The Incursion and Spread of Highly Pathogenic Avian Influenza H5N8 Clade 2.3.4.4 Within South Africa

Abolnik, Célia; Pieterse, Reneé; Peyrot, B. M.; Choma, P.; Phiri, T. P.; Ebersohn, Karen; Heerden, Carel van; Vorster, Alvera; Zel, G. van der; Geertsma, Peter; Laleye, Agnes Tinuke; Govindasamy, Krpasha; Rauff, Dionne Linda

doi:10.1637/11869-042518-reg.1

Cited by 39 publications

(65 citation statements)

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“…Although the three epi-based datasets were built to be fairly balanced in terms of sampling location, collection date and host (Supplementary Methods), the number of sequences from wild birds turned out to be very heterogeneous per region. To overcame this host skewed data for certain geographic areas, such as West and East-Central Africa, South Asia and the Middle East, for which the available sequences from wild birds ranged from 5% (West Africa) to 24% (the Middle East), we repeated the analyses by allowing only host species transitions from wild to domestic birds, as to consider the abundant evidence that during and after 2005, Gs/GD lineage introduction in poultry in multiple regions was associated with wild bird migration 12,13,15,[25][26][27][28][29][30][31][32][33][34][35][36] . Using such enforcement, our estimates reveal a significantly higher rate of viral spread in wild birds compared to domestic ones (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The key role of long-distance migrants in the dispersal of HPAI H5 viruses has been suggested by several authors based on phylogenetic analyses, epidemiological investigations and on the timing and direction of the intercontinental spreads, which coincided with fall bird migrations 25,[28][29][30][31][32][33][34][35][36] . Moreover, HPAI H5-infected wild species have been reported in a variety of countries before or simultaneously with poultry outbreaks, and direct or indirect contacts with wild birds have been frequently identified as the most probable cause of virus introduction into poultry 12,13,15,26,27,29,35 . In some African countries, illegal poaching of wild birds, which are kept in rural communities and then sold at markets, is not uncommon and may represent a possible bridge between wild and domestic birds 59 .…”

Section: Discussionmentioning

confidence: 99%

“…Egypt, Tunisia and Nigeria were the first countries reporting the disease [8][9][10] , followed by Niger, Cameroon and Uganda [11][12][13] . In spring 2017, the virus reached the Democratic Republic of the Congo (DR Congo) 14 , Zimbabwe and South Africa 11,15 and in February 2019 new cases were reported in Namibia 16 . Currently, Gs/GD HPAI H5Nx poses a substantial threat to the poultry population in several African countries, and distinct clades are co-circulating in West Africa ( 17,18 (Supplementary Fig.…”

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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

et al. 2019

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The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

et al. 2019

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“…This study suggested the role of wild birds in the introduction of the H5N8 virus strain from other African countries into South Africa and suspected that western African countries may be serving as the epicenter of the H5N8 virus. This was the first report of the HPAIV strain H5N8 from commercial poultry and captive birds in the country [241].…”

Section: South Africamentioning

confidence: 89%

Systematic Review of Important Viral Diseases in Africa in Light of the ‘One Health’ Concept

et al. 2020

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Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.

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“…1 This followed soon after reported outbreaks in neighboring Zimbabwe. 2 Over the months that followed, the virus rapidly spread across the country to all nine South African provinces resulting in the death and culling of millions of commercially farmed birds as well as mortalities in several species of wild birds. 1 People that are in close contact with infected birds or carcasses are regarded as being at potentially elevated risk of acquiring avian influenza (AI) as the virus may be transmitted through infectious secretions and excretions.…”

Section: Introductionmentioning

confidence: 99%

Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017

Valley‐Omar

Cloete

Pieterse

et al. 2020

Influenza Resp Viruses

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Background: In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives:We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak.Methods: Influenza A(H5N8)-positive veterinary specimens were used to evaluate the ability of real-time PCR-based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next-generation sequencing for phylogenetic characterization and screening for mammalian-adaptive mutations.Results: Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real-time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions:Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression | 267 VALLEY-OMAR Et AL.

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The Incursion and Spread of Highly Pathogenic Avian Influenza H5N8 Clade 2.3.4.4 Within South Africa

Cited by 39 publications

References 15 publications

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

Systematic Review of Important Viral Diseases in Africa in Light of the ‘One Health’ Concept

Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017

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