Quantifying influenza virus diversity and transmission in humans

Influenza A virus is characterized by high genetic diversity.(1–3) However, most of what we know about influenza evolution has come from consensus sequences sampled at the epidemiological scale(4) that only represent the dominant virus lineage within each infected host. Less is known about the extent of intra-host virus diversity and what proportion is transmitted between individuals.(5) To characterize those virus variants that achieve sustainable transmission in new hosts, we examined intra-host virus genetic diversity within household donor/recipient pairs from the first wave of the 2009 H1N1 pandemic when seasonal H3N2 was co-circulating. While the same variants were found in multiple members of the community, the relative frequencies of variants fluctuated, with patterns of genetic variation more similar within than between households. We estimated the effective population size of influenza A virus across donor/recipient pairs to be approximately 100–200 contributing members, which enabled the transmission of multiple lineages including antigenic variants.