Introduction: During the 2021 COVID-19 pandemic, Ghana experienced outbreaks of high pathogenic avian influenza virus (HPAIV) H5N1 among poultry.

Objectives: Here, we describe the distribution and genetic characterisation of clade 2.3.4.4b HPAIV H5N1 isolated among poultry.

Methods: We conducted active surveillance for influenza viruses among animals (poultry and swine) and environmental samples across Ghana from 2021 to 2022. Tracheal/cloacal swabs were collected from poultry while nasal/anal swabs were collected from swine. Environmental samples (bird droppings, feathers, and water) were collected from Ramsar sites. We detected the presence of influenza viruses using specific primers and probes and reverse transcription polymerase chain reactions previously described by the US-CDC. We sequenced and detected viruses using Oxford Nanopore Technologies.

Results: A total of 2847 samples were collected: 2640 from birds, 207 from swine, and 186 from the environment. Out of 2847, 2.2% (63/2847) were positive for HPAIV H5N1. All the H5N1 viruses were detected in poultry populations and none in swine. Again, environmental samples tested negative for influenza. Greater Accra (35), Central (10), and Upper East (7) regions recorded the highest number of H5N1 infections. Phylogenetic analysis of H5N1 showed that these viruses belonged to the clade 2.3.4.4b, which is currently circulating worldwide. Genetic analysis of the HA revealed some mammalian adaptive motifs.

Conclusion: These findings highlight the importance of continuous genomic surveillance for these zoonotic pathogens in-country and further analyses to determine their zoonotic potential. Early detection and local containment are critical for mitigating the threat posed by zoonotic influenza.