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Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic.

ABSTRACT: SARS-CoV-2 is a new form of ?-coronavirus that has been recently discovered and is responsible for COVID 19 pandemic. The earliest infection can be traced back to Wuhan, China. From there it has spread all over the world. Keeping in view the above perspective, an attempt is made in order to find out the epidemiological pattern of COVID 19 pandemic, if any, in different geo-climatological regions of the world in terms of case incidence and mortality. This study is also an endeavor to review and analyze the gradual changes of the genetic makeup of SARS-CoV from evolutionary and epidemiological perspectives. The raw data of COVID-19 cases and death incidences were collected from the World Health Organization (WHO) website from the time period: 1st April to 6th April, 2020. The data that are utilized here for general and Case fatality rate (CFR) based analysis. Western pacific region, European region and Americas have the greatest number of infected cases (P < 0.001); whereas deaths have been found to be significantly higher in Europe (P < 0.001). Total number of confirmed cases and deaths in south-east Asia are comparatively lower (P < 0.001). Case fatality rate (CFR) has also found significant for European region. SARS-CoV-2 is considered to be a strain of SARS-CoV that has a high rate of pathogenicity and transmissibility. Result indicated that the European region has been affected mostly for both cases and death incidences. The novel mutations in SARS-CoV-2 possibly increase the virus infectivity. Genetic heterogeneity of this virus within the human population might originate as the representatives of naturally selected virus quasispecies. In this context, the presence of the asymptomatic individuals could be a significant concern for SARS-CoV-2 epidemiology. Further studies are required to understand its genetic evolution and epidemiological significance.

SUBMITTER: Bhattacharya S

PROVIDER: S-EPMC7419125 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic.

Bhattacharya S S Basu P P Poddar S S

Journal of preventive medicine and hygiene 20200601 2

SARS-CoV-2 is a new form of β-coronavirus that has been recently discovered and is responsible for COVID 19 pandemic. The earliest infection can be traced back to Wuhan, China. From there it has spread all over the world. Keeping in view the above perspective, an attempt is made in order to find out the epidemiological pattern of COVID 19 pandemic, if any, in different geo-climatological regions of the world in terms of case incidence and mortality. This study is also an endeavor to review and a ...[more]

PMID: 32802995

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Project description:BackgroundTransmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries.MethodsThe study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions.ResultsNinety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58% (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation.ConclusionsOur study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes.

Dataset Information

Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic.

Publications

Changing epidemiology of SARS-CoV in the context of COVID-19 pandemic.

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