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

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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.

Section snippets

Background

The emergence of pandemic H1N1/2009 virus provided an unique opportunity to study the dynamics of influenza virus transmission in humans1, 2 and comparative studies of pandemic and seasonal viruses within households may provide important understanding in this regard.3 We previously conducted a prospective household transmission study and concluded that pandemic and seasonal viruses have broadly similar viral-load dynamics, disease severities, and transmissibilities in the household setting.4

Objectives

The aim of this study is to elucidate the genetic sequence variation in HA and NA virus gene segments in these sequential specimens from index cases and secondary cases of infection. In addition, the epidemiological links of these household samples were also studied.

Study design

Three hundred forty-eight index patients with acute respiratory illness from a local network of 14 outpatient clinics were recruited from June to August 2009. We followed the household contacts of 99 index patients who tested positive for influenza A virus on rapid diagnostic testing in an outpatient setting and collected nasal and throat swabs (NTS) from these index cases as well as all household members regardless of illness at three subsequent home visits within 7 days. NTS were sampled and

Results and discussion

A total of 119 influenza viruses were isolated from 98 individuals in 78 households (pandemic H1N1 (pH1N1) = 61; seasonal H1N1 (sH1N1) = 4; seasonal H3N2 (sH3N2) = 54). Of these 119 viral isolates, 42 were sampled from 21 individuals (pH1N1 = 14; sH3N2 = 7) who were positive in two consecutive visits. Twenty pH1N1 and 15 sH3N2 viruses were isolated from households with confirmed secondary transmission (pH1N1 = 8; sH3N2 = 8). On one occasion, a pH1N1 and a sH3N2 viruses were isolated from different members of

Conclusion

Our results demonstrated that there were multiple introductions of pH1N1 and sH3N2 viruses into Hong Kong in 2009. Although multiple clades of pH1N1 and sH3N2 viruses co-circulated at the community level, viruses isolated from the same household were usually derived from the same viral lineage. Natural sequence variations could be detected in some sequential samples from the same person and also within the same household, suggesting influenza viral sequence variations might be more dynamic that

Funding

This study was supported by the Area of Excellence Scheme of the University Grants Committee Hong Kong (AoE/M-12/06), the Research Fund for the Control of Infectious Disease Commissioned Project from Food and Health Bureau, the NIH (NIAID contracts HHS-N266200700005C and N01-AI-70005), and the Harvard Center for Communicable Disease Dynamics from the National Institute of General Medical Sciences (grant number U54 GM088558). The funding bodies were not involved in the collection, analysis and

Conflict of interest

The authors have no commercial or other associations that may pose a conflict of interest.

Ethical approval

The procedures described in this study was reviewed and approved by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (Ref Number: UW 06-350T/1375).

Acknowledgements

We thank Chan Kit Man, Rita Fung, Lai-Ming Ho, Ho Yuk Ling, Lam Yiu Pong, Lincoln Lau, Tom Lui, Tong Hok Leung, Loretta Mak, Gloria Ng, Teresa So, Alfred Yeung, Eileen Yeung and Jenny Yuen for research support.

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