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Volume 6, Issue 1

Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020–21 Open Access

Abstract

Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 (Rufous Horsehoe Bat) six (Lesser Woolly Horseshoe Bat) 15 (Fulvous Fruit Bat) 47 (Bonnet macaques) 35 (Common Palm Civet) five (Small Indian Civet), four (Common Mongoose) ten (Bengal Tiger) eight (Indian Leopard), four (Leopard cats), two (Jungle cats), two (Wild dogs) and one (sloth bear).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Coronavirus , SARS-CoV-2 and wildlife
Funding
This study was supported by the:
  • BBSRC (Award BB/W003546/1)
    • Principle Award Recipient: RachaelTarlinton
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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/content/journal/acmi/10.1099/acmi.0.000686.v3
2024-01-31
2024-05-06
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References

  1. Piewbang C, Poonsin P, Lohavicharn P, Wardhani SW, Dankaona W et al. SARS-CoV-2 transmission from human to pet and suspected transmission from pet to human, Thailand. J Clin Microbiol 2022; 60:e0105822 [View Article] [PubMed]
     [Google Scholar]
  2. Tyson GB, Jones S, Logan N, McDonald M, Marshall L et al. SARS-CoV-2 seroprevalence and cross-variant antibody neutralization in cats, United Kingdom. Emerg Infect Dis 2023; 29:1223–1227 [View Article] [PubMed]
     [Google Scholar]
  3. Oude Munnink BB, Sikkema RS, Nieuwenhuijse DF, Molenaar RJ, Munger E et al. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science 2021; 371:172–177 [View Article] [PubMed]
     [Google Scholar]
  4. Wasniewski M, Boué F, Richomme C, Simon-Lorière E, Van der Werf S et al. Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic. bioRxiv 20232023.02.02.526749 [View Article] [PubMed]
     [Google Scholar]
  5. Kok K-H, Wong S-C, Chan W-M, Wen L, Chu AW-H et al. Co-circulation of two SARS-CoV-2 variant strains within imported pet hamsters in Hong Kong. Emerg Microbes Infect 2022; 11:689–698 [View Article] [PubMed]
     [Google Scholar]
  6. Yen H-L, Sit THC, Brackman CJ, Chuk SSY, Gu H et al. Transmission of SARS-CoV-2 delta variant (AY.127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study. Lancet 2022; 399:1070–1078 [View Article] [PubMed]
     [Google Scholar]
  7. Caserta LC, Martins M, Butt SL, Hollingshead NA, Covaleda LM et al. White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Proc Natl Acad Sci U S A 2023; 120:e2215067120 [View Article] [PubMed]
     [Google Scholar]
  8. McBride D, Garushyants S, Franks J, Magee A, Overend S et al. Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer. Res Sq 2023rs.3.rs-2574993 [View Article] [PubMed]
     [Google Scholar]
  9. Pickering B, Lung O, Maguire F, Kruczkiewicz P, Kotwa JD et al. Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nat Microbiol 2022; 7:2011–2024 [View Article] [PubMed]
     [Google Scholar]
  10. Halfmann PJ, Iida S, Iwatsuki-Horimoto K, Maemura T, Kiso M et al. SARS-Cov-2 Omicron virus causes attenuated disease in mice and Hamsters. Nature 2022; 603:687–692 [PubMed]
     [Google Scholar]
  11. Thakur N, Gallo G, Newman J, Peacock TP, Biasetti L et al. SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges. J Gen Virol 2022; 103: [View Article] [PubMed]
     [Google Scholar]
  12. EFSA Panel on Animal Health and Welfare (AHAW) Nielsen SS, Alvarez J, Bicout DJ, Calistri P et al. SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control. EFSA J 2023; 21:e07822 [View Article] [PubMed]
     [Google Scholar]
  13. Hammer AS, Quaade ML, Rasmussen TB, Fonager J, Rasmussen M et al. SARS-CoV-2 transmission between mink (Neovison vison) and humans, Denmark. Emerg Infect Dis 2021; 27:547–551 [View Article] [PubMed]
     [Google Scholar]
  14. Aguiló-Gisbert J, Padilla-Blanco M, Lizana V, Maiques E, Muñoz-Baquero M et al. First description of SARS-CoV-2 infection in two feral American Mink (Neovison vison) caught in the wild. Animals 2021; 11:1422 [View Article] [PubMed]
     [Google Scholar]
  15. Shriner SA, Ellis JW, Root JJ, Roug A, Stopak SR et al. SARS-CoV-2 exposure in escaped Mink, Utah, USA. Emerg Infect Dis 2021; 27:988–990 [View Article] [PubMed]
     [Google Scholar]
  16. Sikkema RS, Begeman L, Janssen R, Wolters WJ, Geurtsvankessel C et al. Risks of SARS-CoV-2 transmission between free-ranging animals and captive mink in the Netherlands. Transbound Emerg Dis 2022; 69:3339–3349 [View Article] [PubMed]
     [Google Scholar]
  17. Villanueva-Saz S, Giner J, Palomar AM, Gómez MA, Põdra M et al. No evidence of SARS-CoV-2 infection in wild Mink (Mustela lutreola and Neogale vison) from Northern Spain during the first two years of pandemic. Animals 2022; 12:1971 [View Article] [PubMed]
     [Google Scholar]
  18. Wong ACP, Li X, Lau SKP, Woo PCY. Global epidemiology of bat coronaviruses. Viruses 2019; 11:174 [View Article] [PubMed]
     [Google Scholar]
  19. Muylaert RL, Kingston T, Luo J, Vancine MH, Galli N et al. Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health. Proc Biol Sci 2022; 289:20220397 [View Article] [PubMed]
     [Google Scholar]
  20. Cohen LE, Fagre AC, Chen B, Carlson CJ, Becker DJ. Coronavirus sampling and surveillance in bats from 1996-2019: a systematic review and meta-analysis. Nat Microbiol 2023; 8:1176–1186 [View Article] [PubMed]
     [Google Scholar]
  21. Geldenhuys M, Mortlock M, Epstein JH, Pawęska JT, Weyer J et al. Overview of bat and wildlife coronavirus surveillance in Africa: a framework for global investigations. Viruses 2021; 13:936 [View Article] [PubMed]
     [Google Scholar]
  22. Kamau J, Ergunay K, Webala PW, Justi SA, Bourke BP et al. A novel coronavirus and a broad range of viruses in Kenyan cave bats. Viruses 2022; 14:2820 [View Article] [PubMed]
     [Google Scholar]
  23. Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A et al. Full genome Nobecovirus sequences from malagasy fruit bats define a unique evolutionary history for this coronavirus clade. Front Public Health 2022; 10:786060 [View Article] [PubMed]
     [Google Scholar]
  24. Meta Djomsi D, Lacroix A, Soumah AK, Kinganda Lusamaki E, Mesdour A et al. Coronaviruses are abundant and genetically diverse in West and Central African bats, including viruses closely related to human coronaviruses. Viruses 2023; 15:337 [View Article] [PubMed]
     [Google Scholar]
  25. Ntumvi NF, Ndze VN, Gillis A, Le Doux Diffo J, Tamoufe U et al. Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E. Virus Evol 2022; 8:veab110 [View Article] [PubMed]
     [Google Scholar]
  26. Wani H, Menon S, Desai D, D’Souza N, Bhathena Z et al. Wastewater-based epidemiology of SARS-CoV-2: assessing prevalence and correlation with clinical cases. Food Environ Virol 2023; 15:131–143 [View Article] [PubMed]
     [Google Scholar]
  27. Kumar D, Antiya SP, Patel SS, Pandit R, Joshi M et al. Surveillance and molecular characterization of SARS-CoV-2 infection in non-human hosts in Gujarat, India. Int J Environ Res Public Health 2022; 19:21 [View Article] [PubMed]
     [Google Scholar]
  28. Borkakoti R, Karikalan M, Nehul SK, Jogi HR, Sharma K et al. A retrospective study showing a high rate of seropositivity against SARS-CoV-2 in wild felines in India. Arch Virol 2023; 168:109 [View Article] [PubMed]
     [Google Scholar]
  29. Karikalan M, Chander V, Mahajan S, Deol P, Agrawal RK et al. Natural infection of Delta mutant of SARS-CoV-2 in Asiatic lions of India. Transbound Emerg Dis 2022; 69:3047–3055 [View Article] [PubMed]
     [Google Scholar]
  30. Mishra A, Kumar N, Bhatia S, Aasdev A, Kanniappan S et al. SARS-CoV-2 Delta variant among Asiatic Lions, India. Emerg Infect Dis 2021; 27:2723–2725 [View Article] [PubMed]
     [Google Scholar]
  31. Mahajan S, Karikalan M, Chander V, Pawde AM, Saikumar G et al. Detection of SARS-CoV-2 in a free ranging leopard (Panthera pardus fusca) in India. Eur J Wildl Res 2022; 68:59 [View Article] [PubMed]
     [Google Scholar]
  32. Goodale E, Mammides C, Mtemi W, Chen YF, Barthakur R et al. Increasing collaboration between China and India in the environmental sciences to foster global sustainability. Ambio 2022; 51:1474–1484 [View Article] [PubMed]
     [Google Scholar]
  33. Rana AK, Kumar N. Current wildlife crime (Indian scenario): major challenges and prevention approaches. Biodivers Conserv 2023; 32:1473–1491 [View Article] [PubMed]
     [Google Scholar]
  34. Walsh MG, Hossain S. Population structure and diet generalism define a preliminary ecological profile of zoonotic virus hosts in the Western Ghats, India. Epidemics 2020; 33:100416 [View Article] [PubMed]
     [Google Scholar]
  35. Epitools Epitools sample size calculation; 2020 https://epitools.ausvet.com.au/samplesize?page=SampleSize
  36. Tsoleridis T, Ball JK. Discovery of novel coronaviruses in rodents. Methods Mol Biol 2020; 2203:33–40 [View Article] [PubMed]
     [Google Scholar]
  37. Poon LLM, Chu DKW, Chan KH, Wong OK, Ellis TM et al. Identification of a novel coronavirus in bats. J Virol 2005; 79:2001–2009 [View Article] [PubMed]
     [Google Scholar]
  38. Fischer M, Freuling CM, Müller T, Wegelt A, Kooi EA et al. Molecular double-check strategy for the identification and characterization of European Lyssaviruses. J Virol Methods 2014; 203:23–32 [View Article] [PubMed]
     [Google Scholar]
  39. Balasubramaniam KN, Marty PR, Samartino S, Sobrino A, Gill T et al. Impact of individual demographic and social factors on human-wildlife interactions: a comparative study of three macaque species. Sci Rep 2020; 10:21991 [View Article] [PubMed]
     [Google Scholar]
  40. Kadam RG, Karikalan M, Siddappa CM, Mahendran K, Srivastava G et al. Molecular and pathological screening of canine distemper virus in Asiatic lions, tigers, leopards, snow leopards, clouded leopards, leopard cats, jungle cats, civet cats, fishing cat, and jaguar of different states, India. Infect Genet Evol 2022; 98:105211 [View Article] [PubMed]
     [Google Scholar]
  41. Sato S, Kabeya H, Shigematsu Y, Sentsui H, Une Y et al. Small Indian mongooses and masked palm civets serve as new reservoirs of Bartonella henselae and potential sources of infection for humans. Clin Microbiol Infect 2013; 19:1181–1187 [View Article] [PubMed]
     [Google Scholar]
  42. Apaa T, Withers AJ, Staley C, Blanchard A, Bennett M et al. Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology. J Gen Virol 2023; 104: [View Article] [PubMed]
     [Google Scholar]
  43. Wu Z, Han Y, Wang Y, Liu B, Zhao L et al. A comprehensive survey of bat sarbecoviruses across China in relation to the origins of SARS-CoV and SARS-CoV-2. Natl Sci Rev 2023; 10:nwac213 [View Article] [PubMed]
     [Google Scholar]
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Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020–21
Access Microbiology 6, 000686.v3 (2024); https://doi.org/10.1099/acmi.0.000686.v3
/content/journal/acmi/10.1099/acmi.0.000686.v3
/content/journal/acmi/10.1099/acmi.0.000686.v3
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