Reassortment between seasonal and pandemic H1N1 in India

Influenza viruses are named based on only two of their eight genomic segments. This is unfortunate because it leads to confusion when trying to distinguish between viruses that are not closely related but have the same subtype. When the most recent influenza pandemic began in early 2009, the virus that caused it was noted to have the subtype H1N1. However, the virus that caused the 1918 pandemic also had the H1N1 subtype. Even more confusing, there is a seasonal influenza with this same subtype. Thus, since early 2009, two H1N1 viruses, with very different effects on patients, have been infecting people all over the world.

One of the most dangerous possible events with regard to influenza viruses is if two different flu viruses exchange genetic material. If entire genetic segments are exchanged, this is called reassortment. There is evidence consistent with such an event with respect to seasonal H1N1 and pandemic H1N1 in India (Sarkar et al, 2010).

From the paper:

During the peak outbreak (July–September 2009), a total 1886 patients were screened in eastern India, of which 139 (7.37%) and 52 (2.76%) were positive for pH1N1 [pandemic H1N1] and seasonal H1N1, respectively.

[snip]

Consistent with previous reports, the PB1-F2 gene of pH1N1 strains was unique due to a mutation resulting in a truncated protein of 11 aa. The HA, NA and NS1 genes of H1N1/2009 strains clustered with H1N1 strains of 2000–2009, whereas a subset of strains contained a pH1N1-like truncated PB1-F2.

[snip]

Unlike the distinct lineage of HA, NA and NS1 gene of seasonal H1N1/2009 strains, surprisingly, a subset of strains (6/21) contained a truncated PB1-F2 protein similar to those of the pH1N1/2009 strains. This indicates an early reassortment event between co-circulating strains of two different lineages.

In this study, four gene segments were studied, HA, NA, NS and PB1 in both seasonal H1N1 and pandemic H1N1 (pH1N1). Six strains of flu viruses from eastern India were found with HA, NA and NS gene segments which were similar to seasonal H1N1 but PB1 gene segments similar to pandemic H1N1. The six reassortant strains are: A/KOL/2465/2009; A/KOL/2482/2009; A/KOL/2449/2009; A/KOL/2086/2009; A/KOL/927/2009; and A/KOL/230/2009. Notably, if the authors had only sequenced HA and NA gene segments, this reassortment would have been missed. Only by sequencing all eight genomic segments can it be concluded that a reassortment event has *not* occurred.

At this point, there is no evidence that the reassortment event reported in the six strains from eastern India has resulted in a more virulent virus. However, the real importance of this paper is to document that such reassortments are occurring. Given that there are now a multitude of influenza viruses currently circulating, including the extremely lethal H5N1, the risk of a disastrous reassorment is signficant.

Reference

Sarkar et al. (2010) Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India. Arch. Virol.

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