Asia1/WHN/CHA/06 was isolated from pigs in a pig farm in 2006. According to the investigation of the pig farm during the outbreak, about 20% of sows presented typical clinical symptoms of FMD, whereas none of the piglets and boars showed any symptoms and no pigs died. The FMD in the pig farm lasted for about one month. Moreover, there were not any reports about outbreak of FMD in other pig farms around the area at that time. Therefore, we speculated that Asia1/WHN/CHA/06 had low pathogenicity or infectivity to pigs, though high lethality of the strain to sulking mouth was observed in this study. But further study should be carried out to test the virulence of the strain to pigs to approve the inference.
The complete genome sequence of Asia1/WHN/CHA/06 was determined, except Poly(C) tract. Poly(C) tract of FMDV is usually ranging from 100 to 420 cytosine residues interspersed with an occasional uracil residue , so it is difficult to amplify the true sequence of the tract by RT-PCR from the viral RNA genome . In this study, we didn't manage to get the poly(C) tract sequence of Asia1/WHN/CHA/06 either. Pseudoknots (PKs) have been found to be 3-4 tandem repeats of RNA secondary structure in FMDV genome, which probably had some role during viral replication . Additionally, it is reported that partial deletions of FMDV strains in PKs' region correlated with the host range . However, no deletions occurred in PKs' region of Asia1/WHN/CHA/06. In sequence of VP1 protein, the RGD motif is the molecular basis of binding of FMDV to its cellular receptor . Although the RGD bordering region sequence of Asia1/WHN/CHA/06 is highly consistent with the reference strains isolated after the year of 2004, an amino acids' position at RGD +9 mutated (N→D). As several lines of evidence show that the vicinity of the RGD motif, including RGD +1 (leucine) and +4 (leucine) positions, are necessary for the FMDV RGD-mediated receptor recognition [24, 25], it is unclear whether the variation at RGD +9 site influence the receptor recognition of Asia1/WHN/CHA/06. Although non-structural proteins which play important roles for viral propagation are generally more conserved than the structural proteins, 3A is one of the most variable proteins of FMDV . In addition, deletions in 3A have been shown to associate with FMDV attenuation in cattle and high virulence for pigs . Meanwhile, a single amino acid mutation at position 44 in the 3A protein is present in guinea pig-adapted isolates examined . In our study, we found no deletion but 3 amino acid substitutions in the 3A region of Asia1/WHN/CHA/06. Considering that the isolate isolated from a pig, while other FMDV Asia1 type isolates came from cattle, it would be interesting to examine by reverse genetics if the 3 amino acid substitutions may contribute to adaptation of host range.
From a practical point of view, it is important to analyze the nucleotide sequence of the virus from new hosts for subsequent comparison with other isolates to trace the origin and route of the viral spread. To date, there are over 40 complete genome sequences for FMDV Asia1 isolated from cattle available in Genbank, but no data are available on pigs. The present study reported that the complete nucleotide sequence of Asia1/WHN/CHA/06 was isolated from pigs in southwest of China in 2006. In general, the complete genome sequence of Asia1/WHN/CHA/06 exhibited a high level of similarity with JS/CHA/05 strain, which indicated that Asia1/WHN/CHA/06 had a close genetic relationship with JS/CHA/05 strain. Phylogenetic analysis of the virus VP1 region of FMDV has been used extensively to investigate the molecular epidemiology of the disease worldwide . In this study, phylogenetic tree based on VP1 region of Asia1 isolates identified the existence of three groups. Group1a mainly consisted of 11 isolates, which collected in East Asia (China, East of Russia, East of Mongolia, and North Korea) during 2005-2007. However, India/80 and India/81, which were both collected from India in 1980s, also clustered with Group1a. These data suggest that the East Asia strains, including Asia1/WHN/CHA/06, have a close genetic relationship with the two India strains emerged two decades ago.
Recombination plays an important role in FMDV evolution [28, 29]. In this study, supported by Simplot and RDP program, Asia1/WHN/CHA/06 was found to be a mosaic between JS/CHA/05 and HNK/CHA/05, whose breakpoint encompassed partial 3B and 3C genes. Protein 3B, which is present in three similar but nonidentical copies (3B1, 3B2 and 3B3) in FMDV , functions in priming picornavirus RNA synthesis , and the 3C protease is responsible for most of the cleavages during the FMDV polyprotein processing . Recombination in FMDV occurs mainly in non-structural genes , but the recombination over 3B/3C gene boundaries appears to be less frequent . Thus, the role of the mosaicism observed in 3B/3C of FMDV should be targeted for further study. Moreover, JS/CHA/05 and HNK/CHA/05 strains were both isolated from the east of China in 2005, so there was a geographical opportunity for the recombination of the two strains. However, as Asia1/WHN/CHA/06 was isolated from west of China, it was possible that Asia1/WHN/CHA/06 was transmitted from east of China by introduction of pigs or other transmission routes.