Virus database annotations assist in tracing information on patients infected with emerging pathogens

Akiko Nakashima, Mitsue Takeya, Keiji Kuba, Makoto Takano, Noriyuki Nakashima

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


The global pandemic of SARS-CoV-2 has disrupted human social activities. In restarting economic activities, successive outbreaks by new variants are concerning. Here, we evaluated the applicability of public database annotations to estimate the virulence, transmission trends and origins of emerging SARS-CoV-2 variants. Among the detectable multiple mutations, we retraced the mutation in the spike protein. With the aid of the protein database, structural modelling yielded a testable scientific hypothesis on viral entry to host cells. Simultaneously, annotations for locations and collection dates suggested that the variant virus emerged somewhere in the world in approximately February 2020, entered the USA and propagated nationwide with periodic sampling fluctuation likely due to an approximately 5-day incubation delay. Thus, public database annotations are useful for automated elucidation of the early spreading patterns in relation to human behaviours, which should provide objective reference for local governments for social decision making to contain emerging substrains. We propose that additional annotations for past paths and symptoms of the patients should further assist in characterizing the exact virulence and origins of emerging pathogens.

Original languageEnglish
Article number100442
JournalInformatics in Medicine Unlocked
Publication statusPublished - Jan 2020
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Health Informatics


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