OmniVira

Literature detail

Surveillance of avian influenza through bird guano in remote regions of the global south to uncover transmission dynamics.

Dhammika Leshan Wannigama1,2,3,4,5,6 Mohan Amarasiri7,8 Phatthranit Phattharapornjaroen7,9,10 Cameron Hurst7,11,12,13 Charin Modchang14,15,16 John Jefferson V Besa17,18 Kazuhiko Miyanaga19 Longzhu Cui19 Stefan Fernandez20 Angkana T Huang21 Puey Ounjai22 W K C P Werawatte23 Ali Hosseini Rad S M24 Porames Vatanaprasan25 Dylan John Jay7 Thammakorn Saethang26 Sirirat Luk-In27 Phitsanuruk Kanthawee28 Wanwara Thuptimdang29 Ratana Tacharoenmuang30 Bernadina Cynthia31 S P H Spencer Vitharana32 Natharin Ngamwongsatit33 Hitoshi Ishikawa34 Takashi Furukawa35 Yangzhong Wang36 Andrew C Singer37 Naveen Kumar Devanga Ragupathi38,39 Tanittha Chatsuwan40 Kazunari Sei35 Asuka Nanbo41 Asada Leelahavanichkul40,42 Talerngsak Kanjanabuch43,44,45,46 Hiroshi Hamamoto47 Paul G Higgins48,49,50 Daisuke Sano8,51 Anthony Kicic52,53,54,55 José O Valdebenito56,57,58 Jonas Bonnedahl59 Sam Trowsdale60 Parichart Hongsing47,7,61,62 Aisha Khatib63 Kenji Shibuya64 Shuichi Abe47,17
Affiliations 64 institutions
  1. Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan. [email protected].
  2. Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan. [email protected].
  3. Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan. [email protected].
  4. Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata, Japan. [email protected].
  5. The Lygodium Ceylon Health and Environmental Policy Research Center, Colombo, Sri Lanka. [email protected].
  6. Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, UK. [email protected].
  7. Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan.
  8. Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan.
  9. Faculty of Health Science Technology, Chulabhorn Royal Academy, Bangkok, Thailand.
  10. HRH Princess Chulabhorn Disaster and Emergency Medicine Center, Chulabhorn Royal Academy, Bangkok, Thailand.
  11. Department of Clinical Epidemiology, Faculty of Medicine, Thammasat University, Rangsit, Thailand.
  12. Center of Excellence in Applied Epidemiology, Thammasat University, Rangsit, Thailand.
  13. Mater Research Institute, University of Queensland, Brisbane, QLD, Australia.
  14. Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand.
  15. Centre of Excellence in Mathematics, MHESI, Bangkok, Thailand.
  16. Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, Bangkok, Thailand.
  17. Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan.
  18. College of Medicine, University of the Philippines and Philippine General Hospital, Medicine, Manila, Philippines.
  19. Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan.
  20. Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
  21. Department of Genetics, University of Cambridge, Cambridge, UK.
  22. Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand.
  23. Faculty of Medicine, Wayamba University of Sri Lanka, and Teaching Hospital Kuliyapitiya, Kuliyapitiya, Sri Lanka.
  24. Kite Pharma Inc., Santa Monica, CA, USA.
  25. Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
  26. Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand.
  27. Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.
  28. Public Health major, School of Health Science, Mae Fah Luang University, Chiang Rai, Thailand.
  29. Institute of Biomedical Engineering, Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
  30. National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.
  31. Department of General Medicine, St. Carolus Hospital, Jakarta, Indonesia.
  32. The Lygodium Ceylon Health and Environmental Policy Research Center, Colombo, Sri Lanka.
  33. Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
  34. Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata, Japan.
  35. Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa, Japan.
  36. Division of Respiratory and Critical Care Medicine, Affiliated Fuling hospital of Chongqing University, Chongqing, China.
  37. UK Centre for Ecology & Hydrology, Wallingford, UK.
  38. Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, UK.
  39. Division of Microbial Interactions, Department of Research and Development, Bioberrys Healthcare and Research Centre, Vellore, India.
  40. Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand.
  41. The National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan.
  42. Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand.
  43. Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  44. Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  45. Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  46. Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.
  47. Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan.
  48. Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
  49. German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany.
  50. Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
  51. Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan.
  52. Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.
  53. Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA, Australia.
  54. Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, WA, Australia.
  55. School of Population Health, Curtin University, Bentley, WA, Australia.
  56. Departamento de Zoología, Universidad de Concepción, Concepción, Chile.
  57. Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Concepción, Chile.
  58. Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Santiago, Chile.
  59. Department of Infectious Diseases in Kalmar, Region Kalmar County, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
  60. School of Environment, University of Auckland, Auckland, New Zealand.
  61. Women and Marginalized Health Research Alliance, Port Moresby, Papua New Guinea.
  62. Faculty of Social Sciences, Catholic University of Madagascar, Analamanga, Madagascar.
  63. Department of Family & Community Medicine, University of Toronto, Toronto, ON, Canada.
  64. Tokyo Foundation for Policy Research, Minato-ku, Tokyo, Japan.
PMID 40425586 2025 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

Avian influenza viruses (AIVs) pose a growing global health threat, particularly in low- and middle-income countries (LMICs), where limited surveillance capacity and under-resourced healthcare systems hinder timely detection and response. Migratory birds play a significant role in the transboundary spread of AIVs, yet data from key regions along migratory flyways remain sparse. To address these surveillance gaps, we conducted a study between December 2021 and February 2023 using fresh bird guano collected across 10 countries in the Global South. Here, we show that remote, uninhabited regions in previously unsampled areas harbor a high diversity of AIV strains, with H5N1 emerging as the most prevalent. Some of these H5N1 samples also carry mutations that may make them less responsive to the antiviral drug oseltamivir. Our findings documented the presence of AIVs in several underrepresented regions and highlighted critical transmission hotspots where viral evolution may be accelerating. These results underscore the urgent need for geographically targeted surveillance to detect emerging variants, inform public health interventions, and reduce the risk of zoonotic spillover.

Birds Influenza A Virus, H5N1 Subtype Influenza in Birds Animal Migration Animals Antiviral Agents Epidemiological Monitoring Global Health Humans Oseltamivir Phylogeny

Structured evidence records

Evidence records

3 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.80
Key finding

Genetic and phylogenetic analyses of H5N1 avian influenza viruses from bird guano revealed high strain diversity and mutations associated with reduced oseltamivir sensitivity.

Virus
IAV H5N1
Host
Aves
Location
Not specified
Supporting text

We show that remote, uninhabited regions in previously unsampled areas harbor a high diversity of AIV strains, with H5N1 emerging as the most prevalent. Some of these H5N1 samples also carry mutations that may make them less responsive to the antiviral drug oseltamivir. MeSH terms include 'Influenza A Virus, H5N1 Subtype / genetics' and 'Phylogeny'.

Analysis methods
genetic analysis; phylogenetic analysis
Molecular Adaptation 1 records
Molecular Adaptation Extraction confidence 0.70
Key finding

H5N1 avian influenza virus samples were found with mutations potentially conferring reduced susceptibility to oseltamivir.

Virus
IAV H5N1
Host
Not specified
Location
Not specified
Supporting text

Some of these H5N1 samples also carry mutations that may make them less responsive to the antiviral drug oseltamivir.

Mechanism types
drug_resistance
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.98
Key finding

Avian influenza surveillance using bird guano samples from migratory birds across ten countries revealed high viral diversity and widespread H5N1 prevalence.

Virus
IAV H5N1
Host
Aves
Location
Global South
Supporting text

We conducted a study between December 2021 and February 2023 using fresh bird guano collected across 10 countries in the Global South. Here, we show that remote, uninhabited regions in previously unsampled areas harbor a high diversity of AIV strains, with H5N1 emerging as the most prevalent.

Sample type
bird guano
Geographic raw
Global South