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HGNC Genes

SARS-CoV-2 proteins

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    Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

    Authors: Yosuke Hirotsu; Masao Omata

    doi:10.1101/2021.02.24.21251892 Date: 2021-02-26 Source: medRxiv

    On the February 2020, the very first case was an American female from Diamond Princess cruise ship HGNC. Since, we have confirmed 136 patients infected with coronavirus disease 2019 MESHD ( COVID-19 MESHD) until February 2021. Here, we conducted the whole genome sequencing analysis of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) on samples from 70 of 136 patients (51.5%). These patients were infected MESHD in Diamond Princess cruise ship HGNC (n=1), Africa (n=2), Japan (n=66) and Brazil (n=1). The viral genome sequence of a patient on the Diamond Princess cruise ship HGNC in February 2020 was similar to that of original strain found in Wuhan, China (19A clade). Four patients, including two returnees from Africa and two lived in Japan, confirmed at the end of March 2020 had sequences similar to those of lineage with D614G mutation, which was endemic in Europe (20A [n=3] and 20B [n=1] clade). The 64 Japanese patients confirmed from September 2020 to January 2021 had sequences similar to those of the currently prevalent lineage (20B [n=58] and 20C clade [n=6]). Subsequent analysis revealed three mutations (K417T/ E484K / N501Y) in the receptor binding domain of the spike protein PROTEIN in a man in his 40s. The sequence was identical to the P.1 lineage (also known as 20J/501Y.V3) reported in Brazil. This is the first report of SARS-CoV-2 P. MESHD1 lineage identified in the city, Japan.

    The contribution of asymptomatic SARS-CoV-2 infection MESHDs to transmission - a model-based analysis of the Diamond Princess outbreak

    Authors: Jon C Emery; Timothy W Russel; Yang Liu; Joel Hellewell; Carl AB Pearson; - CMMID 2019-nCoV working group; Gwen M Knight; Rosalind M Eggo; Adam J Kucharski; Sebastian Funk; Stefan Flasche; Rein M G J Houben

    doi:10.1101/2020.05.07.20093849 Date: 2020-05-11 Source: medRxiv

    Background: Some key gaps in the understanding of SARS-CoV-2 infection MESHD remain. One of them is the contribution to transmission from individuals experiencing asymptomatic infections. We aimed to characterise the proportion and infectiousness of asymptomatic infections using data from the outbreak on the Diamond Princess cruise ship HGNC. Methods: We used a transmission model of COVID-19 MESHD with asymptomatic and presymptomatic states calibrated to outbreak data from the Diamond Princess, to quantify the contribution of asymptomatic infections to transmission. Data available included the date of symptom onset for symptomatic disease for passengers and crew, the number of symptom agnostic tests done each day, and date of positive test for asymptomatic and presymptomatic individuals. Findings: On the Diamond Princess 74% (70-78%) of infections proceeded asymptomatically, i.e. a 1:3.8 case-to-infection ratio. Despite the intense testing 53%, (51-56%) of infections remained undetected, most of them asymptomatic. Asymptomatic individuals were the source for 69% (20-85%) of all infections. While the data did not allow identification of the infectiousness of asymptomatic infections, assuming no or low infectiousness resulted in posterior estimates for the net reproduction number of an individual progressing through presymptomatic and symptomatic stages in excess of 15. Interpretation: Asymptomatic SARS-CoV-2 infections MESHD may contribute substantially to transmission. This is essential to consider for countries when assessing the potential effectiveness of ongoing control measures to contain COVID-19 MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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