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Since October 2021, outbreaks of highly pathogenic avian influenza (HPAI) A(H5N1) virus belonging to A/Goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b have been reported throughout Europe (1). Transatlantic spread of HPAI H5N1 [...]

Simple Summary: In summary, this report emphasizes the importance of accurate virus characterization using whole-genome sequencing and robust biosecurity practices and training for avian influenza surveillance. Risks must be mitigated to provide accurate disease reporting and limit disease spread, considering this case's avian influenza detection in submitted poultry samples but its attribution to the collector. Highly pathogenic avian influenza (HPAI) surveillance for influenza A virus (IAV) in the United States is conducted using a National Animal Health Laboratory Network (NAHLN) real-time reverse transcriptase–polymerase chain reaction (rRT-PCR). Samples showing the presence of IAV are confirmed and characterized at the national reference laboratory. During the H5N1 HPAI outbreak in 2022, our laboratory reported the detection of IAV in a PA commercial chicken flock using rRT-PCR targeting the matrix gene, which was negative for the H5/H7 subtypes. IAV was not detected by additional sampling of the birds the following day with rRT-PCR. The virus detected was characterized as a human seasonal H3N2 with whole-genome sequencing (WGS). Further investigation revealed that the collector who visited the farm was diagnosed with an IAV infection. This case report emphasizes the importance of farm biosafety and biosecurity, of conducting regular reviews of worker safety protocols, and of advanced molecular techniques like WGS for viral characterization and epidemiology. [ABSTRACT FROM AUTHOR]

The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment. [ABSTRACT FROM AUTHOR]

The Penstylhamaparvovirus species Decapod penstylhamaparvovirus 1, commonly known as infectious hypodermal and hematopoietic necrosis virus (IHHNV), is the smallest of known shrimp viruses belonging to the family Parvoviridae, subfamily Hamaparvovirinae [...]

Highly pathogenic avian influenza viruses (HPAIVs) have devastating impacts on the poultry industries. With infections in poultry, H5 and H7 lowpathogenicity avian influenza viruses (LPAIVs) have spontaneously mutated into HPAIVs [...]

Avian metapneumovirus (aMPV) poses a significant threat to the poultry industry worldwide, primarily affecting turkeys and chickens. The recent detection of aMPV-A and -B subtypes in the United States marks a significant shift after a prolonged period free of aMPV following the eradication of the previously circulating subtype C. Hence, the demand for molecular diagnostic tests for aMPV has arisen due to their limited availability in the US market. In this study, we present the molecular characterization based on the complete genome sequence of aMPV subtype A, which was detected in the US for the first time. Four RT-qPCR positive samples were subjected to next-generation sequencing analysis, resulting in the assembly of one complete and one near-complete genome sequences. Phylogenetic analysis revealed that the isolated strains clustered within the aMPV-A subtype and were most closely related to recent Mexican strains. A detailed amino acid analysis identified unique mutations in the G gene of the US isolates compared to Mexican strains. Additionally, we compared the performance, cross-reactivity, and limit of detection of our revised aMPV subtype-specific RT-qPCR test with two commercial kits, demonstrating similar detection and subtyping capabilities. These findings highlight the importance of accurate diagnostic methods for disease management in the poultry industry, provide valuable insights into the epidemiology of aMPV, and underscore the need for continued vigilance and surveillance to mitigate its impact on poultry production. [ABSTRACT FROM AUTHOR]

Low pathogenicity avian influenza virus (LPAIV) subtype H5N2 has caused outbreaks in poultry in Mexico since 1993 and mutated into highly pathogenic avian influenza virus (HPAIV) H5N2 during 1994-1995 (1). [...]

In the United States during 2012, approximately 300 cases of human infection with influenza A(H3N2) variant (H3N2v) virus were reported; they resulted in 16 hospitalizations and 1 death (1). The [...]

Wild-bird origin influenza A viruses (IAVs or avian influenza) have led to sporadic outbreaks among domestic poultry in the United States and Canada, resulting in economic losses through the implementation of costly containment practices and destruction of birds. We used evolutionary analyses of virus sequence data to determine that 78 H5 low-pathogenic avian influenza viruses (LPAIVs) isolated from domestic poultry in the United States and Canada during 2001 to 2017 resulted from 18 independent virus introductions from wild birds. Within the wild-bird reservoir, the hemagglutinin gene segments of H5 LPAIVs exist primarily as two cocirculating genetic sublineages, and our findings suggest that the H5 gene segments flow within each migratory bird flyway and among adjacent flyways, with limited exchange between the nonadjacent Atlantic and Pacific Flyways. Phylogeographic analyses provided evidence that IAVs from dabbling ducks and swans/geese contributed to the emergence of viruses among domestic poultry. H5 LPAIVs isolated from commercial farm poultry (i.e., turkey) that were descended from a single introduction typically remained a single genotype, whereas those from live-bird markets sometimes led to multiple genotypes, reflecting the potential for reassortment with other IAVs circulating within live-bird markets. H5 LPAIVs introduced from wild birds to domestic poultry represent economic threats to the U.S. poultry industry, and our data suggest that such introductions have been sporadic, controlled effectively through production monitoring and a stamping-out policy, and are, therefore, unlikely to result in sustained detections in commercial poultry operations. [ABSTRACT FROM AUTHOR]