SARS-COV-2 variants

Huamán-Saavedra, Juan Jorge

doi:10.17268/rmt.2020.v16i01.01

Cited by 25 publications

(2 citation statements)

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“…Most vaccines (mRNA, viral vector, DNA and protein subunit) targeted the spike protein encoded by the S gene of SARS-CoV-2, while the whole virion was used in the inactivated vaccines 2 8 9 . D614G was the first globally dominant mutation by June 2020 with no effect on neutralization by pre-existing antibodies 10 . The B.1.1.28 variant was reported in a limited outbreak in Denmark in September 2020 in farmed minks with a potential of mink to human transmission 10 .…”

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“…D614G was the first globally dominant mutation by June 2020 with no effect on neutralization by pre-existing antibodies 10 . The B.1.1.28 variant was reported in a limited outbreak in Denmark in September 2020 in farmed minks with a potential of mink to human transmission 10 . B.1.427/429 mutation was reported from California in June 2020 and was designated as variant of interest (VOI) 11 .…”

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Neutralization assays for SARS-CoV-2

Mukhopadhyay

Gupta

Yadav

et al. 2022

Indian Journal of Medical Research

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The WHO emergency use-listed (EUL) COVID-19 vaccines were developed against early strains of SARS-CoV-2. With the emergence of SARS-CoV-2 variants of concern (VOCs) - Alpha, Beta, Gamma, Delta and Omicron, it is necessary to assess the neutralizing activity of these vaccines against the VOCs. PubMed and preprint platforms were searched for literature on neutralizing activity of serum from WHO EUL vaccine recipients, against the VOCs, using appropriate search terms till November 30, 2021. Our search yielded 91 studies meeting the inclusion criteria. The analysis revealed a drop of 0-8.9-fold against Alpha variant, 0.3-42.4-fold against Beta variant, 0-13.8-fold against Gamma variant and 1.35-20-fold against Delta variant in neutralization titres of serum from the WHO EUL COVID-19 vaccine recipients, as compared to early SARS-CoV-2 isolates. The wide range of variability was due to differences in the choice of virus strains selected for neutralization assays (pseudovirus or live virus), timing of serum sample collection after the final dose of vaccine (day 0 to 8 months) and sample size (ranging from 5 to 470 vaccinees). The reasons for this variation have been discussed and the possible way forward to have uniformity across neutralization assays in different laboratories have been described, which will generate reliable data. Though in vitro neutralization studies are a valuable tool to estimate the performance of vaccines against the backdrop of emerging variants, the results must be interpreted with caution and corroborated with field-effectiveness studies.

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Neutralization assays for SARS-CoV-2

Mukhopadhyay

Gupta

Yadav

et al. 2022

Indian Journal of Medical Research

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The ins and outs of SARS-CoV-2 variants of concern (VOCs)

et al. 2022

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SARS-CoV-2, a newly emerging coronavirus that caused the COVID-19 epidemic, has been spreading quickly throughout the world. Despite immunization and some fairly effective therapeutic regimens, SARS-CoV-2 has been ravaging patients, health workers, and the economy. SARS-CoV-2 mutates and evolves to adapt to its host as a result of extreme selection pressure. As a consequence, new SARS-CoV-2 variants have emerged, some of which are classified as variants of concern (VOC) because they exhibit greater transmissibility, cause more-severe disease, are better able to escape immunity, or cause higher mortality than the original Wuhan strain. Here, we introduce these VOCs and review their characteristics, such as transmissibility, immune escape, mortality risk, and diagnostics.

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In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology

Lee

Yoo

et al. 2022

Genes Genom

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Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began in 2019 but it remains as a serious threat today. To reduce and prevent spread of the virus, multiple vaccines have been developed. Despite the efforts in developing vaccines, Omicron strain of the virus has recently been designated as a variant of concern (VOC) by the World Health Organization (WHO). Objective To develop a vaccine candidate against Omicron strain (B.1.1.529, BA.1) of the SARS-CoV-19. Methods We applied reverse vaccinology methods for BA.1 and BA.2 as the vaccine target and a control, respectively. First, we predicted MHC I, MHC II and B cell epitopes based on their viral genome sequences. Second, after estimation of antigenicity, allergenicity and toxicity, a vaccine construct was assembled and tested for physicochemical properties and solubility. Third, AlphaFold2, RaptorX and RoseTTAfold servers were used to predict secondary structures and 3D structures of the vaccine construct. Fourth, molecular docking analysis was performed to test binding of our construct with angiotensin converting enzyme 2 (ACE2). Lastly, we compared mutation profiles on the epitopes between BA.1, BA.2, and wild type to estimate the efficacy of the vaccine. Results We collected a total of 10 MHC I, 9 MHC II and 5 B cell epitopes for the final vaccine construct for Omicron strain. All epitopes were predicted to be antigenic, non-allergenic and non-toxic. The construct was estimated to have proper stability and solubility. The best modelled tertiary structures were selected for molecular docking analysis with ACE2 receptor. Conclusions These results suggest the potential efficacy of our newly developed vaccine construct as a novel vaccine candidate against Omicron strain of the coronavirus.

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SARS-COV-2 variants

Cited by 25 publications

References 0 publications

Neutralization assays for SARS-CoV-2

Neutralization assays for SARS-CoV-2

The ins and outs of SARS-CoV-2 variants of concern (VOCs)

In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology

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