Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states

Bhattacharjee, Bornali; Pandit, Bhaswati

doi:10.1101/2020.05.28.122143

Cited by 5 publications

(3 citation statements)

References 22 publications

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“…However, the authors suggested that the strain is similar to those strains from Singapore and Philippines [ 54 ]. Furthermore, another study reported that isolate RK100 clustered with the ancestral first isolates from India that were originally reported from Kerala [ 55 ].…”

Section: Resultsmentioning

confidence: 99%

Clinical and whole genome characterization of SARS-CoV-2 in India

et al. 2021

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We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.

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Section: Resultsmentioning

confidence: 99%

Clinical and whole genome characterization of SARS-CoV-2 in India

et al. 2021

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“…CoVs have the largest genomes (29.9-kilobase) among the known RNA viruses with several open reading frames (ORFs). 7 The two ORF (ORF1a/ORF1b) in combination contain two-thirds of the viral genome which directly encodes two polyproteins; namely, pp1a and pp1ab using host cell protein translation machinery. These polyproteins further processed into 16 non-structural proteins (nsps) by viral proteases enzymes like papain-like protease (PLpro) and 3C-like protease (3CLpro).…”

Section: Introductionmentioning

confidence: 99%

<p>An Up-to-Date Overview of Therapeutic Agents for the Treatment of COVID-19 Disease</p>

Belete¹

2020

CPAA

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Acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has a great potential to overwhelm the world healthcare systems that may lead to high morbidity and mortality. It also affects world economic development in the future. Currently, no proven effective drugs or vaccines are available for the management of COVID-19 disease. The pace of normal drug development progression is unacceptable in the context of the current pandemic. Therefore, repurposing the existing drugs that were used for the treatment of malaria, Ebola, and influenza helps rapid drug development for COVID-19. Currently, several repurposing candidate drugs are in a clinical trial including, chloroquine monoclonal antibodies, convalescent plasma, interferon, and antiviral therapies. Antiviral drugs like arbidol, remdesiv and favirnavir are the most promising due to the similarities of the viruses regarding viral entry, fusion, uncoating, and replication. This review article provides an overview of the potential therapeutic agent, which displayed better clinical treatment outcomes. Moreover, with further understanding of the SARS-CoV-2 virus, new drugs targeting specific SARS-CoV-2 viral components arise, and investigations on these novels anti-SARSCoV- 2 agents are also reviewed.

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“…One aspect appears to be least concerned by healthcare professional is the past and ongoing evolution of the virus strain. Recent studies with a relatively limited number of samples for exploring the evolutionary history of SARS-CoV-2 have been restricted to either comparison with the possible ancestral forms (13,14) or a certain region and relatively smaller datasets (15)(16)(17)(18)(19). Here, a comprehensive dataset of 821 SARS-CoV-2 genomes from (13,14), was generated containing 16 non-structural proteins, four structural proteins and six accessory proteins (20)(21)(22)(23).…”

Section: Introductionmentioning

confidence: 99%

Witnessing Evolution of SARS-CoV-2 through Comparative Phylogenomics: The Proximate Origin is Guangdong, not Wuhan

Doğan¹,

Korkmaz²,

Budak³

et al. 2020

Preprint

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A new form of coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) is currently causing a pandemic. A six-month evolutionary history of SARS-CoV-2 is witnessed by characterising the total genome of 821 samples using comparative phylogenomic approaches. Our analyses produced striking inclusive results that may guide scientists/professionals for the past/future of pandemic. Phylogenetic and time estimation analyses suggest the proximate origin of pandemic strain as Guangdong and the origin time as first half of September 2019, not Wuhan and December 2019, respectively. The viral genome experienced a substitution rate similar to other RNA viruses, but it is particularly high in some of the peptides encoding sequences such as leader protein, E gene, orf8, orf10, nsp10, N gene, S gene and M gene and nsp4, while low in nsp11, orf7a, 3C-like proteinase, nsp9, nsp8 and endoRNase. Most strikingly, the divergence rate of amino acid sequences is high proportional to nucleotide divergence. Additionally, specific non-synonymous mutations in nsp3 and nsp6 evolved under positive selection. The exponential growth rate (r), doubling time (Td) and R0 were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. Comparison of synapomorphies distinguishing the SARS-CoV-2 and the candidate ancestor bat coronavirus indicates that mutation pattern in nsp3 and S gene enabled the new strain to invade human and become a pandemic strain. We arrive at the following main conclusions: (i) six months evolution of viral genome is nearly neutral, (ii) origin of pandemic is not Wuhan and predates formal reports, (iii) although viral population is ongoing an exponential growth, the doubling time is evolving towards shortening, and (iv) divergence rate of total genome is similar to other RNA viruses, but it is prominently high in some genes while low in some others and evolution in these genes should be closely monitored as their protein products intervening to pathogenicity, virulence and immune response.

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Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states

Cited by 5 publications

References 22 publications

Clinical and whole genome characterization of SARS-CoV-2 in India

Clinical and whole genome characterization of SARS-CoV-2 in India

<p>An Up-to-Date Overview of Therapeutic Agents for the Treatment of COVID-19 Disease</p>

Witnessing Evolution of SARS-CoV-2 through Comparative Phylogenomics: The Proximate Origin is Guangdong, not Wuhan

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