Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan

Ko, Ko; Nagashima, Shintaro; Bunthen, E; Ouoba, Serge; Akita, Tomoyuki; Sugiyama, Aya; Ohisa, Masayuki; Sakaguchi, Takemasa; Tahara, Hidetoshi; Ohge, Hiroki; Ohdan, Hideki; Kubo, Toshikazu; Kishita, Eisaku; Kuwabara, Masao; Takahashi, Kazuaki; Tanaka, Junko

doi:10.1371/journal.pone.0246383

Cited by 32 publications

(26 citation statements)

References 22 publications

(27 reference statements)

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“…In this study, a significant rise in the rate of mutation was observed in wave-2 samples of Bangladesh compared to the wave-1. A similar pattern was observed in the instance of SARS-CoV-2 pandemic waves in Hiroshima, Japan [ 73 ]. Although both waves in Bangladesh had a higher incidence of amino acid altering SNPs, wave-2 tended to have a higher number of deletion events ( Fig 3 ).…”

Section: Discussionsupporting

confidence: 80%

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

et al. 2021

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As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.

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Section: Discussionsupporting

confidence: 80%

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

et al. 2021

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“…In this study, a significant rise in the rate of mutation was observed in wave-2 samples of Bangladesh compared to the wave-1. A similar pattern was observed in the instance of SARS-CoV-2 pandemic waves in Hiroshima, Japan [72]. Although both waves in Bangladesh had a higher incidence of amino acid altering SNPs, wave-2 tended to have a higher number of deletion events (Fig 3).…”

Section: Discussionsupporting

confidence: 73%

Comparative genomic study for revealing the complete scenario of COVID-19 pandemic in Bangladesh

Ahammad

Hossain

Bhattacharjee

et al. 2020

Preprint

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As the COVID-19 pandemic continues to ravage across the globe and take millions of lives, worldwide efforts to understand its causative agent, SARS-CoV-2 at the genomic level are also running in full swing. Such studies are providing precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of October 1st, 2020, 323 SARS-CoV-2 genomes have been sequenced across Bangladesh. The current study is aimed at answering some vital questions about these sequences. From our analyses, it was discovered that the majority of the SARS-CoV-2 found in Bangladesh belonged to the lineage B 1.1.25 of GR clade. Dhaka and Chittagong division were the most diverse in terms of SARS-CoV-2 clades while Mymensing was the least. There are more variety of clades in southern parts of Bangladesh than the northern parts. The most commonly found SARS-CoV-2 mutations found in the country were Spike_D614G, NSP12_P323L, N_G204R and N_R203K. Even though no significant pattern of distribution could be drawn between mutations found in Bangladesh and the countries with similar mortality rates and the countries with large Bangladeshi diaspora, to a certain degree they match with those in the UK, Oman, Italy, Greece, South Africa and Russia. Therefore, careful eye should be kept on the performance of vaccines in those countries in the near future as they are likely to work well in Bangladesh if they work well there. Mutational events in Bangladesh were found to increase between April and July, 2020 and decrease since August, 2020. The number of mutations per SARS-CoV-2 virus sample in Bangladesh was calculated to be 6.88 which is lower than the global average of 7.23. The decrease and the lower rate of mutation raise the possibility of a vaccine or drug working sustainably to protect the people. Based on these insights, a clear picture about the ongoing pandemic can be drawn in the context of Bangladesh which will help the country take appropriate measures to combat the virus.

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“…Today, we are facing a similar situation all over the world with the second wave of COVID-19 pandemic affecting more persons all over the world [ 4 ]. The emergence of new mutants of SARS-CoV-2 which escape the immunity and the abnormal immune response in patients are possible causes for the rapid rise in cases during the second wave [ 5 , 6 ]. The situation in India is no different from other countries.…”

Section: Discussionmentioning

confidence: 99%

The Increased Burden of SARS-CoV-2 Infection in Orthopaedic Trauma Patients: Comparison of Demographics of Both the Waves of the Pandemic—An Indian Tertiary Center Experience

Patel

Khan

Aggarwal

et al. 2021

JOIO

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Background The second wave of SARS-CoV-2 pandemic has posed new challenges in the management of Orthopedic trauma patients due to the overburdened healthcare facilities and we aim to present the differences in demographics between the first wave and the initial part of the second wave. Methodology This study was a retrospective cross-sectional study of our trauma registry from June 19, 2020 to October 13, 2020 (1st study period) and from April 1, 2021 to the first week of May 2021 (2nd study period). We looked into differences in the following three parameters: (1) infection rate among Orthopaedic patients in the first and second study period of SARS-CoV-2 pandemic, (2) infection rate among the Health Care Workers and (3) hospital-acquired SARS-CoV-2 infections in admitted Orthopaedic trauma patients. Results 35 out of 852 patients (4.1%) were positive for SARS-CoV-2 infection in 1st study period as compared to 48 out of 262 patients (18.3%) in the 2nd study period ( p < 0.001). 23 HCW’s involved in management of Orthopaedic trauma patients tested positive in the second study period compared to none in the first study period. 17 patients had Hospital-acquired SARS-CoV-2 infection in 2nd study period compared to 7 in 1st study period. There were more asymptomatic patients for SARS-CoV-2 infection in the 2nd study period. Conclusion Significant increase in the number of SARS-CoV-2 infection in Orthopaedic trauma patients, and the increased number of HCW’s affected with SARS-CoV-2 infection have been the challenges in 2nd study period.

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Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan

Cited by 32 publications

References 22 publications

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

Comparative genomic study for revealing the complete scenario of COVID-19 pandemic in Bangladesh

The Increased Burden of SARS-CoV-2 Infection in Orthopaedic Trauma Patients: Comparison of Demographics of Both the Waves of the Pandemic—An Indian Tertiary Center Experience

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