Molecular Evolutionary Analysis of the Influenza A(H1N1)pdm, May–September, 2009: Temporal and Spatial Spreading Profile of the Viruses in Japan

Abstract

BackgroundIn March 2009, pandemic influenza A(H1N1) (A(H1N1)pdm) emerged in Mexico and the United States. In Japan, since the first outbreak of A(H1N1)pdm in Osaka and Hyogo Prefectures occurred in the middle of May 2009, the virus had spread over 16 of 47 prefectures as of June 4, 2009.Methods/Principal FindingsWe analyzed all-segment concatenated genome sequences of 75 isolates of A(H1N1)pdm viruses in Japan, and compared them with 163 full-genome sequences in the world. Two analyzing methods, distance-based and Bayesian coalescent MCMC inferences were adopted to elucidate an evolutionary relationship of the viruses in the world and Japan. Regardless of the method, the viruses in the world were classified into four distinct clusters with a few exceptions. Cluster 1 was originated earlier than cluster 2, while cluster 2 was more widely spread around the world. The other two clusters (clusters 1.2 and 1.3) were suggested to be distinct reassortants with different types of segment assortments. The viruses in Japan seemed to be a multiple origin, which were derived from approximately 28 transported cases. Twelve cases were associated with monophyletic groups consisting of Japanese viruses, which were referred to as micro-clade. While most of the micro-clades belonged to the cluster 2, the clade of the first cases of infection in Japan originated from cluster 1.2. Micro-clades of Osaka/Kobe and the Fukuoka cases, both of which were school-wide outbreaks, were eradicated. Time of most recent common ancestor (tMRCA) for each micro-clade demonstrated that some distinct viruses were transmitted in Japan between late May and early June, 2009, and appeared to spread nation-wide throughout summer.ConclusionsOur results suggest that many viruses were transmitted from abroad in late May 2009 irrespective of preventive actions against the pandemic influenza, and that the influenza A(H1N1)pdm had become a pandemic stage in June 2009 in Japan.

Pandemic (H1N1) 2009 virus revisited: An evolutionary retrospective

“…Fereidouni et al (2009) found one subcluster (comprised of Japanese viruses) has seven of eight segments like Cluster I viruses, but has an NP segment most like cluster II viruses, which points to the possibility of reassortment between the two main clusters. Similar observations were found by Shiino et al (2010), where one subcluster consists of the MP and NS segments coming from Cluster I, with the HA, NP and NA segments coming from Cluster II. Our phylogenetic analyses also revealed a likely reassortment in the pandemic May to June Wisconsin viruses (Supplemental File 4).…”

“…First, the earliest outbreak of the pandemic virus was reported in Mexico in March 2009, and the first case was reported in California on April 14, 2009, whereas the cases of infection in New York was first reported on April 24 (CDC, 2009b; Lessler et al, 2009). Secondly, based upon tMRCA, Cluster I viruses appeared two months earlier than Cluster II viruses (Shiino et al, 2010). Thirdly, our study shows the earliest sequences found in Cluster I and Cluster II occur on April 1 and April 24, 2009, respectively.…”

“…Molecular evolutionary analyses of pandemic sequences available as of September 2009 revealed two major clusters, Cluster I originating from Mexico, Texas and California and Cluster II originating from New York (Fereidouni et al, 2009; Shiino et al, 2010). However, the authors caution that further study is needed to determine if the differences between cluster I and cluster II viruses are due to time, geography, or other factors (Fereidouni et al, 2009).…”

Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic

“…The nomenclature of the clusters follows the report of Shiino et al [17]. Bold letters indicate the amino acid substitutions that were previously reported in the parcial sequences we analyzed in this study.…”

Pathogenicity of Pandemic H1N1 Influenza A Virus in Immunocompromised Cynomolgus Macaques

“…The pandemic influenza virus A/Narita/1/2009 (H1N1) pdm (kindly provided by Dr. Takato Odagiri, National Institute of Infectious Disease (NIID), Japan. NCBI taxonomy database ID: 645520) [59,60] was cultured twice in embryonated eggs in NIID and once in MDCK cells at Shiga University of Medical Sciences.…”