Long-term dynamics in different avian influenza viruses in mallard (Anas platyrhynchos) population in Moscow City and region: dependence on the migration activity

The purpose of this study is revealing of the avian influenza virus diversity at the Moscow waterbodies and comparison of the virology changing pattern to the Mallard’s migratory features and wintering capacities at the Moscow waterbodies, as well as an attempt to explain shifting in the virus strain contents and diversity. Mallard droppings were collected in the autumn of 2008–2023 from shores of Moscow and Moscow Region waterbodies. Avian influenza viruses from the feaces were extracted. The extraction process was the standard one with the virus breeding on the chicken embryos. After breeding the extracted viruses were treated by PCR together with specific primaries and then sequences of the type A viruses were obtained. In 2008–2013 European virus strains were prevalent in the Mallard samples, whereas in 2014–2019 the prevalence shifted to the Asian strains. Comparison of these results to the changing of Mallard migration features allow suggesting that European strains were entered into the Moscow Region mainly from the southern Europe. The Asian strains were entered from the Western Europe, since 2014 this part of Europe really became a focus of the Asian strains. For the study period of 2008–2019 in the Mallard feaces extractions from the Moscow waterbodies we observed decreasing of the virus strain numbers. The frequency and the diversity of extracted viruses decreased sharply after 2014. There could be several causes for the decreasing of the strain diversity, in particular this is changing in proportions of hunted ducks during spring and autumn hunting, increasing Mallard numbers on winter grounds within the breeding range, as well as, declining numbers in Black-headed Gulls that are a frequent carrier of the avian influenza.