New Reassortant Clade 2.3.4.4b Avian Influenza A(H5N6) Virus in Wild Birds, South Korea, 2017-18

Rapid and specific on-site H5Nx avian influenza diagnosis via RPA and PAM-independent CRISPR-Cas12a assay combined with anti-NP antibody-based viral RNA purification

Rapid and accurate detection of H5Nx avian influenza viruses is critical for effective surveillance and control measures. Currently, RT-qPCR with spin column RNA extraction is the gold standard for HPAIV surveillance, but its long reaction time and need for specialized equipment limit its effectiveness for rapid response. In this study, we introduce a centrifuge-free, rapid detection method for on-site detection of H5Nx viruses that combines magnetic bead-based ribonucleoprotein (RNP) purification and concentration with a CRISPR-Cas12a system that is independent of the protospacer adjacent motif (PAM) sequence. Our approach employs anti-NP monoclonal antibodies for the targeted isolation of RNA bound to RNPs, facilitating a quick and specific RNA extraction process that negates the need for centrifugation. Additionally, by denaturing the RT-RPA amplicon using 60% DMSO, we activate the trans-ssDNA cleavage activity of the Cas12a protein without the need for a specific PAM (5'-TTTV-3') sequence. This strategy increases flexibility in CRISPR RNA design, providing a significant advantage when targeting genes with high variability. We validated the efficacy of our magnetic RNP purification and concentration method in combined with an RT-RPA/PAM-independent Cas12a assay for detecting the H5 gene. The assay achieved a sensitivity threshold of 101 EID50 with fluorescent detection and 102 EID50 using lateral flow strips. It also exhibited high specificity, yielding positive results solely for H5Nx viruses among various influenza A virus subtypes. Furthermore, in clinical samples, the assay demonstrated 80% sensitivity and 100% specificity. These results highlight the advantages of using NP-specific antibodies for RNP purification and CRISPR-Cas12a with viral gene-specific crRNA to achieve exceptional diagnostic specificity.

Emergence of HPAI H5N6 Clade 2.3.4.4b in Wild Birds: A Case Study From South Korea, 2023

The emergence and evolution of avian influenza A viruses (AIVs) pose significant challenges to both public health and animal husbandry worldwide. Here, we characterized a novel reassortant highly pathogenic avian influenza virus (HPAIV), clade 2.3.4.4b H5N6, that was isolated from a mandarin duck in South Korea in December 2023. Phylogenetic and molecular analyses show that the hemagglutinin (HA) gene of the 23-JBN-F12-36/H5N6 virus clustered with HPAIV clade 2.3.4.4b H5N1 viruses, which were circulating in South Korea and Japan in 2022-2023. The M and polymerase acidic (PA) genes also revealed a close association with the HPAIV clade 2.3.4.4b H5N1 AIV that was identified previously in South Korea during November 2022. Notably, the neuraminidase (NA) gene of the 23-JBN-F12-36/H5N6 virus was estimated to have its origins in the HPAIV clade 2.3.4.4h H5N6 prevalent in poultry in China, and it is clustered with the AIVs that are associated with human infection cases. Taken together, these results show that the virus has been produced by reassortment with H5N1 HPAIV, which is prevalent in wild birds; H5N6 HPAIV, which is circulated in poultry in China; and the internal genes of low pathogenic avian influenza viruses (LPAIVs). In light of the reassortment of HPAIVs circulating in existing wild birds and HPAIVs circulating in poultry in China within the 2.3.4.4b H5Nx clade, it is imperative to strengthen active surveillance across wild bird populations, poultry farms, and live poultry markets, and to inform for the effective design of improved prevention and control strategies.

Caught Right on the Spot: Isolation and Characterization of Clade 2.3.4.4b H5N8 High Pathogenicity Avian Influenza Virus from a Common Pochard (Aythya ferina) Being Attacked by a Peregrine Falcon (Falco peregrinus)

We isolated a high pathogenicity avian influenza (HPAI) virus from a common pochard (Aythya ferina) that was being attacked by a bird of prey in South Korea in December 2020. Genetic analyses indicated that the isolate was closely related to the clade 2.3.4.4b H5N8 HPAI viruses found in South Korea and Japan during the winter season of 2020-2021. The histopathological examination revealed multifocal necrotizing inflammation in the liver, kidney, and spleen. Viral antigens were detected in the liver, kidney, spleen, trachea, intestine, and pancreas, indicating the HPAI virus caused a systemic infection. The presence of immunoreactivity for the viral antigen was observed in the cells involved in multifocal necrotic inflammation. Notably, epitheliotropic-positive patterns were identified in the epithelial cells of the trachea, mucosal epithelium of the intestine, and ductular epithelium of the pancreas. These findings provide direct evidence supporting the possibility of HPAI transmission from infected waterfowl to predators.

Genomic epidemiology of highly pathogenic avian influenza A (H5N1) virus in wild birds in South Korea during 2021-2022: Changes in viral epidemic patterns

Clade 2.3.4.4b highly pathogenic avian influenza A (HPAI) viruses have been detected in wild birds worldwide, causing recurrent outbreaks since 2016. During the winter of 2021-2022, we detected one H5N8 and forty-three H5N1 clade 2.3.4.4b HPAI viruses from wild birds in South Korea. Phylogenetic analysis revealed that HA gene of H5N1 viruses was divided into two genetically distinct groups (N1.G1 and N1.G2). Bayesian phylodynamic analysis demonstrated that wild birds play a vital role in viral transmission and long-term maintenance. We identified five genotypes (N1.G1.1, N1.G2, N1.G2.1, N1.G2.2, and N1.G2.2.1) having distinct gene segment constellations most probably produced by reassortments with low-pathogenic avian influenza viruses. Our results suggest that clade 2.3.4.4b persists in wild birds for a long time, causing continuous outbreaks, compared with previous clades of H5 HPAI viruses. Our study emphasizes the need for enhancing control measures in response to the changing viral epidemiology.

Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders

Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.

Ecological drivers for poultry farms predisposed to highly pathogenic avian influenza virus infection during the initial phase of the six outbreaks between 2010-2021: a nationwide study in South Korea

Background

Highly pathogenic avian influenza (HPAI) has caused substantial economic losses worldwide. An understanding of the environmental drivers that contribute to spillover transmission from wild birds to poultry farms is important for predicting areas at risk of introduction and developing risk-based surveillance strategies. We conducted an epidemiological study using data from six HPAI outbreak events in South Korea.

Materials and methods

An aggregate-level study design was implemented using third-level administrative units in South Korea. Only regions with high natural reservoir suitability were included. The incidence of HPAI at chicken and duck farms during the initial phase (30 and 45 days after the first case) of each outbreak event was used as the outcome variable, assuming that cross-species transmission from wild birds was the dominant exposure leading to infection. Candidate environmental drivers were meteorological factors, including temperature, precipitation, humidity, and altitude, as well as the proportion of protected area, farm density, deforestation level, and predator species richness. Logistic regression models were implemented; conditional autoregression models were used in cases of spatial autocorrelation of residuals.

Results

Lower temperature, higher farm density, and lower predator species richness were significantly associated with a higher risk of HPAI infection on chicken farms. Lower temperature, higher proportion of protected area, and lower predator species richness were significantly associated with a higher risk of HPAI infection on duck farms.

Conclusion

The predicted dominant transmission routes on chicken and duck farms were horizontal and spillover, respectively. These results reveal a potential protective effect of predator species richness against HPAI outbreaks. Further studies are required to confirm a causal relationship.

Surveillance of avian influenza viruses from 2014 to 2018 in South Korea

Surveillance of influenza A viruses (IAVs) among migratory waterfowl is a first step in understanding the ecology, biology, and pathogenicity of IAVs. As part of the nationwide surveillance effort for IAVs in fowl in South Korea, we collected environmental fecal samples in different migratory bird stopover sites in South Korea during the winter seasons within November 2014 through January 2018. We collected a total of 6758 fecal samples, 75 of which were positive for IAV (1.11% positivity). Prevalence of IAVs varied per site and per year. Based on sequencing, the most prevalent hemagglutinin (HA) subtypes were H1, H6, and H5, and the most prevalent neuraminidase (NA) subtypes were N1, N3, and N2. Phylogenetic analyses showed that the genes we isolated clustered with reported isolates collected from other locations along the East Asian-Australasian Flyway. All the H5 and H7 isolates collected in this study were of low pathogenicity. None of the N1 and N2 genes carried amino acid markers of resistance against NA inhibitors. The winter 2016-2017 subset were primarily borne by migratory geese (Anser spp.). These results suggest that majority of the IAVs circulating among migratory wild fowl in South Korea in 2014-2018 were of low pathogenicity.

Analysis of Avian Influenza (H5N5) Viruses Isolated in the Southwestern European Part of the Russian Federation in 2020-2021

In 2021, several isolates of the H5N5 avian influenza virus (AIV) were detected in Europe and the Russian Federation, which differed from those detected in 2020. Genetic analysis revealed a relationship between the highly pathogenic avian influenza H5N5 subtype, detected in Europe, and some isolates detected in the Russian Federation territory in 2020-2021: it was shown that both originated in the Caspian Sea regions around the autumn of 2020. The appearance of H5N5 subtype viruses in the spring of 2021 in Europe and the Russian Federation was not associated with the mass migration of birds from Africa. The results of the analysis revealed the presence of a deletion in the stem of a neuraminidase between bp 139 and 204 (open reading frame). It has been shown that AIVs of the H5N5 subtype are capable of long-term circulation in wild bird populations with the possibility of reassortment. The results also highlighted the need for careful monitoring of the circulation of AIVs in the Caspian Sea region, the role of which, in the preservation and emergence of new antigenic variants of such viruses in Eurasia, is currently underestimated.

Interpolation of Point Prevalence Rate of the Highly Pathogenic Avian Influenza Subtype H5N8 Second Phase Epidemic in South Korea

Humans and animals are both susceptible to highly pathogenic avian influenza (HPAI) viruses. In the future, HPAI has the potential to be a source of zoonoses and pandemic disease drivers. It is necessary to identify areas of high risk that are more vulnerable to HPAI infections. In this study, we applied unbiased predictions based on known information to find points of localities with a high probability of point prevalence rate. To carry out such predictions, we utilized the inverse distance weighting (IDW) and kriging method, with the help of the R statistical computing program. The provinces of Jeollanam-do, Gyeonggi-do, Chungcheongbuk-do and Ulsan have high anticipated risk. This research might aid in the management of avian influenza threats associated with various potential risks.

Subclinical Infection and Transmission of Clade 2.3.4.4 H5N6 Highly Pathogenic Avian Influenza Virus in Mandarin Duck (Aix galericulata) and Domestic Pigeon (Columbia livia domestica)

Since 2014, H5Nx clade 2.3.4.4 highly pathogenic avian influenza viruses (HPAIV) have caused outbreaks in wild birds and poultry in multiple continents, including Asia, Europe, Africa, and North America. Wild birds were suspected to be the sources of the local and global spreads of HPAIV. This study evaluated the infectivity, pathogenicity, and transmissibility of clade 2.3.4.4 H5N6 HPAIV in mandarin ducks (Aixgalericulata) and domestic pigeons (Columbia livia domestica). None of the birds used in this study, 20 mandarin ducks or 8 pigeons, showed clinical signs or mortality due to H5N6 HPAI infection. Two genotypes of H5N6 HPAIV showed replication and transmission by direct and indirect contact between mandarin ducks. H5N6 HPAIV replicated and transmitted by direct contact between pigeons, although the viral shedding titer and duration were relatively lower and shorter than those in mandarin ducks. Influenza virus antigen was detected in various internal organs of infected mandarin ducks and pigeons, indicating systemic infection. Therefore, our results indicate mandarin ducks and pigeons can be subclinically infected with clade 2.3.4.4 H5N6 HPAIV and transfer the virus to adjacent birds. The role of mandarin ducks and pigeons in the spread and prevalence of clade 2.3.4.4 H5N6 viruses should be carefully monitored.

Thermal Image Scanning for the Early Detection of Fever Induced by Highly Pathogenic Avian Influenza Virus Infection in Chickens and Ducks and Its Application in Farms

Highly pathogenic avian influenza (HPAI) is considered as one of the most devastating poultry diseases. It is imperative to immediately report any known outbreaks to the World Organization for Animal Health. Early detection of infected birds is of paramount importance to control virus spread, thus minimizing the associated economic loss. In this study, thermal imaging camera devices were used to detect change in the maximum surface temperature (MST) of chickens (n = 5) and ducks (n = 2) as an early indicator of experimental HPAI infection. The MST of both chickens and ducks increased at least 24 h before the manifestation of clinical signs of HPAI infection, depending on the severity of the infection. The basal MST was recorded for broiler chickens housed under small pen and normal farm conditions without intentional infection. A threshold cutoff of MST was established based on the circadian rhythm of normal MST. This study suggests that thermal imaging of chickens and ducks is a promising tool to screen any potential HPAI-infected flock in order to expedite HPAI diagnosis.

Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance

Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks-in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996-have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.

Highly Pathogenic Avian Influenza Clade 2.3.4.4b Subtype H5N8 Virus Isolated from Mandarin Duck in South Korea, 2020

In October 2020, a highly pathogenic avian influenza (HPAI) subtype H5N8 virus was identified from a fecal sample of a wild mandarin duck (Aix galericulata) in South Korea. We sequenced all eight genome segments of the virus, designated as A/Mandarin duck/Korea/K20-551-4/2020(H5N8), and conducted genetic characterization and comparative phylogenetic analysis to track its origin. Genome sequencing and phylogenetic analysis show that the hemagglutinin gene belongs to H5 clade 2.3.4.4 subgroup B. All genes share high levels of nucleotide identity with H5N8 HPAI viruses identified from Europe during early 2020. Enhanced active surveillance in wild and domestic birds is needed to monitor the introduction and spread of HPAI via wild birds and to inform the design of improved prevention and control strategies.

Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses

From 2013 onwards, the spread of novel H5N6 highly pathogenic avian influenza (HPAI) viruses in China has posed great threats to not only poultry industry but also human health. Since late-2016 in particular, frequent outbreaks of clade 2.3.4.4 H5N6 HPAI viruses among wild birds have promoted viral dissemination in South Korea, Japan, and European countries. In response to those trends, we conducted molecular genetic analysis of global clade 2.3.4.4 H5N6 viruses in order to characterize spatio-temporal patterns of viral diffusion and genetic diversity among wild birds and poultry. The clade 2.3.4.4 H5N6 viruses were classified into three groups (Group B, C, and D). During the cocirculation of Group C/D H5N6 viruses from 2013 to 2017, viral movements occurred between close or adjacent regions of China, Vietnam, South Korea, and Japan. In addition, viral migration rates from Guangdong and Hunan to multiple adjacent provinces seemed to have been highly supported by transmission routes (Bayes factors >100), suggesting that southern China was an epicenter for the spread of H5N6 viruses in poultry during that period. Since the introduction of H5N6 viruses originating in wild birds in late-2016, evolving H5N6 viruses have lost most previous genotypes (e.g. G1, G2, and G1.2), whereas some prevailing genotypes (e.g. G1.1, G1.1.b, and G3) in aquatic birds have been dominated, and in particular, the effective population size of H5N6 originating in wild birds dramatically increased; however, the population size of poultry-origin H5N6 viruses declined during the same period, indicating that wild bird migration might accelerate the genetic diversity of H5N6 viruses. Phylogeographic approaches revealed that two independent paths of H5N6 viruses into South Korea and Japan from 2016 to 2018 and provided evidence of Group B and Group C H5N6 viruses were originated from Europe and China, respectively, as regions located in the East Asia-Australian migration flyway, which accelerated the genetic variability and dissemination. Altogether, our study provides insights to examine time of origin, evolutionary rate, diversification patterns, and phylogeographical approach of global clade 2.3.4.4 H5N6 HPAI viruses for assessing their evolutionary process and dissemination pathways.

Phylogenetic tracing and biological characterization of a novel clade 2.3.2.1 reassortant of H5N6 subtype avian influenza virus in China

In recent years in China, clade 2.3.4.4 H5N6 plus clade 2.3.2.1 H5N1 subtype highly pathogenic avian influenza (HPAI) viruses have gradually become endemic in poultry, and their co-circulation could inevitably facilitate the gene reassortment between each other. During our routine surveillance in live poultry markets (LPMs) in eastern China in 2017-2018, a novel reassortant H5N6 strain with the HA gene derived from clade 2.3.2.1 was isolated from the cloacal swabs of apparently healthy ducks. Phylogenetic tracing analysis indicated that another two clade 2.3.2.1 H5N1 strains with divergent lineages of PB1 gene and one clade 2.3.4.4 H5N6 isolate of the dominant genotype sharing spatio-temporal proximity were intimately involved in the generation of this rarely reported clade 2.3.2.1 H5N6 reassortant. Distinct with the other three HPAI H5 viruses showing moderate virulence in mice, the H5N1 strain of the homologous internal gene constellation against the clade 2.3.2.1 H5N6 reassortant was highly pathogenic, which might probably attribute to the H3 subtype-derived PB1 gene. However, as compared to the clade 2.3.4.4 H5N6 ancestor, the clade 2.3.2.1 H5N6 reassortant displayed a broader tissue distribution and higher viral titres in mice, which could likely facilitate the viral maintenance and spread in nature. Therefore, our results highlight that continuous epidemiological survey of H5 subtype HPAI viruses in LPMs needs to be strengthened to prevent the potential poultry or even public health threat of the novel reassortants from endemic viruses.

Regional Transmission and Reassortment of 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) Viruses in Bulgarian Poultry 2017/18

Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 highly-pathogenic avian influenza (HPAI) viruses. In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the northeastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates a complete lack of reassortment in all segments but the matrix protein gene (MP), which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the hemagglutinin (HA) gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence, we suggest the surveillance of domestic ducks as they are an epidemiologically relevant species for subclinical infection. Monitoring the spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks. The 2.3.4.4b lineage which caused the largest recorded poultry epidemic in Europe continues to circulate, and the risk of further transmission by wild birds during migration remains.

Highly pathogenic H5N6 avian influenza virus subtype clade 2.3.4.4 indigenous in South Korea

The outbreaks of the highly pathogenic avian influenza (HPAI) in 2016–2017 and 2017–2018, caused by novel reassortant clade 2.3.4.4 H5N6 viruses, resulted in the loss of one billion birds in South Korea. Here, we characterized the H5N6 viruses isolated from wild birds in South Korea from December 2017 to August 2019 by next-generation sequencing. The results indicated that clade 2.3.4.4 H5N6 viruses isolated in 2017 and 2019 shared almost identical nucleotide sequences with the HPAI H5N6 viruses from 2016 in South Korea. This repeated detection of evolutionarily identical H5N6 viruses in same region for more than three years may suggest indigenization of the HPAI H5N6 virus in South Korea. Phylogenetic analysis demonstrated that the clade 2.3.4.4 H5N6 viruses isolated in 2017 and 2019 were evolutionarily distinct from those isolated in 2018. Molecular analysis revealed that the H5N6 viruses isolated in 2017 and 2019 had features associated with an increased risk of human infection (e.g. a deletion at position 133 of HA and glutamic acid residue at position 92 of NS1). Overall, these genomic features of HPAI H5N6 viruses highlight the need for continuous monitoring of avian influenza viruses in wild migratory birds as well as in domestic birds.

Introduction of Avian Influenza A(H6N5) Virus into Asia from North America by Wild Birds

An avian influenza A(H6N5) virus with all 8 segments of North American origin was isolated from wild bird feces in South Korea. Phylogenetic analysis suggests that this virus may have been introduced into Asia by wild birds, highlighting the role of wild birds in the dispersal of these viruses.

Pandemic potential of highly pathogenic avian influenza clade 2.3.4.4 A(H5) viruses

The panzootic caused by A/goose/Guangdong/1/96‐lineage highly pathogenic avian influenza (HPAI) A(H5) viruses has occurred in multiple waves since 1996. From 2013 onwards, clade 2.3.4.4 viruses of subtypes A(H5N2), A(H5N6), and A(H5N8) emerged to cause panzootic waves of unprecedented magnitude among avian species accompanied by severe losses to the poultry industry around the world. Clade 2.3.4.4 A(H5) viruses have expanded in distinct geographical and evolutionary pathways likely via long distance migratory bird dispersal onto several continents and by poultry trade among neighboring countries. Coupled with regional circulation, the viruses have evolved further by reassorting with local viruses. As of February 2019, there have been 23 cases of humans infected with clade 2.3.4.4 H5N6 viruses, 16 (70%) of which had fatal outcomes. To date, no HPAI A(H5) virus has caused sustainable human‐to‐human transmission. However, due to the lack of population immunity in humans and ongoing evolution of the virus, there is a continuing risk that clade 2.3.4.4 A(H5) viruses could cause an influenza pandemic if the ability to transmit efficiently among humans was gained. Therefore, multisectoral collaborations among the animal, environmental, and public health sectors are essential to conduct risk assessments and develop countermeasures to prevent disease and to control spread. In this article, we describe an assessment of the likelihood of clade 2.3.4.4 A(H5) viruses gaining human‐to‐human transmissibility and impact on human health should such human‐to‐human transmission occur. This structured analysis assessed properties of the virus, attributes of the human population, and ecology and epidemiology of these viruses in animal hosts.

A novel reassortant clade 2.3.4.4 highly pathogenic avian influenza H5N6 virus identified in South Korea in 2018

Since 2017, clade 2.3.4.4b H5N6 highly pathogenic avian influenza viruses (HPAIVs) have been detected over a broad geographic region, including Eurasia. These viruses have evolved through reassortment with Eurasian low pathogenic avian influenza viruses (LPAIVs), resulting in multiple genotypes. Here, we sequenced the full-length genome of 15 H5N6 HPAIVs collected from wild birds and poultry farms in South Korea from January to March 2018. A comparative phylogenetic analysis was then conducted. Three distinct genotypes were identified in South Korea during 2017/2018, including a novel reassortant genotype, H214. The novel reassortant H5N6 viruses isolated in this study possessed PB2, PA, and NP gene segments of Eurasian LPAIV on a genetic backbone of the H35-like genotype, which was identified in Korea and the Netherlands during 2017. Bayesian molecular clock analysis suggested that the novel reassortant viruses were generated most likely during the fall migration/wintering season of migratory waterfowl in 2017. Considering the continued emergence and spread of clade 2.3.4.4 HPAIV, enhanced surveillance of wild waterfowl is needed for early detection of HPAIV incursions.

Bioengineering a highly productive vaccine strain in embryonated chicken eggs and mammals from a non-pathogenic clade 2·3·4·4 H5N8 strain

The clade 2·3·4·4 H5Nx is a highly pathogenic avian influenza (HPAI) virus, which first appeared in China and has spread worldwide since then, including Korea. It is divided into subclades a - d, but the PR8-derived recombinant clade 2·3·4·4 a viruses replicate inefficiently in embryonated chicken eggs (ECEs). High virus titer in ECEs and no mammalian pathogenicity are the most important prerequisites of efficacious and safer vaccine strains against HPAI. In this study, we have synthesized hemagglutinin (HA) and neuraminidase (NA) genes based on the consensus amino acid sequences of the clade 2·3·4·4a and b H5N8 HPAIVs, using the GISAID database. We generated PR8-derived H5N8 recombinant viruses with single point mutations in HA and NA, which are related to efficient replication in ECEs. The H103Y mutation in HA increased mammalian pathogenicity as well as virus titer in ECEs, by 10-fold. We also successfully eradicated mammalian pathogenicity in H103Y-bearing H5N8 recombinant virus by exchanging PB2 genes of PR8 and 01310 (Korean H9N2 vaccine strain). The final optimized H5N8 vaccine strain completely protected against a heterologous clade 2·3·4·4c H5N6 HPAIV in chickens, and induced hemagglutination inhibition (HI) antibody in ducks. However, the antibody titer of ducks showed age-dependent results. Thus, H103Y and 01310PB2 gene have been successfully applied to generate a highly productive, safe, and efficacious clade 2·3·4·4 H5N8 vaccine strain in ECEs.

Circulation, Evolution and Transmission of H5N8 virus, 2016-2018

OBJECTIVES

A second wave of highly pathogenic avian influenza A virus (HPAIV) H5N8 clade 2.3.4.4 has spread globally, causing outbreaks among wild birds and domestic poultry since autumn 2016. The circulation and evolutionary dynamics of the virus remain largely unknown.

METHODS

We performed surveillance for H5N8 in Qinghai Lake in China since the emergence of the virus (from 2016 to 2018). By analyzing recovered viruses in Qinghai Lake and all related viruses worldwide (449 strains), we identified the genotypes, estimated their genesis and reassortment, and evaluated their global distribution and transmission.

RESULTS

Through surveillance of wild migratory birds around Qinghai Lake between 2016 and 2018, we revealed that the H5N8 was introduced into Qinghai Lake bird populations (QH-H5N8), with distinct gene constellations in 2016 and 2017. A global analysis of QH-H5N8-related viruses showed that avian influenza viruses with low pathogenicity in wild birds contributed to the high diversity of genotypes; the major reassortment events possibly occurred during the 2016 breeding season and the following winters.

CONCLUSIONS

Continued circulation of QH-H5N8-related viruses among wild birds has resulted in the global distribution of high genotypic diversity. Thus, these viruses pose an ongoing threat to wild and domestic bird populations and warrant continuous surveillance.

Spread of Highly Pathogenic Avian Influenza (HPAI) H5N5 Viruses in Europe in 2016-2017 Appears Related to the Timing of Reassortment Events

During the epizootic of highly pathogenic avian influenza (HPAI) H5N8 virus in Europe in 2016-2017, HPAI viruses of subtype H5N5 were also isolated. However, the detection of H5N5 viruses was limited compared to H5N8. In this study, we show that the genetic constellation of a newly isolated H5N5 virus is different from two genotypes previously identified in the Netherlands. The introduction and spread of the three H5N5 genotypes in Europe was studied using spatiotemporal and genetic analysis. This demonstrated that the genotypes were isolated in distinguishable phases of the epizootic, and suggested multiple introductions of H5N5 viruses into Europe followed by local spread. We estimated the timing of the reassortment events, which suggested that the genotypes emerged after the start of autumn migration. This may have prevented large-scale spread of the H5N5 viruses on wild bird breeding sites before introduction into Europe. Experiments in primary chicken and duck cells revealed only minor differences in cytopathogenicity and replication kinetics between H5N5 genotypes and H5N8. These results suggest that the limited spread of HPAI H5N5 viruses is related to the timing of the reassortment events rather than changes in virus pathogenicity or replication kinetics.

The Emergence and Decennary Distribution of Clade 2.3.4.4 HPAI H5Nx

Reassortment events among influenza viruses occur naturally and may lead to the development of new and different subtypes which often ignite the possibility of an influenza outbreak. Between 2008 and 2010, highly pathogenic avian influenza (HPAI) H5 of the N1 subtype from the A/goose/Guangdong/1/96-like (Gs/GD) lineage generated novel reassortants by introducing other neuraminidase (NA) subtypes reported to cause most outbreaks in poultry. With the extensive divergence of the H5 hemagglutinin (HA) sequences of documented viruses, the WHO/FAO/OIE H5 Evolutionary Working Group clustered these viruses into a systematic and unified nomenclature of clade 2.3.4.4 currently known as “H5Nx” viruses. The rapid emergence and circulation of these viruses, namely, H5N2, H5N3, H5N5, H5N6, H5N8, and the regenerated H5N1, are of great concern based on their pandemic potential. Knowing the evolution and emergence of these novel reassortants helps to better understand their complex nature. The eruption of reports of each H5Nx reassortant through time demonstrates that it could persist beyond its usual seasonal activity, intensifying the possibility of these emerging viruses’ pandemic potential. This review paper provides an overview of the emergence of each novel HPAI H5Nx virus as well as its current epidemiological distribution.

Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017-18

Highly pathogenic avian influenza (HPAI) H5 clade 2.3.4.4 viruses were first introduced into Europe in late 2014 and re-introduced in late 2016, following detections in Asia and Russia. In contrast to the 2014-15 H5N8 wave, there was substantial local virus amplification in wild birds in Europe in 2016-17 and associated wild bird mortality, with evidence for occasional gene exchange with low pathogenic avian influenza (LPAI) viruses. Since December 2017, several European countries have again reported events or outbreaks with HPAI H5N6 reassortant viruses in both wild birds and poultry, respectively. Previous phylogenetic studies have shown that the two earliest incursions of HPAI H5N8 viruses originated in Southeast Asia and subsequently spread to Europe. In contrast, this study indicates that recent HPAI H5N6 viruses evolved from the H5N8 2016-17 viruses during 2017 by reassortment of a European HPAI H5N8 virus and wild host reservoir LPAI viruses. The genetic and phenotypic differences between these outbreaks and the continuing detections of HPAI viruses in Europe are a cause of concern for both animal and human health. The current co-circulation of potentially zoonotic HPAI and LPAI virus strains in Asia warrants the determination of drivers responsible for the global spread of Asian lineage viruses and the potential threat they pose to public health.

Adlhoch C, Brouwer A, Kuiken T, Miteva A, Mulatti P, Smietanka K, Staubach C, Gogin A, Muñoz Guajardo I, Baldinelli F. Avian influenza overview August - November 2018

Between 16 August and 15 November 2018, 14 highly pathogenic avian influenza (HPAI) A(H5N8) outbreaks in poultry establishments in Bulgaria and seven HPAI A(H5N6) outbreaks, one in captive birds in Germany and six in wild birds in Denmark and the Netherlands were reported in the European Union (EU). No human infection due to HPAI A(H5N8) and A(H5N6) viruses have been reported in Europe so far. Seroconversion of people exposed during outbreaks in Russia has been reported in one study. Although the risk of zoonotic transmission to the general public in Europe is considered to be very low, appropriate personal protection measures of people exposed will reduce any potential risk. Genetic clustering of the viruses isolated from poultry in Bulgaria suggests three separate introductions in 2016 and a continuing circulation and transmission of these viruses within domestic ducks. Recent data from Bulgaria provides further indication that the sensitivity of passive surveillance of HPAI A(H5N8) in domestic ducks may be significantly compromised. Increased vigilance is needed especially during the periods of cold spells in winter when aggregations of wild birds and their movements towards areas with more favourable weather conditions may be encouraged. Two HPAI outbreaks in poultry were reported during this period from western Russia. Low numbers of HPAI outbreaks were observed in Africa and Asia, no HPAI cases were detected in wild birds in the time period relevant for this report. Although a few HPAI outbreaks were reported in Africa and Asia during the reporting period, the probability of HPAI virus introductions from non‐EU countries via wild birds particularly via the north‐eastern route from Russia is increasing, as the fall migration of wild birds from breeding and moulting sites to the wintering sites continues. Furthermore, the lower temperatures and ultraviolet radiation in winter can facilitate the environmental survival of any potential AI viruses introduced to Europe.