Tracing the possible origins of the clade 2.3.4.4b highly pathogenic avian influenza H5Nx viruses from India

Highly pathogenic avian influenza (HPAI) clade 2.3.4.4b H5Nx viruses are a major zoonotic concern. Clade 2.3.4.4b was first reported in India during the HPAI H5N8 outbreaks in zoological parks, in 2016. Recently, in June 2024, clade 2.3.4.4b HPAI H5N1 virus outbreaks were reported from Kerala. The genetic and molecular characterization of this H5N1 virus revealed that it is a novel reassortant comprising of internal genes derived from LPAI viruses reported from Kerala; and some of European origin. The exact spatio-temporal origins of these viruses were unknown. The present study was undertaken to trace the possible source of the clade 2.3.4.4b HPAI H5N1 and H5N8 viruses reported from India. Molecular clock and phylogeography analyses were carried out using BEAST v1.10.4 for the global and regional datasets of clade 2.3.4.4b H5Nx virus hemagglutinin gene sequences downloaded from the GISAID database. Preliminary phylogeography analysis using the global dataset revealed direct linkages of South Asia with the Middle East, North Africa, Japan, Korea, and China in the transmission network. Further analysis using regional datasets revealed that the H5N1 isolates reported from Kerala in 2024 had been introduced to India from East Asia, around 2022. The two reported H5N8 viruses from 2016 showed separate introductions from East Asian countries, including China and Japan respectively, around the year 2015. In the present study we report the spatio-temporal origins of clade 2.3.4.4b HPAI H5Nx viruses from South Asia. The analyses would be useful in furthering our understanding of this pathogen of human and animal health importance.