Shittu, I. | bioRxiv Science

bioRxiv2026

Community-Based Surveillance for Highly Pathogenic Avian Influenza Viruses among Deceased Birds

Highly pathogenic avian influenza (HPAI) viruses of H5N1 clade 2.3.4.4b, are spreading worldwide, posing a threat to wildlife, domestic animals, and humans. In 2025, a multidisciplinary collaboration for HPAI H5N1 surveillance among birds within Galveston County, Texas, was initiated. Between November and December 2025, oropharyngeal and cloacal swabs were collected from wild and domestic birds reported as dead or dying by Galveston County residents. Specimens were studied with molecular assays, Sanger sequencing, virus isolation, and next-generation sequencing. Molecular evidence of HPAI H5N1 was detected in 7 of 10 (70%) birds, and the virus was successfully cultured in MDCK cells. Next-generation sequencing analysis of eight influenza A genome segments demonstrated a 4:4 gene segment reassortant constellation within clade 2.3.4.4b, consistent with genotype D1.1. Community members exposed to HPAI were offered antiviral prophylaxis. No human infections were identified. This surveillance demonstrates that community involvement combined with cross-sectoral collaboration can ensure rapid detection and characterization of circulating avian influenza viruses. Sustained local surveillance is essential for early warning, risk assessment, and prevention of virus spread to poultry, mammals, and humans.

molecular biology↗

bioRxiv2025

Infectious Bronchitis: Molecular Detection and Characterization in Live Bird Markets in Jos, Plateau State, Nigeria

Infectious bronchitis virus (IBV), the avian coronavirus, is a highly contagious coronavirus of birds. It mostly affects the respiratory, urinary and reproductive tract, leading to considerable economic losses to the poultry industry as a result of drop in egg production, undesirable egg quality and poor weight gain. Thus, this study aimed to detect and characterize the virus in live bird markets (LBMs) in Plateau State, Nigeria. One hundred pooled of cloacal and tracheal swab samples each were collected from two LBMs in Jos. Viral RNA was extracted and screened for IBV using real-time RT-PCR. Subsequently, hyper-variable region of the spike (S1) gene of positive samples were amplified and sequenced. IBV nucleic acid was detected in 42% (42/100) of the pooled samples. Phylogenetic analysis of the resulting sequences of S1 gene showed that IBV detected in this study were diversified into two distinct genotypes: GI-14, and GI-23. These genotypes were closely related to a Poland strain with over 95% nucleotide identity, forming a common cluster within the GI-23 group. One isolate showed a notable relationship with a previously reported Nigerian isolate, sharing 85% nucleotide identity, and formed a common cluster within the GI-14 group. Overall, this study established the widespread of IBV and therefore recommends continuous surveillance to identify the current circulating strain for possible local vaccine development for effective control measures to mitigate the spread of the virus in the study area and the country at large.

microbiology↗