Dataset Information

SARS-CoV-2 viral dynamics of the first 1000 sequences from Vietnam and neighbouring ASEAN countries

ABSTRACT:

OSbjective

: The regional distribution and transmissibility of existing COVID-19 variants of concern (VOC) has led to concerns about increased transmission, given the ability of VOCs to evade immunity as breakthrough infections increase.

Methods

: SARS-CoV-2 genomes were sequenced (n=277) and analysed with all available genomes from Vietnam and ASEAN countries to understand the phylodynamics. The observed lineages were assigned using Pangolin nomenclature and spread patterns were investigated.

Results

: Between January 2020 and 08 November 2021, VOCs including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2), were observed in ASEAN countries. While alpha and delta were the major VOCs in nine ASEAN countries, delta is the predominant. Among ASEAN countries, alpha VOC was first reported by Singapore, beta VOC by Malaysia, gamma VOC by Philippines and delta VOC by Singapore. Of the first 1000 genomes analysed from Vietnam, alpha and delta are the most represented, with delta being the dominant VOC since May 2021. The delta variant was introduced in early January 2021 and forms a large cluster within the representative genomes.

Conclusion

: Spatial and temporal monitoring of SARS-CoV-2 variants is critical to understanding viral phylodynamics and will provide useful guidance to policy makers for infection prevention and control.

SUBMITTER: Hoan N

PROVIDER: S-EPMC8770528 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Background & objectivesSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.MethodsThroat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.ResultsThree cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.Interpretation & conclusionsThe two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.