2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates

Abstract

Background: 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.

Methodology: 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).

Significance: 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.

Figure 1. Reassortment history of the 2009 S-OIV outbreak strain and the Thai reassortants.

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 . Arrows indicate ancestor relationships; additional, unobserved reassortment events may have occurred.

Figure 2. Majority consensus tree for the HA segment computed with MrBayes .

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.

Figure 3. Majority consensus tree for the NA segment, computed and labeled as in Figure 2.