Conceived and designed the experiments: CK NN. Performed the experiments: CK NN. Analyzed the data: CK NN SLS. Wrote the paper: CK NN SLS.
The authors have declared that no competing interests exist.
In April 2009, novel swine-origin influenza viruses (S-OIV) were identified in patients from Mexico and the United States. The viruses were genetically characterized as a novel influenza A (H1N1) strain originating in swine, and within a very short time the S-OIV strain spread across the globe via human-to-human contact.
We conducted a comprehensive computational search of all available sequences of the surface proteins of H1N1 swine influenza isolates and found that a similar strain to S-OIV appeared in Thailand in 2000. The earlier isolates caused infections in pigs but only one sequenced human case, A/Thailand/271/2005 (H1N1).
Differences between the Thai cases and S-OIV may help shed light on the ability of the current outbreak strain to spread rapidly among humans.
In April 2009, a novel strain of the influenza A (H1N1) virus emerged in Mexico, the United States, and multiple other countries. By early June, the World Health Organization reported that the virus had spread to 66 countries with 19,273 confirmed cases including 117 deaths (
In this note, we report the results of the application of a comprehensive, computational search for reassortments between the Eurasian and North American swine influenza lineages. Using the genome sequence of one of the isolates from the current S-OIV outbreak, we conducted a comprehensive computational search among all hemagglutinin (HA) and neuraminidase (NA) sequences from H1N1 swine isolates to identify all reassortments matching the outbreak strain. We found that two similar reassortments had occurred among H1N1 isolates collected in Thailand between 2000 and 2006, resulting in multiple infections among pigs and a single sequenced human case, A/Thailand/271/2005
Colors indicate whether the segment derived from human H3N2, classical H1N1 swine, Eurasian H1N1, or avian influenza. The isolates from Thailand represent the only sequenced examples, prior to S-OIV, of reassortment strains containing the HA segment from classical H1N1 swine and the NA segment from the Eurasian H1N1 swine lineage. The reassortment history of the H1N2 “triple reassortment” was described by Olsen
A second set of reassortants, also from Thailand, involved only the HA segment (A/Sw/Chonburi/NIAH589/2005, A/Sw/Chachoengsao/NIAH587/2005, A/Sw/Ratchaburi/NIAH550/2003, and A/Sw/Ratchaburi/NIAH1481/2000
The Thai reassortants were identified here by an automatic, exhaustive, computational search that compares ensembles of trees sampled from a Markov chain Monte Carlo (MCMC) walk. This search, implemented in a novel reassortment discovery program, exhaustively enumerates all HA-NA tree incompatibilities that have sufficient statistical support to be considered likely reassortments despite the ambiguities in phylogenetic reconstruction. Experiments
The evolutionary relationship among the S-OIV outbreak strain, the Thai isolates, and other influenza strains is illustrated for the HA and NA segments in
Numbers on branches give posterior probabilities. S-OIV (H1N1) 2009 isolates are colored red. To simplify the figure, only three S-OIV isolates are shown; all other sequences from S-OIV are nearly identical and would appear in the same location in the trees. Thai isolates representing the 6+2 and 7+1 reassortments are colored green, with Thai (6+2) reassortants marked by arrows. The human cases of infection with swine-origin influenza that appear in the trees are shown in blue.
The evolutionary history of swine influenza A (H1N1) over the past decade is complex. For many decades, H1N1 influenza in North American swine (also called “classical” H1N1) mutated relatively slowly
The results presented here catalog the complete collection of sequenced reassortments for which a combination of the HA and NA segments similar to the S-OIV outbreak has occurred. Our main novel result is that no other sequenced examples of this pattern besides the discussed Thai isolates could be found. We can confidently say then that among publicly available sequences these isolates represent the complete catalog of such events. The collection shows that this has happened at least twice within the past ten years and that all previous such sequenced reassortments were collected in Thailand. Due to the lack of detailed surveillance of swine populations around the world, this almost certainly represents an underestimate in the frequency of classical-Eurasian reassortment.
Comparisons between these previous reassortant strains and the S-OIV strain may shed light on the cause of S-OIV's virulence. The previous reassortants did not cause a major human outbreak, despite bringing together somewhat similar surface proteins. One hypothesis is that subsequent mutations in the HA or NA proteins was sufficient to facilitate human-to-human transmission of S-OIV. Alternatively, it may be that some combination of the internal proteins not shared with the Thai strains (PA, NP, PB1, and PB2), possibly interacting with changes in the surface proteins, has given S-OIV its ability to cause human outbreaks. Owing to our comprehensive search through the available H1N1 swine isolates, we know the Thai isolates described above represent the complete set of currently available reassortant sequences that are available to answer this question.
The automated reassortment finder
All 74390 flu sequences were downloaded from the influenza virus resource (IVR;
Nucleotide sequences were aligned by the MUSCLE program
Tree for the internal M segment, created as described in the main text. Recent S-OIV isolates are colored red, the Thai 6+2 and 7+1 isolates (described in the main text) are colored green. Red and green boxes draw attention to the clades containing most of the S-OIV and Thai H1N1 reassortant sequences. Human isolates that appear in the trees are colored blue. Because sequences with ≥99% sequence identity were filtered out, some human cases of swine-derived influenza are not shown in the trees.
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Tree for the internal NP segment, created as described in the main text, and colored as described in the caption of Supplementary
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Tree for the internal NS segment, created as described in the main text, and colored as described in the caption of Supplementary
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Tree for the internal PA segment, created as described in the main text, and colored as described in the caption of Supplementary
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Tree for the internal PB1 segment, created as described in the main text, and colored as described in the caption of Supplementary
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Tree for the internal PB2 segment, created as described in the main text, and colored as described in the caption of Supplementary
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