Evolving Insights from <i>SARS-CoV-2</i> Genome from 200K COVID-19 Patients

Desai, Sanket; Rane, Aishwarya; Joshi, Asim; Dutt, Amit

doi:10.1101/2021.01.21.427574

Cited by 5 publications

(7 citation statements)

References 17 publications

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“…Thus after borders reopening and allowing the international travel, the genomic characterization of SARS-CoV-2 strains could be very important tool to better understand and to monitor the COVID-19 epidemiology in the country. This is a very important tool to monitor the emergence of new pathogenic strains including SARS-CoV-2 strains [14,15].…”

Section: Expected Information and Role Of Genomic Characterizationmentioning

confidence: 99%

“…The current emergence of newer SARS-CoV-2 variants in many countries underlines the significance of enhancing efforts to sequence the genome of the virus from across the globe including Mozambique [14]. In the present study the COVID-19 imported cases and severity were analyzed to understand the epidemiology of the disease and to highlight the future information that might be obtained through genomic characterization of SARS-CoV-2 strains in Mozambique.…”

Section: Introductionmentioning

confidence: 99%

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COVID-19 imported cases and severity: expected information from genomic characterization of SARS-CoV-2 strains in Mozambique

Sumbana

Passanduca

Rubino

2021

J Infect Dev Ctries

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Introduction: The novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), etiological agent of coronavirus disease 2019 (COVID-19) was first reported in China in December 2019 and spread worldwide. As of March 6th, 2021, there have been 116,670,105 million confirmed cases globally including 2,592,085 deaths. COVID-19 cases have been reported in 219 countries and territories, creating global panic. Mozambique has witnessed the evolution of COVID-19 epidemic associated with the weakness of health system, mostly in terms of laboratory diagnosis capacity, concerns on compliance to effective public health measures including physical distancing, use of masks in crowded indoor areas, hand hygiene, isolation and quarantine of people. Methodology: The data included in this study were collected from published articles regarding COVID-19 imported cases and severity in Africa, especially in Mozambique. Additionally, official documents of COVID-19 epidemiology from Minister of Health and National Institute of Health of Mozambique from 22nd of March 2020 to 1st of August 2020 were included. Results: The SARS-CoV-2 strains imported mainly from South Africa and European countries might have been playing an important role on COVID-19 epidemic evolution in Mozambique. Conclusions: These circulating strains in the country, might be similar enough to the strains found in other countries, yet the genomic characterization is needed particularly during the phase of borders reopening through understanding the source of infections and guiding the implementation of containment and mitigation measures in the country.

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Section: Expected Information and Role Of Genomic Characterizationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

COVID-19 imported cases and severity: expected information from genomic characterization of SARS-CoV-2 strains in Mozambique

Sumbana

Passanduca

Rubino

2021

J Infect Dev Ctries

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“…The significant progress in the developments of COVID-19 vaccines [2,3], including inactivated vaccine [4], mRNA vaccine [5,6], live vectorial vaccine [7,8] and recombinant protein subunit vaccine [9,10], as well as the neutralizing antibody therapeutics [11,12] is encouraging to prevent the pandemic of SARS-CoV-2. However, the virus is in constant evolution and several more contagious variants have emerged [13][14][15][16]. It is important to investigate the molecular mechanism for the impacts of the naturally occurring mutations on the infectivity of SARS-CoV-2, as well as on the immune effectiveness of the vaccines and the efficacy of the neutralizing antibodies.…”

Section: Introductionmentioning

confidence: 99%

E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

Wang

Liang

Jin

et al. 2021

Preprint

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The pandemic of the COVID-19 disease caused by SARS-CoV-2 has led to more than 100 million infections and over 2 million deaths worldwide. The progress in the developments of effective vaccines and neutralizing antibody therapeutics brings hopes to eliminate the threat of COVID-19. However, SARS-CoV-2 continues to mutate, and several new variants have been emerged. Among the various naturally-occurring mutations, the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to more tight binding interface of RBD with hACE2 and formation of some new hydrogen bonds. The more tight binding interface and the new hydrogen bonds formation also contribute to the improved binding affinity of RBD to the receptor hACE2. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies, indicating reduced effectiveness of these antibodies. Our results provide valuable information for the effective vaccine development and antibody drugs design.

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“…Despite the vast ecological opportunity posed by its recent zoonotic jump and the sheer number of COVID-19 cases worldwide, the global diversity of SARS-CoV-2 measured in late July 2020 was remarkably low, with 46 723 sequenced genomes from 99 countries diverging maximally by 32 SNPs, all of which were considered descendants of a single lineage [54]. However, as of January 2021, global diversity has increased enormously [58], including three novel lineages each characterized by 17 (B.1.1.7), nine (B.1.351), and 16 (P.1) nonsynonymous mutations, of which 38 are distinct [59,60]. Two explanations for this surge of diversity include sufficient time elapsed since emergence for the accumulation of viral diversity and/or transmission of diverse variants that arose in long-term COVID-19 patients [55,59].…”

Section: Evolutionary Controls Of Viral Diversitymentioning

confidence: 99%

“…protein (D614G, N501Y, E484K) associated with within-host advantages and, putatively, increased transmissibility [59,71,77]. Such convergent evolution is a classic sign of adaptation [58,78], and viruses may provide an unexpected opportunity to investigate the relationship between convergence in function (e.g., transmissibility) and convergence of the underlying genetic and/or structural components of the trait [79].…”

Section: Adaptation and Viral Evolutionary Successmentioning

confidence: 99%

SARS-CoV-2: Cross-scale Insights from Ecology and Evolution

Snedden

Makanani

Schwartz

et al. 2021

Trends in Microbiology

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Ecological and evolutionary processes govern the fitness, propagation, and interactions of organisms through space and time, and viruses are no exception. While COVID-19 research has primarily emphasized virological, clinical, and epidemiological perspectives, crucial aspects of the pandemic are fundamentally ecological or evolutionary. Here, we highlight five conceptual domains of ecology and evolution – invasion, consumer-resource interactions, spatial ecology, diversity, and adaptation – that illuminate (sometimes unexpectedly) the emergence and spread of SARS-CoV-2. We describe the applications of these concepts across levels of biological organization and spatial scales, including within individual hosts, host populations, and multi-species communities. Together, these perspectives illustrate the integrative power of ecological and evolutionary ideas and highlight the benefits of interdisciplinary thinking for understanding emerging viruses.

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Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients

Cited by 5 publications

References 17 publications

COVID-19 imported cases and severity: expected information from genomic characterization of SARS-CoV-2 strains in Mozambique

COVID-19 imported cases and severity: expected information from genomic characterization of SARS-CoV-2 strains in Mozambique

E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

SARS-CoV-2: Cross-scale Insights from Ecology and Evolution

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