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We obtained 169 complete genomes of SARS-CoV-2 samples and identified variable sites based on whole genome alignment

Genomic variations of SARS-CoV-2 suggest multiple outbreak sources of transmission

MedRxiv, (2020)

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Abstract

We examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type I and Type II. Type I can be further divided into Type IA and IB. Our phylogenetic analysis showed that the Type IA resembles the ancestral SARS-CoV-2 most. Type II was likely evolved from Type I and predominant in the infections. Ou...More

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Introduction
  • The outbreak of the coronavirus disease 2019 (COVID-19), caused by a novel coronavirus named “Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) ”, has been detected in over 60 nations and lead to more than 80,000 confirmed cases and ~3,000 deaths.
  • Revealing the evolutionary history of different SARS-CoV-2 samples allows them to infer the virus transmission routes and to identify novel mutations associated with the transmissions.
  • Such information will be valuable for vaccine development and disease control
Highlights
  • The outbreak of the coronavirus disease 2019 (COVID-19), caused by a novel coronavirus named “Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) ”, has now been detected in over 60 nations and lead to more than 80,000 confirmed cases and ~3,000 deaths
  • The complete genomes of SARS-CoV-2 samples were obtained from GISAID, NCBI and NMDC
  • We obtained 169 complete genomes of SARS-CoV-2 samples and identified variable sites based on whole genome alignment (Figure 1)
  • The number of genomes belonging to Type IA, IB and II are 11, 37, and 121, respectively
  • We found that the three sites in Type IA and two in Type IB are identical to those in three bat viruses BatCoV RaTG13 [3], bat-SL-CoVZC45 and bat-SL-CoVZXC21[2](Figure 1B), suggesting that the Type I may be more closely related to the ancestral human-infecting strain than Type II
  • To better understand why the Type II virus is more prevalent, we focused on the three variable genomic sites that distinguish Type II from Type I strains
Methods
  • The complete genomes of SARS-CoV-2 samples were obtained from GISAID, NCBI and NMDC. Alignment of the complete genome sequences and that of BatCoV RaTG13 was carried out by MAFFT [4].

    The authors identified genome variable sites from the sequence alignment using Noisy [5].
  • The complete genomes of SARS-CoV-2 samples were obtained from GISAID, NCBI and NMDC.
  • Alignment of the complete genome sequences and that of BatCoV RaTG13 was carried out by MAFFT [4].
  • Some samples have unusually large number of mutation sites, which could be due to due to sequencing or assembly errors.
  • These sequences were excluded in the analysis
Results
  • Results and discussions

    The authors obtained 169 complete genomes of SARS-CoV-2 samples and identified variable sites based on whole genome alignment (Figure 1).
  • A total number of 207 variable sites were identified (Figure S2)
  • It shows that the amplitude of mutations is small, and their evolution history can be inferred from these variable sites.
  • Their phylogenetic relationships reveal two major genotypes from the SARS-CoV-2 samples, namely Type I and II (Figures 1A, S3 and S4).
  • The number of genomes belonging to Type IA, IB and II are 11, 37, and 121, respectively
Conclusion
  • The authors examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type I and Type II.
  • By analyzing three genomic sites that distinguish Type I and Type II strains, the authors found that synonymous changes at two of the three sites confer higher protein translational efficiencies in Type II strains than in Type I strains, which might explain why Type II strains are predominant, implying that Type II is more contagious than Type I.
  • These findings could be valuable for the current epidemic prevention and control
Funding
  • Examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type ands Type II
  • Ands Type II strains, found that synonymous changes at two of the three sites confer higher protein translational efficiencies in Type II strains than in Type strainss, which might explain why Type II strains are predominant, implying that Type II is more contagious than Type I
  • Identified genome variable sites from the sequence alignment using Noisy
  • Found that the three sites in Type IA and two in Type IB are identical to those in three bat viruses BatCoV RaTG13 , bat-SL-CoVZC45 and bat-SL-CoVZXC21 (Figure 1B), suggesting that the Type may be more closely related to the ancestral human-infecting strain than Type II
Study subjects and analysis
genomes: 169
. We examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type I and Type II. Type I can be further divided into Type IA and IB

samples: 2
Alignment of the complete genome sequences and that of BatCoV RaTG13 was carried out by MAFFT [4].

We identified genome variable sites from the sequence alignment using Noisy [5]. Variants that are present in at least two samples were used in our subsequence analysis. Some samples have unusually large number of mutation sites, which could be due to due to sequencing or assembly errors

samples: 2
We identified genome variable sites from the sequence alignment using Noisy [5]. Variants that are present in at least two samples were used in our subsequence analysis. Some samples have unusually large number of mutation sites, which could be due to due to sequencing or assembly errors

confirmed cases: 80000
These findings could be valuable for the current epidemic prevention and control. The outbreak of the coronavirus disease 2019 (COVID-19), caused by a novel coronavirus named “Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) ”, has now been detected in over 60 nations and lead to more than 80,000 confirmed cases and ~3,000 deaths (http://2019ncov.chinacdc.cn/2019-nCoV/global.html). Although the spread of SARS-CoV-2 in China seems to be largely contained, the confirmed cases outside China have been rising

samples: 2
We identified genome variable sites from the sequence alignment using Noisy [5]. Variants that are present in at least two samples were used in our subsequence analysis. Some samples have unusually large number of mutation sites, which could be due to due to sequencing or assembly errors

complete genomes: 169
Results and discussions. We obtained 169 complete genomes of SARS-CoV-2 samples and identified variable sites based on whole genome alignment (Figure 1). In most cases, different SARS-CoV-2 genomes only differ in 0 to 3 sites

environmental samples: 2
In addition, Type II may have originated from a Type IB strain by accumulating mutations at sites 8750 and 28112. Two environmental samples isolated from the Huanan market (Wuhan/IVDC-HB-envF13-20 and 21) belong to Type II, and no samples from Type I have a direct link to the Huanan market (such as Wuhan/WH04/2020 [7]). These observations suggest that the outbreak in the Huanan market was triggered by the Type II virus and that the initial transmission of Type I viruses to humans might have occurred somewhere else in Wuhan, probably preceding the outbreak of Type II in the Huanan market

cases: 41
These observations suggest that the outbreak in the Huanan market was triggered by the Type II virus and that the initial transmission of Type I viruses to humans might have occurred somewhere else in Wuhan, probably preceding the outbreak of Type II in the Huanan market. Our speculation is in line with earlier reports that 14 of the first reported 41 cases had no link to the Huanan market [7,8,9]. In addition to the above-mentioned transmission sources, we also found that there are several large clades in Type II (Group 1-3)

Reference
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Author
Liangsheng Zhang
Liangsheng Zhang
Zhenguo Zhang
Zhenguo Zhang
Zhenguo Lin
Zhenguo Lin
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