Local-Scale Diversity and Between-Year “Frozen Evolution” of Avian Influenza A Viruses in Nature

Abstract

Influenza A virus (IAV) in wild bird reservoir hosts is characterized by the perpetuation in a plethora of subtype and genotype constellations. Multiyear monitoring studies carried out during the last two decades worldwide have provided a large body of knowledge regarding the ecology of IAV in wild birds. Nevertheless, other issues of avian IAV evolution have not been fully elucidated, such as the complexity and dynamics of genetic interactions between the co-circulating IAV genomes taking place at a local-scale level or the phenomenon of frozen evolution. We investigated the IAV diversity in a mallard population residing in a single pond in the Czech Republic. Despite the relative small number of samples collected, remarkable heterogeneity was revealed with four different IAV subtype combinations, H6N2, H6N9, H11N2, and H11N9, and six genomic constellations in co-circulation. Moreover, the H6, H11, and N2 segments belonged to two distinguishable sub-lineages. A reconstruction of the pattern of genetic reassortment revealed direct parent-progeny relationships between the H6N2, H11N9 and H6N9 viruses. Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically unchanged form in the close proximity of the original sampling locality. The almost absolute nucleotide sequence identity of all the respective genomic segments between the two H6N9 viruses indicates frozen evolution as a result of prolonged conservation in the environment. The persistence of the H6N9 IAV in various abiotic and biotic environmental components was also discussed.

Survivability of highly pathogenic avian influenza virus (H5N1) in naturally preened duck feathers at different temperatures

“…Similarly, LPAI H5N1 at 0°C and 10°C showed a T‐90 value (90% reduction in infectivity) of 75 days and 16 days respectively in faeces (Nazir et al., ). However, studies on abiotic reservoirs of AIVs like faeces, intact pond water and pond sediments demonstrated that these fomites did not provide sufficient protection for optimum durations to ensure the year‐to‐year preservation of the virus (Keeler et al., ; Nagy et al., ; Nazir et al., ). Detached duck feathers present in the environment might result in longer environmental persistence of the AIVs compared to faeces and contaminated water (Yamamoto et al., ).…”

“…The progressive dilution of infectious faeces in water would reduce the probability of virushost interactions, implying that there should be certain natural mechanisms that concentrate AIVs from water onto bird's bodies, especially the feathers as even unfavourable environmental conditions during summer do not prevent circulation of AIVs in the environment (Hénaux, Samuel, Dusek, Fleskes, & Ip, 2012). The abiotic reservoirs of AIVs studied so far like faeces, intact pond water and pond sediments did not provide sufficient protection for optimum durations to ensure the year-to-year preservation of the virus (Keeler, Lebarbenchon, & Stallknecht, 2013;Nagy, Černíková, Jiřincová, Havlíčková, & Horníčková, 2014;Nazir, Haumacher, Ike, & Marschang, 2011). Feathers could be a potential source of infection for unaffected birds in nature (Yamamoto et al, 2007).…”

Phylogenetic study of H5 low pathogenic avian influenza viruses detected in wild birds in Poland in 2010−2015

“…This may suggest that Polish 2013-2014-year H5N3 isolates are a “closed circle”, in which genes such as NP underwent complete rearrangement, but PB2-HA gene constellation was preserved for three years, which may indicate their increased compatibility. An extensive reassortment of AIVs at a local level over short time was demonstrated ( 16 , 29 ). On the other hand, circulation of specific gene constellation without reassortment for a prolonged time was also observed ( 4 , 15 ), to which the existence of frozen evolution of AIV may contribute as a result of persistence in the environment without replication ( 16 ).…”

Genetic Characterization of Avian Influenza A (H11N9) Virus Isolated from Mandarin Ducks in South Korea in 2018

“…Unlike various combinations such as H2N2, H3N2, and H1N1, which threaten human health, H11N9 strains have mostly unknown effects for either avians or humans. H11N9 strains were first isolated in Europe (Great Britain) in 1982 [5], after which they were continuously detected through worldwide surveillance, showing low virulence in avians such as in Australia in 1987 and then in 2006, in Europe in 2002-2014 [6][7][8][9][10]; southern Africa in 2008-2009 [11]; Asian countries in 2009 to 2011-2012 [12][13][14]; USA in 2007 [15]; and for the first time in South America in 2014 [16] followed by in 2015 [17].…”