Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays

Jain, Abhinav; Rophina, Mercy; Mahajan, Saurabh; Krishnan, Bhavya Balaji; Sharma, Manasa; Mandal, Sreya; Fernandez, Teresa de Souza; Sultanji, Sumayra; Jolly, Bani; Mathew, Samatha; Sivasubbu, Sridhar; Scaria, Vinod

doi:10.1016/j.ijid.2020.10.086

Cited by 28 publications

(33 citation statements)

References 8 publications

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“…Mutation in the Spike gene, such as 69-70del that is amplified by RT-PCR has shown to affect specificity and sensitivity of the assay (91). Similar results may also be observed for other genetic variation in the RBD sites if the 132 publicly available primers and probes are used to amplify the Spike gene of SARS-CoV-2 (92). Mass screening and sero-surveillance require rapid testing kits rather than RT-PCR (93).…”

Section: Features Of Sars-cov-2 Functions/implications Referencesmentioning

confidence: 78%

The Spike of SARS-CoV-2: Uniqueness and Applications

et al. 2021

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The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point‐of‐care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.

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Section: Features Of Sars-cov-2 Functions/implications Referencesmentioning

confidence: 78%

The Spike of SARS-CoV-2: Uniqueness and Applications

et al. 2021

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“…The spread of a new variant in September in Marseille (named marseille-4, which was found to originate from a mink farmer) [44], supported by the appearance of new variants in the world (UK variant, South African variant, Brazilian variant, etc.) [45,46] may potentially be an explanation for these differences in mortality associated with COVID-19 [47]. Genetic analysis of these first wave strains must be conducted.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Strategies to Fight COVID-19: The French Paradigm

Giraud-Gatineau

Colson

Chaudet

et al. 2021

JCM

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(1) Background: We collected COVID-19 mortality data and the age distribution of the deceased in France and other European countries, as well as specifically in the cities of Paris and Marseille, and compared them. (2) Methods: Data on mortality related to COVID-19 and the associated age distribution were collected from government institutions in various European countries. In France, data were obtained from INSEE and Santé Publique France. All-cause mortality was also examined in order to study potential excess mortality using EuroMOMO. The Marseille data came from the epidemiological surveillance system. (3) Results: France is one of the European countries most impacted by COVID-19. Its proportion of deaths in people under 60 years of age is higher (6.5%) than that of Italy (4.6%) or Spain (4.7%). Excess mortality (5% more deaths) was also observed. Ile-de-France and the Grand-Est are the two French regions with the highest mortality. The proportion of deaths in the under-60 age group was considerable in Ile-de-France (9.9% vs. 4.5% in the Southern region). There are significantly higher numbers of patients hospitalized, in intensive care and deceased in Paris than in Marseille. (4) Conclusions: No patient management, i.e., from screening to diagnosis, including biological assessment and clinical examination, likely explains the high mortality associated with COVID-19.

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“…In addition, countless efforts have been put forward using in silico drug screening approaches to identify potential inhibitors of the SARS-CoV2 proteins. Some of the works from India also highlighted the genomic diversity and the phylogenetic profiles of the prevalent strains in the country (Banu et al, 2020;Thakur et al, 2020;INDICOV, 2021;Jain et al, 2021;Phylovis, 2021). However, most of these works are discrete in nature, and a combined unified effort characterizing a country-or region-specific mutational profile of the SARS-CoV2 proteins, especially for the NSPs, is warranted.…”

Section: Figure 7 | (A)mentioning

confidence: 99%

Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients

et al. 2021

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The novel coronavirus 2 (nCoV2) outbreaks took place in December 2019 in Wuhan City, Hubei Province, China. It continued to spread worldwide in an unprecedented manner, bringing the whole world to a lockdown and causing severe loss of life and economic stability. The coronavirus disease 2019 (COVID-19) pandemic has also affected India, infecting more than 10 million till 31st December 2020 and resulting in more than a hundred thousand deaths. In the absence of an effective vaccine, it is imperative to understand the phenotypic outcome of the genetic variants and subsequently the mode of action of its proteins with respect to human proteins and other bio-molecules. Availability of a large number of genomic and mutational data extracted from the nCoV2 virus infecting Indian patients in a public repository provided an opportunity to understand and analyze the specific variations of the virus in India and their impact in broader perspectives. Non-structural proteins (NSPs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus play a major role in its survival as well as virulence power. Here, we provide a detailed overview of the SARS-CoV2 NSPs including primary and secondary structural information, mutational frequency of the Indian and Wuhan variants, phylogenetic profiles, three-dimensional (3D) structural perspectives using homology modeling and molecular dynamics analyses for wild-type and selected variants, host-interactome analysis and viral–host protein complexes, and in silico drug screening with known antivirals and other drugs against the SARS-CoV2 NSPs isolated from the variants found within Indian patients across various regions of the country. All this information is categorized in the form of a database named, Database of NSPs of India specific Novel Coronavirus (DbNSP InC), which is freely available at http://www.hpppi.iicb.res.in/covid19/index.php.

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Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays

Abstract: Graphical abstract Hightlights

Cited by 28 publications

References 8 publications

The Spike of SARS-CoV-2: Uniqueness and Applications

The Spike of SARS-CoV-2: Uniqueness and Applications

Evaluation of Strategies to Fight COVID-19: The French Paradigm

Structural and Drug Screening Analysis of the Non-structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Virus Extracted From Indian Coronavirus Disease 2019 Patients

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