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The Ecology of Influenza A Viruses in Wild Birds in Southern Africa

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Avian influenza viruses (AIVs) are pathogens of global concern, but there has been little previous research on avian influenza in southern Africa and almost nothing is known about the dynamics of AIVs in the region. We counted, captured and sampled birds regularly at five sites, two in South Africa (Barberspan and Strandfontein) and one in each of Botswana (Lake Ngami), Mozambique (Lake Chuali) and Zimbabwe (Lakes Manyame and Chivero) between March 2007 and May 2009. The South African and Zimbabwean sites were visited every 2 months and the sites in Botswana and Mozambique every 4 months. During each visit we undertook 5–7 days of standardised bird counts followed by 5–10 days of capturing and sampling water-associated birds. We sampled 4,977 birds of 165 different species and completed 2,503 half-hour point counts. We found 125 positive rRT-PCR cases of avian influenza across all sites. Two viruses (H1N8 and H3N8) were isolated and additional H5, H6 and H7 strains were identified. We did not positively identify any highly pathogenic H5N1. Overall viral prevalence (2.51%) was similar to the lower range of European values, considerable spatial and temporal variation occurred in viral prevalence, and there was no detectable influence of the annual influx of Palearctic migrants. Although waterbirds appear to be the primary viral carriers, passerines may link wild birds and poultry. While influenza cycles are probably driven by the bird movements that result from rainfall patterns, the epidemiology of avian influenza in wild birds in the subregion is complex and there appears to be the possibility for viral transmission throughout the year.

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We thank the many people who helped us during the course of this study. Logistics and permits were facilitated by Deon Hignett (Cape Nature), Dalton Gibbes (City of Cape Town), Daan Buijs (NorthWest Parks Board), Ongai Musemburi (Zimbabwe Parks and Wildlife Authority), Dr. Pious Makaya and Dr. Chris Foggin (Zimbabwe Veterinary Services), Felix Monggae (Kalahari Conservation Society), Dr. Neo Mapitse (Government of Botswana) and Raimundo Matisse (Government of Mozambique). Sampie van Der Merwe provided accommodation and field support at Barberspan. We are grateful to our >80 field assistants, especially those who helped with three or more sampling missions: Jonathan Aaronson, Joel Avni, Tertius Gous, Dominic Henry, Rhinos Kambanje, Mmapula Kgagodi, Mike Kock, Amos Koloti, Innocent Magunje, Josphine Mundava, Admire Muzeziwa, Andrew Mvundle, David Nkosi, Khumbulani Nyathi and Sydwell Setuki. This research was funded by a USAID-sponsored Global Avian Influenza Network for Surveillance subcontract from the Wildlife Society to GSC, with additional contributions from the DST/NRF Centre of Excellence at the Percy FitzPatrick Institute. Steve Osofsky and Scott Newman facilitated parts of the funding process. Analyses by ARC-OVI were funded by the South African National Department of Agriculture, Forestry and Fisheries; and by IZSVe, by the Italian Ministry of Health and a grant from the Food and Agriculture Organization of the United Nations (FAO). In Zimbabwe we benefited from the “Mesures d’Urgence” and GRIPAVI projects funded by the French Ministry of Foreign Affairs and the scientific and logistical support of the Research Platform Produce and Conserve in Partnership (RP-PCP).

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Correspondence to Graeme S. Cumming.

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Appendix 1 The number of individuals of each of the 165 species that we sampled during this study (includes scientific, common, and family names); and a summary of the numbers and species of Palearctic migrants observed during point counts (RTF 507 kb)

Appendix 2 Dates of each sampling mission and precise coordinates of counting points (RTF 316 kb)


Appendix 3 Background information on study sites, bird counting and capture protocols, and laboratory methods (RTF 65 kb)

Appendix 4 Additional supporting figures (RTF 295 kb)

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Cumming, G.S., Caron, A., Abolnik, C. et al. The Ecology of Influenza A Viruses in Wild Birds in Southern Africa. EcoHealth 8, 4–13 (2011).

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