Experience in organizing monitoring of wild animal viruses potentially dangerous to humans and farm animals: The specifics of organization of field material sampling

Aim. Wild animals serve as an important natural reservoir for dangerous viruses. Their migration and interaction with domestic or farm animals and also humans may create conditions for the transmission and spreading of zoonotic infections. This emphasises the importance and necessity of monitoring and research in this area for potential outbreaks of human and animal diseases for prevention. In this regard, an important question arises of how to organize properly the sampling from wild animals. This is the first and the most important stage of monitoring for pathogens and, depending on its optimal implementation, we will subsequently receive adequate results on viral pathogens introduced or circulating in the study area.
In this analytical work, we tried to summarise our twenty‐five years of experience in studying viral pathogens in wild animals throughout almost the entire territory of Russia. The choice of key sampling sites (locations) for monitoring zoonotic infections in bats and birds is substantiated. Depending on the region, the periods for the principal sampling activities are determined. The criteria for selecting a list of bird and bat species and the number of collecting samples are described.
Collection of field material from wildlife is a basic and very important task for monitoring the circulation of viral pathogens in wild animals. Inadequate collection methods can lead to erroneous results and, accordingly, to erroneous conclusions about the presence of potentially dangerous viruses in the surveyed area surveyed.

1. Lvov D.K., Ilyichev V.D. Migracii ptic I perenos vosbuditeley infekcii [Bird migration and transmission of infectious agents: (Ecol.‐ geogr. connections of birds with infectious agents)]. Moscow, Nauka Publ., 1979, 270 p. (In Russian)

2. Daszak P., Cunningham A.A., Hyatt A.D. Anthropogenic environmental change and the emergence of infectious diseases in wildlife. Acta Tropica, 2001, vol. 78, iss. 2, pp. 103–116. https://doi.org/10.1016/s0001‐706x(00)00179‐0

3. Daszak P., Epstein J.H., Kilpatrick A.M., Aguirre A.A., Karesh W.B., Cunningham A.A. Collaborative research approaches to the role of wildlife in zoonotic disease emergence. Current Topics in Microbiology and Immunology, 2007, vol. 315, pp. 463–475. https://doi.org/10.1007/978‐3‐540‐70962‐6_18

4. Shestopalov A.M., Alekseev A.Y., Glupov V.V., Voevoda M.I. Wild Animal Migration As a Potential Threat of Introduction of New Viruses into Russia. Herald of the Russian Academy of Sciences, 2022, vol. 92, no. 8, pp. 766–774. https://doi.org/10.1134/S1019331622040220

5. Taylor L.H., Latham S.M., Woolhouse M.E.J. Risk factors for human disease emergence. Philosophical Transactions of the Royal Society B: Biological Sciences, 2001, vol. 356(1411), pp. 983–989. https://doi.org/10.1098/rstb.2001.0888

6. Jones K.E., Patel N.G., Levy M., Storeygard A., Balk D., Gittleman J.L., Daszak P. Global trends in emerging infectious diseases. Nature, 2008, vol. 451(7181), pp. 990–993. https://doi.org/10.1038/nature06536

7. Schatz J., Fooks A.R., McElhinney L., Horton D., Echevarria J., Vázquez‐Moron S., Kooi E.A., Rasmussen T.B., Müller T., Freuling C.M. Bat rabies surveillance in Europe. Zoonoses and Public Health, 2013, vol. 60(1), pp. 22–34. https://doi.org/10.1111/zph.12002

8. Latinne A., Hu B., Olival K.J., Zhu G., Zhang L.‐B., Li H., Chmura A.A., Field H.E., Zambrana‐Torrelio C., Epstein J.H., Li B., Zhang W., Wang L.‐F., Shi Z.‐L., Daszak P. Origin and cross-species transmission of bat coronaviruses in China. Nature Communications, 2024, vol. 15, article number: 10705. https://doi.org/10.1038/s41467‐024‐55384‐7

9. Olsen B., Munster V.J., Wallensten A., Waldenström J., Osterhaus A. D. M. E., Fouchier R. A. M. Global patterns of influenza A virus in wild birds. Science, 2006, vol. 312(5772), pp. 384–388. https://doi.org/10.1126/science.1122438

10. Hesterberg U., Harris K., Stroud D.A., Guberti V., Busani L., Pittman M., Piazza V., Cook A., Brown I. Avian influenza surveillance in wild birds in the European Union in 2006. Influenza and Other Respiratory Viruses, 2009, vol. 3(6), pp. 271–279. https://doi.org/10.1111/j.1750‐2659.2008.00058.x

11. Pannwitz G., Wolf C., Harder T. Active surveillance for avian influenza virus infection in wild birds by analysis of hunter‐ harvested specimens in Germany, 2006–2008. Journal of Wildlife Diseases, 2009, vol. 45(2), pp. 421–426. https://doi.org/10.7589/0090‐3558‐45.2.421

12. Han H.J., Wen H.L., Zhou C.M., Chen F.F., Luo L.M., Liu J.W., Yu X.J. Bats as reservoirs of severe emerging infectious diseases. Virus Research, 2015, vol. 205, iss. 2, pp. 1–6. https://doi.org/10.1016/j.virusres.2015.05.006

13. Ivanitzky A.N., Alekseev A.Yu. Distribution of bats in the subtropical regions of the Black Sea coast and adjacent territories. South of Russia: ecology, development, 2023, vol. 18, no. 4, pp. 8– 30. (In Russian) https://doi.org/10.18470/1992‐1098‐2023‐4‐8‐30

14. Smirnov D.G., Jamirzoev G.S., Vechnik V.P., Bykov Yu.A., Gazaryan S.V. Assessment of the study of the fauna of bats (Chiroptera) Dagestan. Russian Journal of Ecosystem Ecology, 2021, no. 4. (In Russian) https://doi.org/10.21685/2500‐0578‐2021‐4‐1

15. Snitko V.P. Summer habitats of sedentary bat species in the Southern Urals. Plecotus et al, 2005, no. 8, pp. 43–53. (In Russian)

16. Zhigalin A.V., Gadzhiev A.A., Daudova M.G., Salimkhanov N.G., Shestopalov A.M. Ecology of chiroptera bats in Altai‐Sayan region of southern Siberia. South of Russia: ecology, development, 2019, vol. 14, no. 1, pp. 9–25. (In Russian) https://doi.org/10.18470/1992‐1098‐2019‐1‐9‐25

17. Botvinkin A.D., Belikov D.S., Kazakov D.V., Matveev V.A., Rosina V.V., Hutson A.M., Shumkina A.P. Diversity and relative abundance of bats in the southern Baikal region in habitats with varying degrees of urbanization. Baikal Zoological Journal, 2016, vol. 19, no. 2, pp. 101–106. (In Russian)

18. Kartavtseva I.V., Gorobeyko U.V., Tiunov M.P. The current state of chromosomal studies of bats (Chiroptera) The Russian Far East. Zoological Journal, 2014, vol. 93, no. 7, pp. 1–14. (In Russian)

19. Newman S.H., Field H.E., de Jong C.E, Epstein J.H. Investigating the role of bats in emerging zoonoses: Balancing ecology, conservation and public health interests. Food and Agricultural Organization of the United Nations. Rome: FAO Animal Production and Health Manual N 12, 2011

20. Sasaki M., Setiyono A., Handharyani E., Rahmadani I., Taha S., Adiani S., Subangkit M., Sawa H., Nakamura I., Kimura T. Molecular detection of a novel paramyxovirus in fruit bats from Indonesia. Virology Journal, 2012, iss. 19, article number: 240. https://doi.org/10.1186/1743‐422X‐9‐240

21. Irving A.T., Ahn M., Goh G., Anderson D.E., Wang L.F. Lessons from the host defences of bats, a unique viral reservoir. Nature, 2021, iss. 589, pp. 363–370. https://doi.org/10.1038/s41586‐020‐03128‐0

22. Streicker D.G., Turmelle A.S., Vonhof M.J., Kuzmin I.V., McCracken G.F., Rupprecht C.E. Host phylogeny constrains cross‐ species emergence and establishment of rabies virus in bats. Science, 2010, vol. 329, iss. 5992, pp. 676–679. https://doi.org/10.1126/science.1188836

23. Chan J.F., To K.K., Chen H., Yuen K.Y. Cross‐species transmission and emergence of novel viruses from birds. Current Opinion in Virology, 2015, vol. 10, pp. 63–69. https://doi.org/10.1016/j.coviro.2015.01.006

24. Verhagen J.H., Fouchier R.A.M., Lewis N. Highly Pathogenic Avian Influenza Viruses at the Wild‐Domestic Bird Interface in Europe: Future Directions for Research and Surveillance. Viruses, 2021, vol. 13, iss. 2, pp. 212. https://doi.org/10.3390/v13020212

25. Hesterberg U., Harris K., Stroud D., Guberti V., Busani L., Pittman M., Piazza V., Cook A., Brown I. Avian influenza surveillance in wild birds in the European Union in 2006. Influenza Other Respir Viruses, 2009, vol. 3, iss. 1, pp. 1–14. https://doi.org/10.1111/j.1750‐2659.2008.00058.x

26. Snit’ko V.P. Bats (Chiroptera, Vespertilionidae) from the Cis-Urals and South Urals (Republic of Bashkortostan). Biology Bulletin, 2016, iss. 43, pp. 587–598. https://doi.org/10.1134/S1062359016070177

27. Pannwitz G., Wolf C., Harder T. Active surveillance for avian influenza virus infection in wild birds by analysis of hunter‐ harvested specimens in Germany, 2006–2008. Journal of Wildlife Diseases, 2009, vol. 45, iss. 2, pp. 421–426. https://doi.org/10.7589/0090‐3558‐45.2.421

28. Machalaba C.C., Elwood S.E., Forcella S., Smith K.M., Hamilton K., Jebara K.B., Swayne D.E., Webby R.J., Mumford E., Mazet J.A., Gaidet N., Daszak P., Karesh W.B. Global avian influenza surveillance in wild birds: a strategy to capture viral diversity. Emerging Infectious Diseases, 2015, vol. 21, iss. 4, pp. e1–e7. https://doi.org/10.3201/eid2104.141415

29. Verhagen J.H., Fouchier R.A.M., Lewis N. Highly pathogenic avian influenza viruses at the wild–domestic bird interface in Europe. Viruses, 2021, vol. 13, iss. 2, pp. 212. https://doi.org/10.3390/v13020212

30. Veen J., Yurlov A.K., Delany S., Mihantiev A.I., Selivanova M., Boere G.C. An Atlas of Movements of Southwest Siberian Waterbirds. Wageningen: Wetlands International. Netherlands, 2005, 60 p.

31. Boere G.C., Galbraith C.A., Stroud D.A. Waterbirds around the world. Edinburgh: TSO Scotland Ltd. UK., 2006, 940 p.

32. Rozenfeld S.B., Strelnikov E.G., Volkov S.V. Migration routes and key stopovers of Anser fabalis fabalis (Anseriformes): critical protection gaps. Nature Conservation Research, 2024, vol. 9, iss. 4, pp. 80–92. https://doi.org/10.24189/ncr.2024.033

33. Boere G.C., Galbraith C.A., Stroud D.A. A Bird’s-Eye View on Flyways: A Brief Tour by the Convention on Migratory Species of Wild Animals (second edition). Bonn: UNEP/ CMS Secretariat, Germany, 2012, 64 p. Available at: https://www.cms.int/sites/default/files/publication/cms_pub_pop-series_bird-eye-view-flyways_2ed_web.pdf (accessed 12.04.2025)

34. Verhagen J.H., Fouchier R.A.M., Lewis N. Highly pathogenic avian influenza viruses at the wild–domestic bird interface in Europe: Future Directions for Research and Surveillance. Viruses, 2021, vol. 13, iss. 2, pp. 212. https://doi.org/10.3390/v13020212

35. Klenina A.A., Ruchin A., Bykov E. Occurrence of the birds of the Middle Volga Region (South‐East of the European part of Russia). Biodiversity Data Journal, 2021, vol. 9, article number: e72075. https://doi.org/10.3897/BDJ.9.e72075

36. Golubev S. Status of the Pallas’s Gull Ichthyaetus ichthyaetus during Summer/Autumn in the Fairway Volga–Kama Reservoirs (East European Plain) in Russia. Birds, 2023, no. 4, pp. 46–60. https://doi.org/10.3390/birds4010004

37. Zakharov V.D. The influence of climate change on the dates of bird arrival to the Ilmen State Reserve, Southern Urals. Russian Journal of Ecology, 2016, vol. 47, pp. 543–550. https://doi.org/10.1134/S1067413616060138

38. Yurlov K.T. Ekologiya i biotsenoticheskie svyazi pereletnykh ptits Zapadnoi Sibiri [Ecology and biocenotic relationships of migratory birds of Western Siberia]. Novosibirsk, Nauka: Siberian Branch Publ., 1981, 288 p. (In Russian)

39. Onishchenko G.G., Berezhnov S.P., Shestopalov A.M., Alekseev A.Yu., Ternovoy V.A., Khaytovich A.B., Krovyakova M.T., Netesov S.V., Drozdov I.G. Molecular biological analysis of influenza virus isolates that caused epizootics in the South of Western Siberia and in the Republic of Crimea. Zhurnal mikrobiologii, epidemiologii i immunobiologii [Journal of Microbiology, epidemiology and immunobiology]. 2007, no. 5, pp. 28–32. (In Russian)

40. Melnikov Yu.I. Waterfowl of the Baikal region: spatial structure and breeding success. Izvestiya Irkutskogo gosudarstvennogo universiteta: Seriya «Biologiya. Ekologiya» [Izvestiya Irkutsk State University: Series "Biology. Ecology"]. 2010, vol. 3, no. 1, pp. 49– 59. (In Russian)

41. Degtyarev A.G. Okhotnich'e‐promyslovye ptitsy Respubliki Sakha (Yakutiya) [Hunting and commercial birds of the Republic of Sakha (Yakutia)]. Yakutsk, Siberian Branch of the Russian Academy of Sciences Publ., 2004, 142 p. (In Russian)

42. Shan T., Yang S., Wang H., Wang H., Zhang J., Gong G., Xiao Y., Yang J., Wang X., Lu J., Zhao M., Yang Z., Lu X., Dai Z., He Y., Chen X., Zhou R., Yao Y., Kong N., Zeng J., Ullah K., Wang X., Shen Q., Deng X., Zhang J., Delwart E., Tong G., Zhang W. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. Microbiome, 2022, vol. 10, iss. 1, pp. 60. https://doi.org/10.1186/s40168‐022‐01246‐7

43. Michel F., Fischer D., Eiden M., Fast C., Reuschel M., Müller K., Rinder M., Urbaniak S., Brandes F., Schwehn R., Lühken R., Groschup M.H., Ziegler U. West Nile Virus and Usutu Virus Monitoring of Wild Birds in Germany. International Journal of Environmental Research and Public Health, 2018, vol. 15, iss. 1, pp. 171. https://doi.org/10.3390/ijerph15010171

44. Chamings A., Nelson T.M., Vibin J., Wille M., Klaassen M., Alexandersen S. Detection and characterisation of coronaviruses in migratory and non‐migratory Australian wild birds. Scientific Reports, 2018, no. 8, article number: 5980. https://doi.org/10.1038/s41598‐018‐24407‐x

45. Ng D.Y.M., Sun W., Sit T.H.C., Brackman C.J., Tse A.C.N., Bui C.H.T., Tang A.W.Y., Wong A.N.C., Tsang A.T.L., Koo J.C.T., Cheng S.M.S., Peiris M., Samborskiy D.V., Gorbalenya A.E., Chin A.W.H., Poon L.L.M. Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in the Deltacoronavirus. Virus Evolution, 2025, vol. 11, iss. 1, article number: veaf049. https://doi.org/10.1093/ve/veaf049