Genome Sequence of a SARS-CoV-2 P.1 Variant of Concern (20J/501Y.V3) from Bangladesh

Sarkar, Md. Murshed Hasan; Rabbi, Mohammad Fazle Alam; Akter, Shahina; Banu, Tanjina Akhtar; Goswami, Barna; Jahan, Iffat; Hossain, Md. Saddam; Osman, Eshrar; Uzzaman, Mohammad Samir; Habib, Md. Ahasan; Mahmud, Abu Sayeed Mohammad; Kabir, Firoz; Hasan, Kazi Nadim; Rahman, Md. Mizanur; Khaleque, Md. Abdul; Akhteruzzaman, Sharif; Khan, Mala

doi:10.1128/mra.00524-21

Cited by 5 publications

(6 citation statements)

References 4 publications

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“…Our finding is supported by reports of high anti-S protein IgG on the day of positive swab among unvaccinated COVID-19 patients in the United Kingdom having confirmed SARS-CoV-2 re-infection [39]. On this basis, we conclude that the patients with the delta variant likely have pre-existing antibodies from either the first Bangladesh pandemic wave in April to June 2020 [29][30][31][32] or the second Bangladesh pandemic wave in March 2021, which were predominantly of the SARS CoV-2 alpha or beta variants [25][26][27][28]40].…”

Section: Discussionsupporting

confidence: 88%

“…The extensive genomic surveillance of SARS CoV-2 viral isolates in Bangladesh throughout the pandemic is motivated by the urgency to identify the next strains of SARS CoV-2 carrying S-protein mutations or other genetic changes [25][26][27][28][29][30][31][32][33][34]. In the first and second pandemic waves in Bangladesh, the alpha and beta variants of the B.1.1.7 and B.1.351 lineages were associated with an Ro of approximately 1.2 [27].…”

Section: Discussionmentioning

confidence: 99%

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Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Ghosh

Kaiser

Molla

et al. 2021

Viruses

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Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Ghosh

Kaiser

Molla

et al. 2021

Viruses

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“…Since December 2020, approximately 42% of SARS-CoV-2 positive tested samples were analyzed with P.1 lineage infection ( Hoffmann et al., 2021 ). These mutations are closely linked with antibody-mediated immune evasion high infection rate (+161%), the mortality rate was also observed to be high, up to 50%, making it 2.2 times more transmissible than the baseline virus ( Sarkar et al., 2021 ). P.1 and P.1-like clades are more infective in younger people.…”

Section: Sars-cov-2 Vaccine and Variantsmentioning

confidence: 99%

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

Singh

Parveen

Yadav

2021

Front. Cell. Infect. Microbiol.

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The emergence of SARS-CoV-2 variants may cause resistance at the immunity level against current vaccines. Some emergent new variants have increased transmissibility, infectivity, hospitalization, and mortality. Since the administration of the first SARS-CoV-2 vaccine to a human in March 2020, there is an ongoing global race against SARS-CoV-2 to control the current pandemic situation. Spike (S) glycoprotein of SARS-CoV-2 is the main target for current vaccine development, which can neutralize the infection. Companies and academic institutions have developed vaccines based on the S glycoprotein, as well as its antigenic domains and epitopes, which have been proven effective in generating neutralizing antibodies. The effectiveness of SARS-CoV-2 vaccines and other therapeutics developments are limited by the new emergent variants at the global level. We have discussed the emergent variants of SARS-CoV-2 on the efficacy of developed vaccines. Presently, most of the vaccines have been tremendously effective in severe diseases. However, there are still noteworthy challenges in certifying impartial vaccines; the stories of re-infections are generating more stressful conditions, and this needs further clinical evaluation.

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“…Until February 2021, more than 51.1% of cases suffered from SARS-CoV-2 P.1 variant in all COVID-19 patients who were identified in Umbria, Italy ( 67 ). And the Gamma variant began to emerge in more than 45 countries until March 30, 2021, according to the release of the epidemiological information by WHO, including the United States ( 68 ), Spain ( 69 ), Bangladesh ( 70 ), Uruguay ( 71 ), Italy ( 72 ), etc.…”

Section: Predominant Variations Of Sars-cov-2mentioning

confidence: 99%

The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines

Jiang

Song

et al. 2022

Front. Med.

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Over the past 2 years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) and rapidly spread worldwide. In the process of evolution, new mutations of SARS-CoV-2 began to appear to be more adaptable to the diverse changes of various cellular environments and hosts. Generally, the emerging SARS-CoV-2 variants are characterized by high infectivity, augmented virulence, and fast transmissibility, posing a serious threat to the prevention and control of the global epidemic. At present, there is a paucity of effective measurements to cure COVID-19. It is extremely crucial to develop vaccines against SARS-CoV-2 and emerging variants to enhance individual immunity, but it is not yet known whether they are approved by the authority. Therefore, we systematically reviewed the main characteristics of the emerging various variants of SARS-CoV-2, including their distribution, mutations, transmissibility, severity, and susceptibility to immune responses, especially the Delta variant and the new emerging Omicron variant. Furthermore, we overviewed the suitable crowd, the efficacy, and adverse events (AEs) of current vaccines.

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Genome Sequence of a SARS-CoV-2 P.1 Variant of Concern (20J/501Y.V3) from Bangladesh

Cited by 5 publications

References 4 publications

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021

SARS-CoV-2: Emergence of New Variants and Effectiveness of Vaccines

The Variation of SARS-CoV-2 and Advanced Research on Current Vaccines

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