., Hamilton-West, C. N., Schultz-Cherry, S.. 2023-02-03. Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022. https://doi.org/10.1101/2023.02.01.526205

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