Figure 3.

Maximum clade credibility (MCC) phylogenetic tree of the HA genes of Asian H1 IAVs-S. All available H1 HA gene sequences with complete HA coding regions from IAVs-S isolated in the nine Asian countries in Figure 2 were downloaded from GISAID on 8 July 2021. Sequence data from the Philippines were unavailable at the time of the download. Sequence data for each country or region underwent cd-hit clustering [69] (threshold, 98.5% identity) to reduce the number of sequences and increase visualization. ‘China’ refers to mainland China, and Hong Kong and Taiwan were considered as separate regions because they differ in pig trade and other livestock-related practices that might affect the prevalence of IAV-S. For the calculation, when only the year was available as the isolation date from GISAID, 1 July was used as the tentative isolation date; when only the year and month were available, the 15th was used as the day. This tree was constructed to illustrate the overall evolutionary pathway of Asian IAVs-S, not for precise calculation of the divergence time. Various the human seasonal IAVs and IAVs-S from other countries have been included as clade indicators.