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Case Reports
. 2015 Dec:73:108-111.
doi: 10.1016/j.jcv.2015.11.008. Epub 2015 Nov 5.

Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus

Sareth Rith  1 , Savuth Chin  2 , Borann Sar  3 , Phalla Y  1 , Srey Viseth Horm  1 , Sovann Ly  4 , Philippe Buchy  1 , Philippe Dussart  1 , Paul F Horwood  5
Affiliations
Case Reports

Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus

Sareth Rith et al. J Clin Virol. 2015 Dec.

Abstract

Background: Despite annual co-circulation of different subtypes of seasonal influenza, co-infections between different viruses are rarely detected. These co-infections can result in the emergence of reassortant progeny.

Study design: We document the detection of an influenza co-infection, between influenza A/H3N2 with A/H1N1pdm09 viruses, which occurred in a 3 year old male in Cambodia during April 2014. Both viruses were detected in the patient at relatively high viral loads (as determined by real-time RT-PCR CT values), which is unusual for influenza co-infections. As reassortment can occur between co-infected influenza A strains we isolated plaque purified clonal viral populations from the clinical material of the patient infected with A/H3N2 and A/H1N1pdm09.

Results: Complete genome sequences were completed for 7 clonal viruses to determine if any reassorted viruses were generated during the influenza virus co-infection. Although most of the viral sequences were consistent with wild-type A/H3N2 or A/H1N1pdm09, one reassortant A/H3N2 virus was isolated which contained an A/H1N1pdm09 NS1 gene fragment. The reassortant virus was viable and able to infect cells, as judged by successful passage in MDCK cells, achieving a TCID50 of 10(4)/ml at passage number two. There is no evidence that the reassortant virus was transmitted further. The co-infection occurred during a period when co-circulation of A/H3N2 and A/H1N1pdm09 was detected in Cambodia.

Conclusions: It is unclear how often influenza co-infections occur, but laboratories should consider influenza co-infections during routine surveillance activities.

Keywords: A/H1N1pdm09; A/H3N2; Co-infection; Influenza; Reassortant; Reassortment; Seasonal.

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Figures

Fig. 1
Fig. 1
Phylogenetic tree based on NS1 sequences of A/H1N1pdm09 and A/H3N2 viruses, generated in MEGA 6 by using the Maximum Likelihood method based on the Tamura 3-parameter model . The numbers next to the branches indicate the percentage of 1000 bootstrap replicates that support each phylogenetic branch. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. (□) Vaccine strains in 2014: A/Texas/50/2012 (A/H3N2), A/California/07/2009 (A/H1N1pdm09). (■) A/H3N2 reassortant virus clone on MDCK cells, passage 1 and 2. (●) A/H3N2 virus clone on MDCK, passage 1.
See this image and copyright information in PMC

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