Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community

Abstract

Background: There are few data in the literature on viral sequence variation between host generations/successive transmission events. Relatively little is known about the sequence heterogeneity of the influenza viruses transmitted within families.

Objectives: To study the molecular epidemiology of influenza virus and to determine the sequence variation within an individual, a household and a community during the first wave of influenza pandemic in 2009.

Study design: A prospective study of household transmission of influenza A in Hong Kong was conducted during the pandemic in 2009. The HA and NA sequences of pandemic and seasonal influenza A viral isolates identified in this household transmission study were sequences and analyzed.

Results: Our results indicated that there were multiple introductions of influenza viruses into Hong Kong. Sequence analysis of these isolates suggested that members of these family clusters acquired the infection by household transmissions. Interestingly, unlike those concluded from previous household transmission studies, we observed sequence variations between sequential samples from the same person and also within the same household.

Conclusions: Family clusters of influenza A viral infection are predominantly the result of secondary transmission within a household. Our results also suggested that the intra-host viral sequence variation might be more common that than previously thought.

Figure 1

Phylogenetic analysis of pH1N1 HA. Viruses isolated from households with household transmissions (Household 1–8) were marked by colored symbols. Within the name of each virus, the number after “V” and the number in the brackets denotes the sampling occasion (Visits 1 to 3) and household member identity (Index case=0), respectively. Viruses isolated from the same individuals, but at different sampling occasions, were highlighted in bold. The phylogenetic tree was constructed by neighbor-joining method with default parameters in MEGA4. Bootstrap values of the phylogenetic tree constructed were generated by doing 1,000 replicates. Bootstrap values ≥ 70% were considered well-supported. The scale bar represents genetic distance between homologues (nucleotide substitutions per site). The GenBank accession numbers of reference sequences are shown.

Figure 2

Phylogenetic analysis of sH3N2 HA. Viruses isolated from households with household transmissions (Household 9–18) were marked by colored symbols. Within the name of each virus, the number after “V” and the number in the brackets denotes the sampling occasion (Visits 1 to 3) and household member identity (Index case=0), respectively. Viruses isolated from the same individuals, but at different sampling occasions, were highlighted in bold. The phylogenetic tree was constructed by neighbor-joining method with default parameters in MEGA4. Bootstrap values of the phylogenetic tree constructed were generated by doing 1,000 replicates. Bootstrap values ≥ 70% were considered well-supported. The scale bar represents genetic distance between homologues (nucleotide substitutions per site). The GenBank accession numbers of reference sequences are shown.