Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006–2016)

Rimondi, Agustina; Gonzalez‐Reiche, Ana S.; Olivera, Valeria; Decarre, Julieta; Castresana, Gabriel; Romano, Marcelo Munhões; Nelson, Martha I.; Bakel, Harm van; Pereda, Ariel; Ferreri, Lucas; Geiger, Ginger; Pérez, Daniel R.

doi:10.1038/s41426-018-0190-2

Cited by 22 publications

(27 citation statements)

References 59 publications

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“…Overall, our phylogenetic analysis suggests that many of the gene segments collected from wild birds in South America were distinct from those collected from wild birds in North America; the H3, PA, NP, and NS1 genes were more closely related to the 1963 H3N8 EIV, supporting the hypothesis that the 1963 H3N8 EIV originated from wild birds in South America. Our results are consistent with those of Rimondi et al, who reported that viruses from birds from Argentina also carry PA and NP sequences with homology to the EIV ( 12 ). These sequences are closely related to the highlighted sequences from Chile.…”

Section: Resultssupporting

confidence: 93%

“…The origin of the H3N8 lineage is unknown; however, phylogenetic studies and uracil content analysis suggest that these viruses originated in wild birds ( 9 ). The H3N8 EIV-like polymerase acidic (PA), nucleoprotein (NP), and nonstructural (NS) genes have been identified in avian influenza viruses (AIV) isolated from South American wild birds since the mid-2000s; the most recent isolation was in Argentina during 2016 ( 10 – 12 ). Time to most recent common ancestor (tMRCA) analysis suggests that these genes likely originated in AIVs during the 1950s ( 9 , 12 ).…”

mentioning

confidence: 99%

“…The H3N8 EIV-like polymerase acidic (PA), nucleoprotein (NP), and nonstructural (NS) genes have been identified in avian influenza viruses (AIV) isolated from South American wild birds since the mid-2000s; the most recent isolation was in Argentina during 2016 ( 10 – 12 ). Time to most recent common ancestor (tMRCA) analysis suggests that these genes likely originated in AIVs during the 1950s ( 9 , 12 ). However, an EIV-like H3 hemagglutinin (HA) has yet to be identified in AIVs from wild birds.…”

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confidence: 99%

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Equine-Like H3 Avian Influenza Viruses in Wild Birds, Chile

Bravo-Vasquez¹,

Yao²,

Jimenez‐Bluhm³

et al. 2020

Emerg. Infect. Dis.

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A quatic birds are the reservoir of influenza A viruses and responsible for the evolution and longdistance spread of the virus (1-3). Occasionally, spillover into domestic poultry or domesticated mammals can result in human infections (2,4,5) and sustained transmission within a new mammalian host, as shown by equine influenza virus (H3N8) (EIV) (3). The H3N8 EIVs were reported in the southern United States in 1963 during an outbreak in horses imported from Argentina (6,7). This emergence resulted in a pandemic that led to international cocirculation of H7N7 and H3N8 EIVs during the 1960s and 1970s, causing heterosubtypic reassortment that might have contributed to the extinction of H7N7 EIV (8). Today, H3N8 EIVs represent a single genetic lineage capable of inducing serious respiratory disease in susceptible horses. The origin of the H3N8 lineage is unknown; however, phylogenetic studies and uracil content analysis suggest that these viruses originated in wild birds (9). The H3N8 EIV-like polymerase acidic (PA), nucleoprotein (NP), and nonstructural (NS) genes have been identified in avian influenza viruses (AIV) isolated from South American wild birds since the mid-2000s; the most recent isolation was in Argentina during 2016 (10-12). Time to most recent common ancestor (tMRCA) analysis suggests that these genes likely originated in AIVs during the 1950s (9,12). However, an EIV-like H3 hemagglutinin (HA) has yet to be identified in AIVs from wild birds. We performed active surveillance of wild birds in Chile and isolated 6 distinct AIVs with HA, NP, NS, and PA genes having high nucleotide homology with the 1963 H3 EIV. The AIVs were isolated from resident waterfowl belonging to the families Anatidae and Rallidae, suggesting that circulation of these viruses might be restricted to nonmigratory species found only in the Southern Cone of South America. Although viruses from Chile had nucleotide similarity with H3 EIVs, they were antigenically like avian influenza viruses and could be transmitted into chickens, suggesting adaptations to the avian host. These studies provided the initial evidence that an H3 EIVlike HA continues to circulate in wild birds.

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Section: Resultssupporting

confidence: 93%

mentioning

confidence: 99%

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confidence: 99%

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Equine-Like H3 Avian Influenza Viruses in Wild Birds, Chile

Bravo-Vasquez¹,

Yao²,

Jimenez‐Bluhm³

et al. 2020

Emerg. Infect. Dis.

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“…The entire process is time-consuming and occasionally requires multiple ECE passages before a virus is isolated. Our group has been performing IAV surveillance in wild birds in Guatemala and Argentina for more than a decade (Gonzalez-Reiche et al, 2012, 2017Pereda et al, 2008;Rimondi et al, 2018Rimondi et al, , 2011Xu et al, 2012). In both of these countries, we have described the circulation of highly diverse IAVs in terms of subtype combinations as well as phylogenetic characteristics.…”

Section: Discussionmentioning

confidence: 99%

Improved detection of influenza A virus from blue‐winged teals by sequencing directly from swab material

Ferreri

Ortiz

Geiger

et al. 2019

Ecology and Evolution

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The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real‐time RT‐PCR (rRT‐PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next‐generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT‐PCR‐positive swabs collected during the 2013–14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT‐PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.

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“…While surveillance for notifiable AIV subtypes (H5 and H7) is common practice, for neglected subtypes, including H10Nx, surveillance is typically poor. Surveillance of AIV is often limited to subtype prevalence in bird populations based on sequences of HA and NA glycoproteins, but some studies are able to investigate internal genes to examine viral evolution and possible virulence factors ( 24 – 26 ). Internal viral genes are sequenced to determine presence of zoonotic risk mutations or virulence markers of specific segments ( 27 ) or to track the reassortment of internal genes ( 24 , 25 , 28 ), which is of particular importance for H10Nx infections, as they have been shown to frequently reassort with other circulating subtypes.…”

Section: History and Emergence Of H10nx Virusesmentioning

confidence: 99%