Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer.
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Pandemic 2009 influenza A virus (A/H1N1/2009) has emerged globally. In this study, we performed a comprehensive detection of potential pathogens by de novo sequencing using a next-generation DNA sequencer on total RNAs extracted from an autopsy lung of a patient who died of viral pneumonia with A/H1N1/2009. Among a total of 9.4x10(6) 40-mer short reads, more than 98% appeared to be human, while 0.85% were identified as A/H1N1/2009 (A/Nagano/RC1-L/2009(H1N1)). Suspected bacterial reads such as Streptococcus pneumoniae and other oral bacteria flora were very low at 0.005%, and a significant bacterial infection was not histologically observed. De novo assembly and read mapping analysis of A/Nagano/RC1-L/2009(H1N1) showed more than x200 coverage on average, and revealed nucleotide heterogeneity on hemagglutinin as quasispecies, specifically at two amino acids (Gly(172)Glu and Gly(239)Asn of HA) located on the Sa and Ca2 antigenic sites, respectively. Gly239 and Asn239 on antigenic site Ca2 appeared to be minor amino acids compared with the highly distributed Asp239 in H1N1 HAs. This study demonstrated that de novo sequencing can comprehensively detect pathogens, and such in-depth investigation facilitates the identification of influenza A viral heterogeneity. To better characterize the A/H1N1/2009 virus, unbiased comprehensive techniques will be indispensable for the primary investigations of emerging infectious diseases.
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P. gingivalis is the most important periodontitis pathogen, while Streptococcus sp., in general, constitute the main component of oral flora.
“P. gingivalis is the most important periodontitis pathogen, while Streptococcus sp., in general, constitute the main component of oral flora (Kuroda et al., 2010).”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Kuroda et al., 2010
In an autopsied lung of a patient who died of A/H1N1/2009, Streptococcus pneumoniae and Porphyromonas gingivalis were detected, though in small quantities.
“comprehensive detection of potential pathogens was performed using next-generation DNA sequencing of total RNAs extracted from an autopsied lung of a patient died of A/H1N1/2009. Streptococcus pneumoniae and Porphyromonas gingivalis were detected, though in small quantities.”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Kuroda et al., 2010
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- Authors
- Kuroda, M., Katano, H., Nakajima, N., Tobiume, M., Ainai, A., Sekizuka, T., Hasegawa, H., Tashiro, M., Sasaki, Y., Arakawa, Y., Hata, S., Watanabe, M., & Sata, T.
- Affiliations
- National Institute of Infectious Diseases (JP)
- Nagano Red Cross Hospital (JP)
- Corresponding author
- Kuroda, Makoto
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-04-23
- Volume
- 5
- Issue
- 4
- Pages
- e10256
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2859049
- OpenAlex
- W2083925087
- Cited by
- 111
- References
- 34
- Citations by year
- 2025: 1 · 2024: 4 · 2023: 4 · 2022: 5 · 2021: 5 · 2020: 4 · 2019: 9 · 2018: 2 · 2017: 8 · 2016: 10 · 2015: 8 · 2014: 8 · 2013: 15 · 2012: 14
- FWCI
- 10.00
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Topics
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
- Keywords
- 2009 H1N1 influenza A virus, quasispecies, hemagglutinin, viral heterogeneity, viral pneumonia, de novo sequencing, bacterial co-infection, Streptococcus pneumoniae, emerging infectious diseases
- MeSH terms
- Humans, Lung, Pneumonia, Viral, RNA, RNA, Viral, Genetic Variation, Sequence Analysis, DNA, Hemagglutinin Glycoproteins, Influenza Virus, Influenza A Virus, H1N1 Subtype, Pandemics
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