Genetic characterization of highly pathogenic avian Influenza H5Nx clade 2.3.4.4b reveals independent introductions in nigeria

Laleye, Agnes Tinuke; Bianco, Alice; Shittu, Ismaila; Sulaiman, Lanre; Fusaro, Alice; Inuwa, Bitrus; Oyetunde, Joshua Seyi; Zecchin, Bianca; Bakam, Judith; Pastori, Ambra; Olawuyi, Kayode Abraham; Schivo, Alessia; Meseko, Clement; Vakuru, Columba; Fortin, Andrea; Monne, Isabella; Joannis, Tony M.

doi:10.1111/tbed.14000

Cited by 8 publications

(12 citation statements)

References 35 publications

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“…2 ). The H5 clade 2.3.4.4b had evolved at around 2016 and currently this clade predominates worldwide ( World Health Organization, 2018 ; Lee et al, 2017b ; Lee et al, 2017a ; Chen et al, 2019 ; Le & Nguyen, 2014 ; Yamaji et al, 2020 ; Gu et al, 2013 ; Tarek et al, 2021 ; Zhang et al, 2020 ; Pohlmann et al, 2019 ; Laleye et al, 2021 ; Lewis et al, 2021 ; Globig et al, 2017 ; Liang et al, 2020 ; Baek et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

Amirgazin

Shevtsov

Karibayev³

et al. 2022

PeerJ

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Background Large poultry die-offs happened in Kazakhstan during autumn of 2020. The birds’ disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia. Methods Samples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions. Results Phylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan’s viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan’s viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds. Conclusion The findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination.

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Section: Resultsmentioning

confidence: 99%

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

Amirgazin

Shevtsov

Karibayev³

et al. 2022

PeerJ

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“…A total of 3131 tracheal ( n = 1566) and cloacal ( n = 1565) samples from 13 bird species were collected by field officers of the Veterinary and Pest Control Services Department, Federal Ministry of Agriculture and Rural Development, Abuja. The samples were collected using polyester cotton swab into viral transport medium and analyzed at National Veterinary Research Institute (NVRI), Nigeria for avian influenza viruses as described previously [ 8 , 9 ].…”

Section: Methodsmentioning

confidence: 99%

“…Following the first episode of HPAI in Nigeria, several subtypes and reassortant strains of AI including H5N1 [ 5 ], H5N2 [ 6 ], H5N8 [ 7 , 8 ] and more recently H5N6 [ 9 ] have been detected in LBMs across the country but no evidence yet of the presence of H9N2 in Nigeria. However, seroconversion to the H9 subtype has been reported in poultry sampled at LBMs in a limited study in Southwestern Nigeria [ 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Live Bird Markets in Nigeria: A Potential Reservoir for H9N2 Avian Influenza Viruses

Sulaiman

Shittu

Fusaro

et al. 2021

Viruses

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Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats.

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“…The affected area is geographically, tem- The tMRCA analysis dated the MRCA with the best statistical support for the genotype 6 cluster to late 2017, that is 2-3 months prior to introduction into SA. The SA and Nigerian genotype 6 strains were similar in all eight genome segments; therefore, the reverse movement of virus from SA to Nigeria was postulated (Laleye et al, 2022). This reverse movement of virus would, however, be unprecedented and highly unlikely because SA has shown itself to be an ecological sink for avian influenza viruses of various subtypes that originated in northern hemisphere, but never a source to northern hemisphere countries, including Nigeria, based on the sequencing of hundreds of AIV genome segments in the past 20 years (NCBI database records).…”

Section: Estimation Of the Tmrca Of Southern African Virusesmentioning

confidence: 99%

“…Clinical signs included diarrhoea, corneal oedema, weakness and incoordination, circling and/or the inability to fly, neurological signs like head tremors, poor balance, torticollis, seizures and death (Roberts, 2018). a Guineafowl sampled at a live bird market in July 2019 (Laleye et al, 2022), and in an outbreak in commercial turkeys in Poland at the end of December 2019 (Świętoń et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary dynamics of the clade 2.3.4.4B H5N8 high‐pathogenicity avian influenza outbreaks in coastal seabirds and other species in southern Africa from 2017 to 2019

Peyrot

Abolnik

Anthony³

et al. 2022

Transbounding Emerging Dis

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From late 2017 to early 2018, clade 2.3.4.4B H5N8 highly pathogenic avian influenza (HPAI) viruses caused mass die‐offs of thousands of coastal seabirds along the southern coastline of South Africa. Terns (Laridae) especially were affected, but high mortalities in critically endangered and threatened species like African Penguins (Spheniscus demersus) caused international concern and, exactly a year later, the disease recurred at a key African Penguin breeding site on Halifax Island, Namibia. Twenty‐five clade 2.3.4.4B H5N8 HPAI viruses from coastal seabirds and a Jackal Buzzard (Buteo rufofuscus) were isolated and/or sequenced in this study. Phylogenetic analyses of the full viral genomes and time to the most recent common ancestor (tMRCA) analyses of the HA, NA, PB1 and PA genes determined that the South African coastal seabird viruses formed a monophyletic group nested within the South African genotype 4 viruses. This sub‐lineage likely originated from a single introduction by terrestrial birds around October 2017. Only the HA and NA sequences were available for the Namibian penguin viruses, but the phylogenetic data confirmed that the South African coastal seabird viruses from 2017 to 2018 were the source and the most closely related South African virus was found in a gull. tMRCA analyses furthermore determined that the progenitors of the five genotypes implicated in the earlier 2017 South African outbreaks in wild birds and poultry were dated at between 2 and 4 months prior to the index cases. tMRCA and phylogenetic data also showed that the novel genotype 6 virus introduced to South Africa in 2018, and later also detected in Nigeria and Poland in 2019, most likely arose in late 2017 in West, Central or East Africa. We propose that it continued to circulate there, and that an unidentified reservoir was the source of both the South African outbreaks in early 2018 and in Nigeria in mid‐2019.

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Genetic characterization of highly pathogenic avian Influenza H5Nx clade 2.3.4.4b reveals independent introductions in nigeria

Cited by 8 publications

References 35 publications

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

Live Bird Markets in Nigeria: A Potential Reservoir for H9N2 Avian Influenza Viruses

Evolutionary dynamics of the clade 2.3.4.4B H5N8 high‐pathogenicity avian influenza outbreaks in coastal seabirds and other species in southern Africa from 2017 to 2019

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