Molecular and In Vivo Characterization of the High Pathogenicity H7N6 Avian Influenza Virus That Emerged in South African Poultry in 2023

Abstract

A high pathogenicity avian influenza (HPAI) subtype H7N6 virus emerged in South African poultry in 2023 and later spread to Mozambique, the first documented emergence of H7 HPAI in the African continent. A total of 6.82 million birds succumbed to the disease or were culled, representing about 20% of the South African egg‐laying flock and almost 30% of the broiler breeder flock. The complete genomes of 68 outbreak viruses were sequenced and analyzed, tracing the phylogenetic origins of the ancestral H7N6 virus to a reassortment of various subtypes that circulated in southern African wild birds. Molecular clock analysis determined that the virus emerged in the first week of May 2023, probably in a smallholder chicken flock, before spreading to commercial farms, where the disease was first reported in early June. The multibasic hemagglutinin protein cleavage site (HA0) was derived from a nonhomologous recombination event with chicken 28S ribosomal ribonucleic acid (RNA). Few genetic markers associated with an increased risk to humans were present in the translated viral proteins. The intravenous pathogenicity index (IVPI) value of the index case isolate was 1.67, reflecting that 50% of the specific pathogen‐free chickens died within 4 days of infection. Surviving birds showing mostly mild clinical signs and recovered by day 10 postinfection. Prior to death, chickens shed the virus primarily through the respiratory route, with lower amounts shed from the cloaca, but in the survivors, the virus was still being shed from the cloaca on day 10. Fomites were the likely source of disease spread between farms, and the amount of H7N6 HPAI virus per gram of feces was calculated at ~383,193 (5.58 log10) egg infectious dose 50 (EID50) equivalents, chicken feather follicles contained on average 739,712.43 (5.87 log10) EID50 equivalents, and 20 µg of feather dust contained 14,976.96 (4.175 log10) EID50 equivalents.