Outbreaks of Clade 2.3.4.4 H5N8 highly pathogenic avian influenza in 2018 in the northern regions of South Africa were unrelated to those of 2017

The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021-2022

In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021-2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho's outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana's outbreaks in 2021 were unrelated, but viruses of Botswana's unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA's commercial poultry cases in 2021-2022 were point introductions from wild birds. Like H5N8 HPAI in 2017-2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.

Descriptive Epidemiology of and Response to the High Pathogenicity Avian Influenza (H5N8) Epidemic in South African Coastal Seabirds, 2018

High pathogenicity avian influenza (HPAI) clade 2.3.4.4b H5N8 virus was detected in coastal seabirds in late 2017 in South Africa, following a devastating epidemic in the commercial poultry and ostrich industries. By May 2018, the infection had been confirmed in fifteen seabird species at 31 sites along the southern coast, with the highest mortality recorded in terns (Family Laridae, Order Charadriiformes). Over 7,500 positive or suspected cases in seabirds were reported. Among those infected were three endangered species: African penguins (Spheniscus demersus Linnaeus, 1758), Cape cormorants (Phalacrocorax capensis Wahlberg, 1855), and Cape gannets (Morus capensis Lichtenstein, 1823). The scale and impact of this outbreak were unprecedented in southern African coastal seabirds and raised logistical challenges in resource allocation, risk mitigation, and outbreak response. It required the collaboration of multiple stakeholder groups, including a variety of government departments and nongovernmental organizations. With another HPAI outbreak in South African seabirds in 2021 and major incursions in seabird species in the northern hemisphere in 2022, it is vital to share and consolidate knowledge on the subject. We describe the epidemic, the lessons learned, and recommendations for developing contingency plans.

Assessing potential pathogenicity of novel highly pathogenic avian influenza (H5N6) viruses isolated from Mongolian wild duck feces using a mouse model

Several novel highly pathogenic avian influenza (HPAIVs) A(H5N6) viruses were reported in Mongolia in 2020, some of which included host-specific markers associated with mammalian infection. However, their pathogenicity has not yet been investigated. Here, we isolated and evaluate two novel genotypes of A(H5N6) subtype in Mongolia during 2018–2019 (A/wildDuck/MN/H5N6/2018-19). Their evolution pattern and molecular characteristics were evaluated using gene sequencing and their pathogenicity was determined using a mouse model. We also compared their antigenicity with previous H5 Clade 2.3.4.4 human isolates by cross-hemagglutination inhibition (HI). Our data suggests that A/wildDuck/MN/H5N6/2018-19 belongs to clade 2.3.4.4h, and maintains several residues associated with mammal adaptation. In addition, our evaluations revealed that their isolates are less virulent in mice than the previously identified H5 human isolates. However, their antigenicity is distinct from other HPAIVs H5 clade 2.3.4.4, thus supporting their continued evaluation as potential infection risks and the preparation of novel candidate vaccines for their neutralization.

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

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.

Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction

Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.

A systematic review of influenza A virus prevalence and transmission dynamics in backyard swine populations globally

Background

Backyard swine farming is critical to generating subsistence and food security in rural and peri-urban households in several developing countries. The objective of this systematic review was to analyze the molecular and serological prevalence of influenza A virus (IAV) in backyard swine populations globally.

Results

We identified 34 full-text research articles in NCBI-PubMed and Google Scholar databases that have reported IAV sero- and/or virological prevalence in backyard swine up to 11 July 2021. The highest number of studies were reported from Asia (n = 11) followed by North America (n = 10), South America (n = 6), Africa (n = 6), and Europe (n = 1). While the maximum number of studies (44.12%) reported human-to-swine transmission of IAV, swine-to-human (5.88%), poultry-to-swine (5.88%), and wild birds-to-swine (2.94%) transmissions were also reported. An overall higher IAV seroprevalence (18.28%) in backyard swine was detected compared to the virological prevalence (1.32%). The human-origin pandemic A(H1N1)pdm09 virus clade 1A.3.3.2 was the more frequently detected IAV subtype in virological studies (27.27%) than serological studies (18.92%). In addition, the avian-origin highly pathogenic H5N1 and H5N8 viruses were also detected, which further substantiated the evidence of avian–swine interactions in the backyards.

Conclusion

Human–swine and avian–swine interactions in backyards may transmit IAV between species. Monitoring the circulation and evolution of IAV in backyard swine would help stakeholders make informed decisions to ensure sustainable backyard swine farming and public safety.

Multiple Reassortants of H5N8 Clade 2.3.4.4b Highly Pathogenic Avian Influenza Viruses Detected in South Korea during the Winter of 2020-2021

During October 2020–January 2021, we isolated a total of 67 highly pathogenic avian influenza (HPAI) H5N8 viruses from wild birds and outbreaks in poultry in South Korea. We sequenced the isolates and performed phylogenetic analysis of complete genome sequences to determine the origin, evolution, and spread patterns of these viruses. Phylogenetic analysis of the hemagglutinin (HA) gene showed that all the isolates belong to H5 clade 2.3.4.4 subgroup B (2.3.4.4b) and form two distinct genetic clusters, G1 and G2. The cluster G1 was closely related to the 2.3.4.4b H5N8 HPAI viruses detected in Europe in early 2020, while the cluster G2 had a close genetic relationship with the 2.3.4.4b H5N8 viruses that circulated in Europe in late 2020. A total of seven distinct genotypes were identified, including five novel reassortants carrying internal genes of low pathogenic avian influenza viruses. Our Bayesian discrete trait phylodynamic analysis between host types suggests that the viruses initially disseminated from migratory waterfowl to domestic duck farms in South Korea. Subsequently, domestic duck farms most likely contributed to the transmission of HPAI viruses to chicken and minor poultry farms, highlighting the need for enhanced, high levels of biosecurity measures at domestic duck farms to effectively prevent the introduction and spread of HPAI.

Comparative infectivity and transmissibility studies of wild-bird and chicken-origin highly pathogenic avian influenza viruses H5N8 in chickens

Despite the recent advances in avian influenza viruses surveillance and genomic data, fundamental questions concerning the ecology and evolution of these viruses remain elusive. In Egypt, H5N8 highly pathogenic avian influenza viruses (HPAIVs) are co-circulating simultaneously with HPAIVs of subtypes H5N1 and low-pathogenic avian influenza viruses (LPAIVs) of subtype H9N2 in both commercial and backyard poultry. In order to isolate AIVs from wild birds and to assess their potential in causing infection in commercial poultry, a total of thirty-four cloacal swab samples were collected from apparently healthy migratory wild birds (Anas acuta, Anas crecca, Rallus aquaticus, and Bubulcus ibis) from four Egyptian Governorates (Giza, Menoufia, Gharbia, and Dakahlia). Based on matrix (M) gene-targeting real-time reverse transcriptase PCR and subsequent genetic characterization, our results revealed two positive isolates (2/34) for H5N8 whereas no H5N1 and H9N2 subtypes were detected. Genetic characterization of the full-length haemagglutinin (HA) genes revealed the clustering of two reported isolates within genotype 5 of clade 2.3.4.4b. The potential of a wild bird-origin H5N8 virus isolated from a cattle egret for its transmission capability within and between chickens was investigated in compare to chicken origin H5N8 AIV. Chickens inoculated with cattle egret isolate showed varying clinical signs and detection of virus shedding. In contrast, the contact chickens showed less levels of virus secretion indicating efficient virus inter/intra-species transmission. These results demonstrated the possibility for spreading of wild bird origin H5N8 viruses between chicken. In conclusion, our study highlights the need for continuous and frequent monitoring of the genetic diversity of H5N8 AIVs in wild birds as well as commercial poultry sectors for better understanding and determining the genetic nature of these viruses, which is fundamental to predict any future threat through virus reassortment with the potential to threaten human and animal health. Likewise, an assessment of coverage and efficacy of different vaccines and or vaccination regimes in the field conditions should be reconsidered along with strict biosecurity measures.

Development and evaluation of a TaqMan MGB RT-PCR assay for detection of H5 and N8 subtype influenza virus

Background

Highly pathogenic influenza A (H5N8) viruses have caused several worldwide outbreaks in birds and are of potential risk to humans. Thus, a specific, rapid and sensitive method for detection is urgently needed.

Methods

In the present study, TaqMan minor groove binder probes and multiplex real-time RT-PCR primers were designed to target the H5 hemagglutinin and N8 neuraminidase genes. A total of 38 strains of avian influenza viruses and other viruses were selected to test the performance of the assay.

Results

The results showed that only H5 and N8 avian influenza viruses yielded a positive signal, while all other subtypes avian influenza viruses and other viruses were negative. High specificity, repeatability, and sensitivity were achieved, with a detection limit of 10 copies per reaction.

Conclusions

The developed assay could be a powerful tool for rapid detection of H5N8 influenza viruses in the future.

Sub-Saharan Africa and Eurasia Ancestry of Reassortant Highly Pathogenic Avian Influenza A(H5N8) Virus, Europe, December 2019

We report detection of a highly pathogenic avian influenza A(H5N8) clade 2.3.4.4b virus in Europe. This virus was generated by reassortment between H5N8 subtype virus from sub-Saharan Africa and low pathogenicity avian influenza viruses from Eurasia.

Avian influenza overview February - May 2020

Between 16 February and 15 May 2020, 290highly pathogenic avian influenza (HPAI) A(H5) virus outbreakswere reported in Europe in poultry (n=287), captive birds (n=2) and wild birds (n=1)in Bulgaria, Czechia,Germany,Hungary andPolandand two low pathogenic avian influenza (LPAI) A(H7N1) virus outbreaks were reported in poultry in Italy. 258 of 287 poultry outbreaks detected in Europe were secondary outbreaks, suggesting that in the large majoryty of cases the spread of the virus was not due to wild birds.Allthe HPAI outbreaks were A(H5N8) apart from three,which were reported as A(H5N2) from Bulgaria. Genetic analysis of the HPAI A(H5N8) viruses isolated from the eastern and central European countries indicates that this is a reassortant between HPAI A(H5N8) viruses from Africa and LPAI viruses from Eurasia. Two distict subtypes were identified in Bulgaria, a novel reassortant A(H5N2) and A(H5N8) that is persisting in the country since 2016. There could be several reasons why only very few HPAI cases were detected in wild birds in this 2019-2020 epidemic season and a better knowledge of wild bird movements and virus-host interaction (e.g. susceptibility of the hosts to this virus) could help to understand the reasons for poor detection of HPAI infected wild birds. In comparison with the last reporting period, a decreasing number of HPAI A(H5)-affected countries and outbreaks were reported from outside Europe. However, there is considerable uncertainty regarding the current epidemiological situation in many countries out of Europe. Four human cases due to A(H9N2) virus infection were reported during the reporting period from China.

Avian influenza overview November 2019- February2020

Between 16 November 2019 and 15 February 2020, 36 highly pathogenic avian influenza (HPAI) A(H5N8) virus outbreakswere reported in Europe in poultry (n=34), captive birds (n=1) and wild birds (n=2), in Poland, Hungary, Slovakia, Romania, Germany, Czechiaand Ukraine,one HPAI outbreakcaused by a simultaneous infection with A(H5N2) and A(H5N8) was reported in poultry in Bulgaria, andtwo low pathogenic avian influenza (LPAI) A(H5) virus outbreaks were reported in poultryin the United Kingdom and in Denmark. Genomic characterisation of the HPAI A(H5N8) viruses suggests that they are reassortants of HPAI A(H5N8) viruses from Africa and LPAI viruses from Eurasia. It is likely that this reassortment occurred in wild migratory birds in Asia during the summer and then spread to eastern Europe with the autumnmigration. This is the first time that wild bird migration from Africa to Eurasia has been implicated in the long-distance spread of HPAI viruses to the EU. Given the late incursion of HPAI A(H5N8) virus into the EU in this winter season (first outbreak reported on 30 December 2019), its overall restriction to eastern Europe, and the approaching spring migration, the risk of the virus spreadingfurther in the west via wild birds is decreasing for the coming months. Genetic analysis of the HPAI A(H5N2) and A(H5N8) viruses detected in the Bulgarian outbreak reveals that these virusesare both related to the 2018-19 Bulgarian HPAI A(H5N8) viruses and not to the HPAI A(H5N8) viruses currently circulating in Europe.An increasing number of HPAI A(H5N1), A(H5N2), A(H5N5) and A(H5N6) virus outbreaks in poultry in Asia were reported during the time period for this report compared with the previous reporting period. Single outbreaks of HPAI A(H5N8) virus were notified by Saudi Arabia and South Africa. Furthermore, in contrast to the last report, HPAI virus-positive wild birds were reported from Israel and one of the key migration areas in northern China.Two human cases due to A(H9N2) virus infection were reported during the reporting period.