New incursions of H5N1 clade 2.3.4.4b highly pathogenic avian influenza viruses in wild birds, South Korea, October 2024 DOI Creative Commons
Young‐Jae Si, Dong‐Ju Kim, Sun-Hak Lee

et al.

Frontiers in Veterinary Science, Journal Year: 2025, Volume and Issue: 11

Published: Jan. 10, 2025

Highly pathogenic avian influenza (HPAI) subtype H5Nx viruses of the A/Goose/Guangdong/1/1996 (Gs/Gd) lineage have led to substantial economic losses within poultry industry and represent an ongoing public health threat [1]. The Gs/Gd H5 not only evolved into ten primary clades 0-9 with their subclades but also reassorted other A [2; 3; 4]. Notably, since 2020, clade 2.3.4.4b HPAI H5N1 caused outbreaks across a broad geographic range, including Asia, Europe, Africa, North America, South Antarctica [5; 6; 7]. infections in mammals wild, domestic humans underscore potential zoonotic risk pandemic these evolving [8].In Korea, multiple outbreaks. During October 2022-March 2023, total 16 different genotypes HPAIV, Kor22-23A-P, were reported wild birds, showing high genetic diversity HPAIVs generated through frequent reassortment [9]. December 2023-May 2024, H5N6 [10; 11] 32 cases farms (home.kahis.go.kr) 19 birds (http://wadis.go.kr). No virus had been detected Korea June despite large-scale active surveillance targeting both poultry. Here, we report detection isolated from captured Mandarin duck (Aix galericulata) on 15, Northern pintail (Anas acuta) found dead 17, during early-stage fall migration waterfowl Korea. To facilitate timely information sharing, conducted complete genome sequencing using Illumina next-generation (NGS) technology submitted sequences GISAID database (https://www.gisaid.org). comparative phylogenetic analysis was carried out determine virus's origin genotype.Materials MethodsOn 15 8 ducks along Cheongmicheon stream Gyeonggi-do Province, (GPS coordinate: 37°8'31.25"N, 127°22'52.23"E) as part national bird program (Supplementary Figure 1). On 17 at Yongsu reservoir Jeju island 33°30'18.28"N, 126°53'33.4"E). We collected oropharyngeal cloacal swabs birds. Swab samples placed phosphate-buffered saline (PBS) containing 400 mg/mL gentamicin thoroughly homogenized by vortexing for 1 min. supernatant filtered 0.45-μm Minisart Syringe Filter (Sartorius, Göttingen, Germany) after centrifugation sample 3000 rpm 10 min inoculated 10-day-old specific-pathogen-free (SPF) embryonated chicken eggs. After 72 h incubation 37•C, allantoic fluids harvested tested hemagglutination activity (HA) 10% red blood cells. RNA extracted hemagglutination-activity-positive fluid Maxwell RSC simply Tissue Kit (Promega, Madison, WI, USA) according manufacturer's instructions screened matrix (M) genes real-time reverse transcription-PCR (rRT-PCR) previously described [12].Complementary DNA SuperScript III First-Strand Synthesis system (Invitrogen, Carlsbad, CA, USA), eight gene segments amplified AccuPrime Pfx Polymerase [13]. libraries prepared Nextera Flex Library Prep (Illumina, San Diego, which utilizes transposon-mediated tagmentation adapter ligation, dual-index barcodes instructions. sequenced paired-end 150 Miseq sequencing-by-synthesis platform. NGS raw reads trimmed adapters low-quality bases BBDuk version 38.84 setting minimum quality 30 [14]. Trimmed assembled de novo SPAdes assembler 3.15.5. mapped top result EpiFlu database, identified contigs, Minimap 2.24 (https://github.com/lh3/minimap2) default options visualized Geneious Prime software.The produced reference-guided assembly used generate final consensus sequences. dataset presented this study can be online repositories. names repositories accession ID is available GISAID(https://www.gisaid.org) EPIFlu (accession ID: EPI_ISL_19528860 EPI_ISL_19531393). classification performed subspecies tool BV-BRC (https://www.bvbrc.org/app/SubspeciesClassification). examined identify molecular markers associated mammalian host adaptation, pathogenicity, drug resistance. utilized FluSurver mutation Initiative [15] manual screening based known impacting AIV biological properties [16]. Identified amino acid substitutions HA segment are referenced numbering.All analyzed BLAST query function (https://gisaid.org/). From 500 hits, identical ElimDupes software (https://www.hiv.lanl.gov/content/sequence/elimdupesv2/elimdupes.html). Genome aligned MAFFT [17]. Phylogenetic tree construction each RAxML v8.0 [18] general time reversible model nucleotide substitution Gamma rate heterogeneity, 1,000 bootstrap replicates. Interactive Tree Life (iTOL) employed visualize [19]. cluster regarded distinct when it support value > 70 sequence identity 97%. genotype G2b G2d 2021 2022 [20; 21] verify viruses. A/goose/Hunan/SE284/2022(SE284) (H5N1) [22] categorize G2c viruses.A Bayesian relaxed-clock phylogeny reconstructed BEAST 1.10.4 [23], applying Hasegawa, Kishino, Yano uncorrelated log-normal distribution Gaussian Markov Random Field (GMRF) skyride coalescent prior [24]. Chain Monte Carlo (MCMC) process run parallel three chains, 50 million iterations, results combined burn-in. All parameters achieved effective sizes >200 TRACER v1.5 (http://tree.bio.ed.ac.uk/software/tracer/) [25]. maximum credibility (MCC) created TreeAnnotator FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/). most recent common ancestor (tMRCA) estimated height values nodes.A live 2024 positive via embryo inoculation rRT-PCR.We successfully viruses, designated A/Mandarin duck/Korea/24WS005-2/H5N1/2024 (hereafter MD/24WS005-2) A/Northern pintail/Korea/24WC025/H5N1/2024 NP/24WC025). 52,864 136,268 generated, respectively, resulting coding (CDS) all average depth (>350). presence basic acids proteolytic cleavage site (PLREKRRKR/G) [26] classified 2.3.4.4b.The NP/24WC025 MD/24WS005-2 constellations, suggesting independently introduced (Figure that circulating Japan 2023-2024.The belonged sub-lineage 21]. shared ancestry A/white-tailed eagle/Hokkaido/2024, A/chicken/Hokkaido/E012/2024, concurrently Japan, tMRCA April 28, (95% BCI: January 10, -July 29, 2024), descendants circulated early-mid 2024.For virus, HA, NA, M clustered mainly 2022-2024 Asia did form wellsupported monophyletic 1D,F,G). [22]. In gene, 1A,B,C,E,H). PB1, NP, A/eagle/Korea/22WC464/2023(H5N1) 1B, D-G) minor genotype, Kor22-23P, winter season 2022-2023 PB2, PA, NS derived Eurasian LPAI pool population 1A,C,H). has contributed generation donor lineages [27]. long branch length new suggest undetected approximately two years undergone prevailing population.Genetic mutations increased binding affinity α-2,6 sialic receptors protein, N110S S154N S133A T156A (Table Both V588T PB2 enhance pathogenicity mice. K482R, polymerase cell lines, virus. PB1 D3V D622G, enhanced viral replication lines virulence mice, present viruses.Mutations protein (N30D, I43M, T215A, P42S), increase murine models, ESEV motif C-terminal NS1 protein.The

Language: Английский

Pinnipeds and avian influenza: a global timeline and review of research on the impact of highly pathogenic avian influenza on pinniped populations with particular reference to the endangered Caspian seal (Pusa caspica) DOI Creative Commons
А. А. Гаджиев, Guy Petherbridge, Kirill Sharshov

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2024, Volume and Issue: 14

Published: June 26, 2024

This study reviews chronologically the international scientific and health management literature resources relating to impacts of highly pathogenic avian influenza (HPAI) viruses on pinnipeds in order reinforce strategies for conservation endangered Caspian seal (

Language: Английский

Citations

5
An overview of avian influenza surveillance strategies and modes DOI Creative Commons

Chenlin Duan,

Chao Li,

Ruiqi Ren

et al.

Science in One Health, Journal Year: 2023, Volume and Issue: 2, P. 100043 - 100043

Published: Jan. 1, 2023

The global epidemic of avian influenza has imposed a substantial disease burden, inciting societal panic and economic losses. high variability associated uncertainty the virus present significant challenges in its prevention control. As pivotal strategy for mitigation influenza, surveillance network shown considerable growth at both regional levels. This includes expansion coverage, continuous refinement monitoring content scope, rapid enhancement quality. Although ultimate goal remains uniform, strategies models vary, reflecting or national differences system frameworks their implementation. review collates examines features experiences global, regional, efforts. Furthermore, it delves into modalities light "One Health" concept, which establishment interdisciplinary cross-sectoral coordination cooperation among medical, veterinary, public health institutions, sharing information timely alerts.

Language: Английский

Citations

12
Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic DOI Creative Commons
Alexander Nagy,

Martina Stará,

Lenka Černíková

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(2), P. 221 - 221

Published: Jan. 31, 2024

In 2022/2023, Europe experienced its third consecutive season of high-pathogenicity avian influenza. During this period, the Czech Republic was again severely affected. For first time, number culled birds approached one million, which three times higher than in previous seasons. parallel to outbreaks poultry, mass die-offs gulls were also observed. present study, we performed whole-genome sequencing and phylogenetic analysis 137 H5N1 strains collected 2022/2023 (94.6% all or locations). The revealed four distinct genotypes: AB, CH, BB AF. Phylogenetic suggested that AF genotype persisted from without reassortment. addition, BB, detected mainly gulls, showed a noticeable strain diversity at local level. This virus responsible for single outbreak commercially bred turkeys. Finally, an interesting spatio-temporal cluster with co-circulating genotypes, CH AF, identified no evidence intrasubtype Highly sensitive molecular surveillance timely sharing genomic sequences associated metadata could greatly assist tracking spread detecting changes increased virulence potentially zoonotic pathogen.

Language: Английский

Citations

4
Phylodynamics of avian influenza A(H5N1) viruses from outbreaks in Brazil DOI Creative Commons

Anselmo Vasconcelos Rivetti,

Dilmara Reischak, Cairo Henrique Sousa de Oliveira

et al.

Virus Research, Journal Year: 2024, Volume and Issue: 347, P. 199415 - 199415

Published: June 19, 2024

Our study identified strains of the A/H5N1 virus in analyzed samples subsistence poultry, wild birds, and mammals, belonging to clade 2.3.4.4b, genotype B3.2, with very high genetic similarity from Chile, Uruguay, Argentina. This suggests a migratory route for birds across Pacific, explaining phylogenetic relatedness. The Brazilian displayed that had already been previously detected South America. Phylogeographic analysis transmission US viruses Europe Asia, co-circulating other lineages American continent. As mutations can influence virulence host specificity, genomic surveillance is essential detect those changes, especially critical regions, such as hot spots HA, NA, PB2 sequences. Mutations gene (D701N Q591K) associated adaptation mammals were suggesting potential zoonotic risk. Nonetheless, resistance neuraminidase inhibitors (NAIs) was not identified, however, continued crucial resistance. also mapped spread Southern hemisphere, identifying possible entry routes highlighting importance prevent outbreaks protect both human animal populations.

Language: Английский

Citations

4
New incursions of H5N1 clade 2.3.4.4b highly pathogenic avian influenza viruses in wild birds, South Korea, October 2024 DOI Creative Commons
Young‐Jae Si, Dong‐Ju Kim, Sun-Hak Lee

et al.

Frontiers in Veterinary Science, Journal Year: 2025, Volume and Issue: 11

Published: Jan. 10, 2025

Highly pathogenic avian influenza (HPAI) subtype H5Nx viruses of the A/Goose/Guangdong/1/1996 (Gs/Gd) lineage have led to substantial economic losses within poultry industry and represent an ongoing public health threat [1]. The Gs/Gd H5 not only evolved into ten primary clades 0-9 with their subclades but also reassorted other A [2; 3; 4]. Notably, since 2020, clade 2.3.4.4b HPAI H5N1 caused outbreaks across a broad geographic range, including Asia, Europe, Africa, North America, South Antarctica [5; 6; 7]. infections in mammals wild, domestic humans underscore potential zoonotic risk pandemic these evolving [8].In Korea, multiple outbreaks. During October 2022-March 2023, total 16 different genotypes HPAIV, Kor22-23A-P, were reported wild birds, showing high genetic diversity HPAIVs generated through frequent reassortment [9]. December 2023-May 2024, H5N6 [10; 11] 32 cases farms (home.kahis.go.kr) 19 birds (http://wadis.go.kr). No virus had been detected Korea June despite large-scale active surveillance targeting both poultry. Here, we report detection isolated from captured Mandarin duck (Aix galericulata) on 15, Northern pintail (Anas acuta) found dead 17, during early-stage fall migration waterfowl Korea. To facilitate timely information sharing, conducted complete genome sequencing using Illumina next-generation (NGS) technology submitted sequences GISAID database (https://www.gisaid.org). comparative phylogenetic analysis was carried out determine virus's origin genotype.Materials MethodsOn 15 8 ducks along Cheongmicheon stream Gyeonggi-do Province, (GPS coordinate: 37°8'31.25"N, 127°22'52.23"E) as part national bird program (Supplementary Figure 1). On 17 at Yongsu reservoir Jeju island 33°30'18.28"N, 126°53'33.4"E). We collected oropharyngeal cloacal swabs birds. Swab samples placed phosphate-buffered saline (PBS) containing 400 mg/mL gentamicin thoroughly homogenized by vortexing for 1 min. supernatant filtered 0.45-μm Minisart Syringe Filter (Sartorius, Göttingen, Germany) after centrifugation sample 3000 rpm 10 min inoculated 10-day-old specific-pathogen-free (SPF) embryonated chicken eggs. After 72 h incubation 37•C, allantoic fluids harvested tested hemagglutination activity (HA) 10% red blood cells. RNA extracted hemagglutination-activity-positive fluid Maxwell RSC simply Tissue Kit (Promega, Madison, WI, USA) according manufacturer's instructions screened matrix (M) genes real-time reverse transcription-PCR (rRT-PCR) previously described [12].Complementary DNA SuperScript III First-Strand Synthesis system (Invitrogen, Carlsbad, CA, USA), eight gene segments amplified AccuPrime Pfx Polymerase [13]. libraries prepared Nextera Flex Library Prep (Illumina, San Diego, which utilizes transposon-mediated tagmentation adapter ligation, dual-index barcodes instructions. sequenced paired-end 150 Miseq sequencing-by-synthesis platform. NGS raw reads trimmed adapters low-quality bases BBDuk version 38.84 setting minimum quality 30 [14]. Trimmed assembled de novo SPAdes assembler 3.15.5. mapped top result EpiFlu database, identified contigs, Minimap 2.24 (https://github.com/lh3/minimap2) default options visualized Geneious Prime software.The produced reference-guided assembly used generate final consensus sequences. dataset presented this study can be online repositories. names repositories accession ID is available GISAID(https://www.gisaid.org) EPIFlu (accession ID: EPI_ISL_19528860 EPI_ISL_19531393). classification performed subspecies tool BV-BRC (https://www.bvbrc.org/app/SubspeciesClassification). examined identify molecular markers associated mammalian host adaptation, pathogenicity, drug resistance. utilized FluSurver mutation Initiative [15] manual screening based known impacting AIV biological properties [16]. Identified amino acid substitutions HA segment are referenced numbering.All analyzed BLAST query function (https://gisaid.org/). From 500 hits, identical ElimDupes software (https://www.hiv.lanl.gov/content/sequence/elimdupesv2/elimdupes.html). Genome aligned MAFFT [17]. Phylogenetic tree construction each RAxML v8.0 [18] general time reversible model nucleotide substitution Gamma rate heterogeneity, 1,000 bootstrap replicates. Interactive Tree Life (iTOL) employed visualize [19]. cluster regarded distinct when it support value > 70 sequence identity 97%. genotype G2b G2d 2021 2022 [20; 21] verify viruses. A/goose/Hunan/SE284/2022(SE284) (H5N1) [22] categorize G2c viruses.A Bayesian relaxed-clock phylogeny reconstructed BEAST 1.10.4 [23], applying Hasegawa, Kishino, Yano uncorrelated log-normal distribution Gaussian Markov Random Field (GMRF) skyride coalescent prior [24]. Chain Monte Carlo (MCMC) process run parallel three chains, 50 million iterations, results combined burn-in. All parameters achieved effective sizes >200 TRACER v1.5 (http://tree.bio.ed.ac.uk/software/tracer/) [25]. maximum credibility (MCC) created TreeAnnotator FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/). most recent common ancestor (tMRCA) estimated height values nodes.A live 2024 positive via embryo inoculation rRT-PCR.We successfully viruses, designated A/Mandarin duck/Korea/24WS005-2/H5N1/2024 (hereafter MD/24WS005-2) A/Northern pintail/Korea/24WC025/H5N1/2024 NP/24WC025). 52,864 136,268 generated, respectively, resulting coding (CDS) all average depth (>350). presence basic acids proteolytic cleavage site (PLREKRRKR/G) [26] classified 2.3.4.4b.The NP/24WC025 MD/24WS005-2 constellations, suggesting independently introduced (Figure that circulating Japan 2023-2024.The belonged sub-lineage 21]. shared ancestry A/white-tailed eagle/Hokkaido/2024, A/chicken/Hokkaido/E012/2024, concurrently Japan, tMRCA April 28, (95% BCI: January 10, -July 29, 2024), descendants circulated early-mid 2024.For virus, HA, NA, M clustered mainly 2022-2024 Asia did form wellsupported monophyletic 1D,F,G). [22]. In gene, 1A,B,C,E,H). PB1, NP, A/eagle/Korea/22WC464/2023(H5N1) 1B, D-G) minor genotype, Kor22-23P, winter season 2022-2023 PB2, PA, NS derived Eurasian LPAI pool population 1A,C,H). has contributed generation donor lineages [27]. long branch length new suggest undetected approximately two years undergone prevailing population.Genetic mutations increased binding affinity α-2,6 sialic receptors protein, N110S S154N S133A T156A (Table Both V588T PB2 enhance pathogenicity mice. K482R, polymerase cell lines, virus. PB1 D3V D622G, enhanced viral replication lines virulence mice, present viruses.Mutations protein (N30D, I43M, T215A, P42S), increase murine models, ESEV motif C-terminal NS1 protein.The

Language: Английский

Citations

0