Dataset Information

Antigenic and genetic characterization of influenza C viruses which caused two outbreaks in Yamagata City, Japan, in 1996 and 1998.

ABSTRACT: During the 3 years from January 1996 to December 1998, a total of 33 strains of influenza C virus were isolated from 10,726 throat swab specimens collected from children with acute respiratory illness who visited two pediatric clinics in Yamagata City, Japan. These 33 strains were isolated in clusters during two different periods, 20 strains in May to August 1996 and the remaining 13 in March to June 1998. Antigenic analysis with monoclonal antibodies to the hemagglutinin-esterase (HE) glycoprotein and phylogenetic analysis of seven RNA segments showed that the 33 influenza C viruses isolated were antigenically and genetically similar and that they were reassortant viruses which had obtained PB2, PB1, HE, M, and NS genes from a C/pig/Beijing/115/81-like virus and P3 and NP genes from a C/Mississippi/80-like virus. These observations suggest strongly that during the survey period of 3 years, two outbreaks of influenza C occurred in Yamagata City, both of which were caused by a reassortant virus having the genome composition described above.

SUBMITTER: Matsuzaki Y

PROVIDER: S-EPMC153379 | biostudies-literature | 2002 Feb

REPOSITORIES: biostudies-literature

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Antigenic and genetic characterization of influenza C viruses which caused two outbreaks in Yamagata City, Japan, in 1996 and 1998.

Matsuzaki Y Y Sugawara K K Mizuta K K Tsuchiya E E Muraki Y Y Hongo S S Suzuki H H Nakamura K K

Journal of clinical microbiology 20020201 2

During the 3 years from January 1996 to December 1998, a total of 33 strains of influenza C virus were isolated from 10,726 throat swab specimens collected from children with acute respiratory illness who visited two pediatric clinics in Yamagata City, Japan. These 33 strains were isolated in clusters during two different periods, 20 strains in May to August 1996 and the remaining 13 in March to June 1998. Antigenic analysis with monoclonal antibodies to the hemagglutinin-esterase (HE) glycoprot ...[more]

PMID: 11825952

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Project description:In Osaka City, Japan, between April 1996 and March 1999, a total of 350 fecal specimens from 64 outbreaks of acute nonbacterial gastroenteritis were examined to investigate infection by "Norwalk-like viruses" (NLVs). By reverse transcription (RT)-PCR, 182 samples (52.0%) from 47 outbreaks (73.4%) were NLV positive. During those three years, the incidence of NLV-associated outbreaks showed seasonality, being higher during January to March (winter to early spring). The ingestion of contaminated oysters was the most common transmission mode (42.6%). The amplicons of the 47 outbreak strains that were NLV positive by RT-PCR were tested using Southern hybridization with four probe sets (Ando et al., J. Clin. Microbiol. 33:64-71, 1995). Forty of the outbreak strains were classified as 4 probe 1-A (P1-A) strains, 6 P1-B strains, 10 P2-A strains, 17 P2-B strains, and 3 untypeable strains, and the other 7 outbreaks were determined to be mixed-probe-type strains. Probe typing and partial sequence analysis of the outbreak strains indicated that a predominant probe type of NLVs in Osaka City had drastically changed; P2-B strains (77.8%) with multiple genetic clusters were observed during the 1996-97 season, the P2-A common strain (81.3%) related to the Toronto virus cluster was observed during the 1997-98 season, and P1-B strains (75.0%) with a genetic similarity were observed during the 1998-99 season. For the three untypeable outbreak strains (96065, 97024, and 98026), the 98026 outbreak strain had Southampton virus (SOV)-like sequences, and each of the other outbreak strains had a unique 81-nucleotide sequence. Newly designed probes (SOV probe for the 98026 outbreak strain and the 96065 probe for the 96065 and 97024 outbreak strains) were hybridized with relative strains and without other probe type strains. The prevalent NLV probe types in Osaka City during those three years were classified in six phylogenetic groups: P1-A, P1-B, P2-A, P2-B, SOV, and 96065 probe types.

Project description:The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strains make sequence-based antigenic distance estimates an attractive approach to researchers. Antigenic mismatch between circulating strains and vaccine strains results in significantly decreased vaccine effectiveness. Furthermore, antigenic relatedness between the vaccine strain and the strains an individual was originally primed with can affect the cross-reactivity of the antibody response. Thus, understanding the antigenic relationships between influenza viruses that have circulated is important to both vaccinologists and immunologists.Here we develop a method of mapping antigenic relationships between influenza virus stains using a sequence-based antigenic distance approach (SBM). We used a modified version of the p-all-epitope sequence-based antigenic distance calculation, which determines the antigenic relatedness between strains using influenza hemagglutinin (HA) genetic coding sequence data and provide experimental validation of the p-all-epitope calculation. We calculated the antigenic distance between 4838 H1N1 viruses isolated from infected humans between 1918 and 2016. We demonstrate, for the first time, that sequence-based antigenic distances of H1N1 Influenza viruses can be accurately represented in 2-dimenstional antigenic cartography using classic multidimensional scaling. Additionally, the model correctly predicted decreases in cross-reactive antibody levels with 87% accuracy and was highly reproducible with even when small numbers of sequences were used.This work provides a highly accurate and precise bioinformatics tool that can be used to assess immune risk as well as design optimized vaccination strategies. SBM accurately estimated the antigenic relationship between strains using HA sequence data. Antigenic maps of H1N1 virus strains reveal that strains cluster antigenically similar to what has been reported for H3N2 viruses. Furthermore, we demonstrated that genetic variation differs across antigenic sites and discuss the implications.

Dataset Information

Antigenic and genetic characterization of influenza C viruses which caused two outbreaks in Yamagata City, Japan, in 1996 and 1998.

Publications

Antigenic and genetic characterization of influenza C viruses which caused two outbreaks in Yamagata City, Japan, in 1996 and 1998.

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