Reassortment patterns in Swine influenza viruses - PubMed (original) (raw)

Reassortment patterns in Swine influenza viruses

Hossein Khiabanian et al. PLoS One. 2009.

Abstract

Three human influenza pandemics occurred in the twentieth century, in 1918, 1957, and 1968. Influenza pandemic strains are the results of emerging viruses from non-human reservoirs to which humans have little or no immunity. At least two of these pandemic strains, in 1957 and in 1968, were the results of reassortments between human and avian viruses. Also, many cases of swine influenza viruses have reportedly infected humans, in particular, the recent H1N1 influenza virus of swine origin, isolated in Mexico and the United States. Pigs are documented to allow productive replication of human, avian, and swine influenza viruses. Thus it has been conjectured that pigs are the "mixing vessel" that create the avian-human reassortant strains, causing the human pandemics. Hence, studying the process and patterns of viral reassortment, especially in pigs, is a key to better understanding of human influenza pandemics. In the last few years, databases containing sequences of influenza A viruses, including swine viruses, collected since 1918 from diverse geographical locations, have been developed and made publicly available. In this paper, we study an ensemble of swine influenza viruses to analyze the reassortment phenomena through several statistical techniques. The reassortment patterns in swine viruses prove to be similar to the previous results found in human viruses, both in vitro and in vivo, that the surface glycoprotein coding segments reassort most often. Moreover, we find that one of the polymerase segments (PB1), reassorted in the strains responsible for the last two human pandemics, also reassorts frequently.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Pair-wise hamming distances at the third codon positions in PB2 vs. PB1.

The colors demonstrate the logarithm of the cumulative probability for the points, among which the ones with a cumulative probability of less than 10−7 indicate possible reassortment events. Left: The results from 150 strains in the dataset, where there are candidates for reassortment events in both PB2 and PB1. Right: The results when the dataset is limited to the classical H1N1 strains isolated in the 70's, 80's, and 90's, where there are distinctively more candidates for reassortment events in PB1.

Figure 2

Figure 2. History overlap for segments PB1 and NP of the swine influenza strain A/Swine/Tennessee/23/1976.

NP and all the other segments except PB1 share a common recent history, whereas the recent history of PB1 is different from the other seven segments, indicating a reassortment event at PB1. The small history overlap of M1 with PB1 and NP at lower identities can be attributed to a possible slower evolutionary rate of M1 and a fork in its lineage to a line of human viruses. The fluctuations in the history overlap of NP at 99% identity are due to small number of sample points at that level of identity.

Figure 3

Figure 3. Diversity measurements in swine influenza viruses and the corresponding 95% bootstrap percentile confidence intervals.

Left: Considering the 150 strains in the dataset, NA, HA, and PB1 present a higher diversity than the rest. Right: When the dataset is limited to the classical H1N1 strains isolated in the 70's, 80's, and 90's, which fixes the HA and NA variations in the population, shows a higher diversity in PB1 than the rest of the segments.

Figure 4

Figure 4. Pair-wise Pearson correlation of the distances at the third codon positions of the viral segments.

Left: The HA, NA, and PB1 segments have the least correlation in regards to the rest of the segments. Right: When the HA and NA variations are fixed in the population by limiting the dataset to the classical H1N1 strains isolated in the 70's, 80's, and 90's, PB1 presents a distinctively lower correlation relative to the other segments.

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