Full-Genome Analysis of Avian Influenza A(H5N1) Virus from a Human, North America, 2013

Kanti Pabbaraju, Raymond Tellier, Sallene Wong, Yan Li, Nathalie Bastien, Julian W. Tang, Steven J. Drews, Yunho Jang, C. Todd Davis, Kevin Fonseca

, and Graham A. Tipples

Author affiliations: Provincial Laboratory for Public Health, Calgary, Alberta, Canada (K. Pabbaraju, R. Tellier, S. Wong, J.W. Tang, S.J. Drews, K. Fonseca, G.A. Tipples); Public Health Agency of Canada, Winnipeg, Manitoba, Canada (Y. Li, N. Bastien); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (Y. Jang, C.T. Davis); University of Calgary, Calgary (R. Tellier, K. Fonseca, S.J. Drews); University of Manitoba, Winnipeg (Y. Li); and University of Alberta, Edmonton, Alberta, Canada (J.W. Tang, G.A. Tipples)

Abstract

Full-genome analysis was conducted on the first isolate of highly pathogenic avian influenza A(H5N1) virus from a human in North America. The virus has a hemagglutinin gene of clade 2.3.2.1c and is a reassortant with an H9N2 subtype lineage polymerase basic 2 gene. No mutations conferring resistance to adamantanes or neuraminidase inhibitors were found.

Since the 1997 emergence of highly pathogenic avian influenza (HPAI) A(H5N1) virus in Hong Kong, China, 648 HPAI A(H5N1) infections and 384 associated deaths in humans have been reported. During 2013, Cambodia reported the most human infections, followed by Egypt, Indonesia, China, and Vietnam (www.who.int/influenza/human_animal_interface/H5N1_cumulative_table_archives/en/, December 10, 2013, report). In December 2013, an HPAI A(H5N1) infection was reported in a Canadian resident who recently returned from China. No human or poultry HPAI A(H5N1) infections had been previously reported in North America.

Case Report and Laboratory Investigations

Preliminary details of this case have been reported (1) (Technical Appendix 1

[PDF - 57 KB - 4 pages]). The patient initially sought care for respiratory symptoms; however, the probable cause of death was listed as meningoencephalitis, an unusual outcome for HPAI A(H5N1) infections in humans. Detailed interviews with close contacts have not identified exposure to infected avian sources or environmental contamination, although these investigations are continuing. Because symptom onset occurred during a return flight from China, it is probable that the patient was exposed to the virus while in China.

Nasopharyngeal swab (NP) samples, bronchoalveolar lavage (BAL), and cerebrospinal fluid (CSF) samples tested positive for influenza A(H5N1) virus by various molecular testing methods, including sequencing, at the Provincial Laboratory for Public Health and the National Microbiology Laboratory, Public Health Agency of Canada (1). An isolate cultured from BAL (A/Alberta/01/2014) underwent full-genome sequencing (methods available in online Technical Appendix 1); analysis results are presented here.

Partial sequences of virus from the primary specimens (shown in parentheses) included 1,378 bp of the hemagglutinin (HA) gene (CSF, BAL, NP), 1,350 bp of the neuraminidase gene (BAL), 810 bp of the matrix gene (NP), and 687 bp of the polymerase basic 2 (PB2) gene (NP). These sequences were identical to corresponding sequences obtained from the isolate, suggesting the absence of cell culture–induced changes.