Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes

Cao, Canhui; He, Liang; Tian, Yuan; Yu, Qin; Sun, Haiyin; Ding, Wencheng; Gui, Liming; Wu, Peng

doi:10.1016/j.meegid.2021.104831

Cited by 12 publications

(8 citation statements)

References 38 publications

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“…The question of the differences in clinical courses—specifically, in disease severity and outcome—between the different SARS-CoV-2 variants has been studied extensively [ 18 , 19 , 20 , 21 , 22 ]. By undergoing mutations in genes responsible for the expression of viral proteins (specifically, spike and nucleocapsid proteins), the SARS-CoV-2 virion changes its properties, e.g., its ability to infect new cells, to further reproduce, and to evade host immune responses [ 23 , 24 ].…”

Section: Discussionmentioning

confidence: 99%

A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants

Korobova

Arsentieva

Любимова

et al. 2022

IJMS

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Background. Infection caused by SARS-CoV-2 mostly affects the upper and lower respiratory tracts and causes symptoms ranging from the common cold to pneumonia with acute respiratory distress syndrome. Chemokines are deeply involved in the chemoattraction, proliferation, and activation of immune cells within inflammation. It is crucial to consider that mutations within the virion can potentially affect the clinical course of SARS-CoV-2 infection because disease severity and manifestation vary depending on the genetic variant. Our objective was to measure and assess the different concentrations of chemokines involved in COVID-19 caused by different variants of the virus. Methods. We used the blood plasma of patients infected with different variants of SARS-CoV-2, i.e., the ancestral Wuhan strain and the Alpha, Delta, and Omicron variants. We measured the concentrations of 11 chemokines in the samples: CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL7/MCP-3, CCL11/Eotaxin, CCL22/MDC, CXCL1/GROα, CXCL8/IL-8, CXCL9/MIG, CXCL10/IP-10, and CX3CL1/Fractalkine. Results. We noted a statistically significant elevation in the concentrations of CCL2/MCP-1, CXCL8/IL-8, and CXCL1/IP-10 independently of the variant, and a drop in the CCL22/MDC concentrations. Conclusions. The chemokine concentrations varied significantly depending on the viral variant, leading us to infer that mutations in viral proteins play a role in the cellular and molecular mechanisms of immune responses.

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Section: Discussionmentioning

confidence: 99%

A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants

Korobova

Arsentieva

Любимова

et al. 2022

IJMS

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“…Three studies (one bigdata analysis [50] and two clinical studies [17,51]) reported that the SARS-CoV-2 variants were significantly associated with decrease in severity of disease. The remaining 27 studies (one animal study [18], 22 bigdata analyses [8][9][10][11][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69] and four clinical studies [70][71][72][73]) described the positive association between the different variants with severity of COVID-19 (Table 3). A clinical study by Long et al showed that infection with SARS-CoV-2 variants harboring the D614G substitution was not associated with disease severity, overall mortality, transfer to ICU, mechanical ventilation and length of stay at hospital [41].…”

Section: Relation Between Viral Mutations and Severity Of Covid-19 Infectionmentioning

confidence: 99%

SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence

Dao

Hoang

Colson

et al. 2021

JCM

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Background: We conducted this review to summarize the relation between viral mutation and infectivity of SARS-CoV-2 and also the severity of COVID-19 in vivo and in vitro. Method: Articles were identified through a literature search until 31 May 2021, in PubMed, Web of Science and Google Scholar. Results: Sixty-three studies were included. To date, most studies showed that the viral mutations, especially the D614G variant, correlate with a higher infectivity than the wild-type virus. However, the evidence of the association between viral mutation and severity of the disease is scant. A SARS-CoV-2 variant with a 382-nucleotide deletion was associated with less severe infection in patients. The 11,083G > U mutation was significantly associated with asymptomatic patients. By contrast, ORF1ab 4715L and S protein 614G variants were significantly more frequent in patients from countries where high fatality rates were also reported. The current evidence showed that variants of concern have led to increased infectivity and deteriorating epidemiological situations. However, the relation between this variant and severity of COVID-19 infection was contradictory. Conclusion: The COVID-19 pandemic continues to spread worldwide. It is necessary to anticipate large clinical cohorts to evaluate the virulence and transmissibility of SARS-CoV-2 mutants.

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“…Major NSPs are 3, 5, 12, and 13 shown in Figure 1. Frequency of variation in >1900 SARS-CoV-2 genome samples examined varied from 5.48 in coding regions to 6.96 in the noncoding regions [18]. The variation sites included S: 23403 (D614G), ORF1ab: 14408 (NSP12b: P314L),17747 (NSP13: P504L) and 17858 (NSP13:Y541C), and ORF8: 28144 (L84S).…”

Section: Genome Organisation Of Sars-cov-2mentioning

confidence: 99%

Diversity due to mutations in circulating virus strains of SARS-CoV-2 may delay control of COVID-19

S.¹,

Shivamallu²,

Dharmashekara³

et al. 2022

J Appl Biol Biotech

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Severe acute respiratory syndrome (SARS)-coronavirus-2 (CoV-2) is a beta-coronavirus (beta-CoV; sarbecovirus), like its predecessors SARS and MERS CoVs. Of the structural proteins of the virus, the Spike (S) protein on the virion envelope binds to the host cell ACE2 through viral epitopes in the receptor-binding domain (RBD). Deletions in the ORF8 as well as mutations in the S gene of SARS-CoV of 2003 were related to adaptation of the virus to humans. The emergence of novel variants of viz., B.1.1.7, B.1.427 and B.1.429, B.1.617 and its Kappa and Delta strains/ variants, B.1.351, and P.1 in the United Kingdom, Americas, India, South Africa and Brazil, respectively, has been found be associated with the current waves of the COVID-19 pandemic. These variants are antigenically dissimilar, whereas the current COVID-19 vaccines are monovalent. This is a handicap in the control program. The Delta variant has been reported in 74 countries as of 14 June 2021 and the anticipated third wave involving this variant is of concern to the countries (www.gavi.org). Of late, on 17 June 2021, Delta Plus variant was identified in India (AIIMS, Bhopal, India). Circulation of virus in vaccinated population may lead to endemicity, and this can be monitored by regular serosurveillance for antibodies against select non-structural proteins (NSPs) of the virus; antibodies to NSPs will indicate virus replication in the host. Endemic areas will have higher NSP reactors. It is predicted that the Delta B.1 variant may ignite the third wave of the disease in many countries. As it has been difficult to achieve uniformity in time and density of the vaccination even in the districts, circulation of the virus in partially immune population may lead to the selection of newer variants of SARS-CoV-2. The presence of monoclonal antibody resistant mutants and neutralization-escape mutants in quasispecies structure of another + sense RNA virus, i.e., Aphthovirus (FMD virus; foot and mouth disease virus) in the family Picornaviridae is well documented. The situation could be similar in the Coronaviridae member SARS-CoV-2. Previous immunity may not protect against current/ future mutants thereby pro-longing the COVID-19 control Programme.

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Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes

Cited by 12 publications

References 38 publications

A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants

A Comparative Study of the Plasma Chemokine Profile in COVID-19 Patients Infected with Different SARS-CoV-2 Variants

SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence

Diversity due to mutations in circulating virus strains of SARS-CoV-2 may delay control of COVID-19

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