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

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 TCID 50 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.
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https://hal-riip.archives-ouvertes.fr/pasteur-03214733
Contributor : Philippe Dussart <>
Submitted on : Sunday, May 2, 2021 - 6:23:49 PM
Last modification on : Monday, June 21, 2021 - 6:01:59 PM
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Sareth Rith, Savuth Chin, Borann Sar, Phalla Y, Srey Viseth Horm, et al.. Natural co-infection of influenza A/H3N2 and A/H1N1pdm09 viruses resulting in a reassortant A/H3N2 virus. Journal of Clinical Virology, Elsevier, 2015, 73, pp.108-111. ⟨10.1016/j.jcv.2015.11.008⟩. ⟨pasteur-03214733⟩

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