Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

AbstractRecently classified as a pandemic by WHO, novel Corononavirus 2019 has affected almost every corner of the globe causing human deaths in a range of hundred thousands. The virus having its roots in Wuhan (China) has been spread over the world by its own property to change itself accordingly. These changes correspond to its transmission and pathogenicity due to which the concept of social distancing appeared into the picture. In this paper, a few findings from the whole genome sequence analysis of viral genome sequences submitted from India are presented. The data used for analysis comprises 440 collective genome sequences of virus submitted in GenBank, GISAID, and SRA projects, from around the world as well as 28 viral sequences from India. Multiple sequence alignment of all genome sequences was performed and analysed. A novel non-synonymous mutation 4809C>T (S1515F) in NSP3 gene of SARS-CoV2 Indian strains is reported along with other frequent and important changes from around the world: 3037C>T, 14408C>T, and 23403A>G. The novel change was observed in samples collected in the month of March, whereas was found to be absent in samples collected in January with the respective persons’ travel history to China. Phylogenetic analysis clustered the sequences with this change as one separate clade. Mutation was predicted as stabilising change by insilco tool DynaMut. A second patient in the world to our knowledge with multiple (Wuhan and USA) strain contraction was observed in this study. The infected person is among the two early infected patients with travel history to China. Strains sequenced in Iran stood out to have different variants, as most of the reported frequent variants were not observed. The objective of this paper is to highlight the similarities and changes observed in the submitted Indian viral strains. This helps to keep track on the activity, that how virus is changing into a new subtype. Major strains observed were European with the novel change in India and other being emergent clade of Iran. Its important to observe the changes in NSP3 gene, as this gene has been reported with extensive positive selection as well as potential drug target. Extensive Positive Selection Drives the Evolution of Nonstructural Proteins. With the limited number of sequences this was the only frequent novel non-synonymous change observed from Indian strains, thereby making this change vulnerable for investigation in future. This paper has a special focus on tracking of Indian viral sequences submitted in public domain.

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Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

10.1101/2020.03.04.976662 ◽

2020 ◽

Cited By ~ 5

Author(s):

Bin Fang ◽

Linlin Liu ◽

Xiao Yu ◽

Xiang Li ◽

Guojun Ye ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Sliding Window ◽

The Novel ◽

Population Demography ◽

Short Term ◽

Genome Wide ◽

The World ◽

Genome Wide Data ◽

Neutrality Tests

AbstractAs the highly risk and infectious diseases, the outbreak of coronavirus disease 2019 (COVID-19) poses unprecedent challenges to global health. Up to March 3, 2020, SARS-CoV-2 has infected more than 89,000 people in China and other 66 countries across six continents. In this study, we used 10 new sequenced genomes of SARS-CoV-2 and combined 136 genomes from GISAID database to investigate the genetic variation and population demography through different analysis approaches (e.g. Network, EBSP, Mismatch, and neutrality tests). The results showed that 80 haplotypes had 183 substitution sites, including 27 parsimony-informative and 156 singletons. Sliding window analyses of genetic diversity suggested a certain mutations abundance in the genomes of SARS-CoV-2, which may be explaining the existing widespread. Phylogenetic analysis showed that, compared with the coronavirus carried by pangolins (Pangolin-CoV), the virus carried by bats (bat-RaTG13-CoV) has a closer relationship with SARS-CoV-2. The network results showed that SARS-CoV-2 had diverse haplotypes around the world by February 11. Additionally, 16 genomes, collected from Huanan seafood market assigned to 10 haplotypes, indicated a circulating infection within the market in a short term. The EBSP results showed that the first estimated expansion date of SARS-CoV-2 began from 7 December 2019.

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Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽

10.3390/genes12111803 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1803

Author(s):

Jitendra Singh ◽

Anvita Gupta Malhotra ◽

Debasis Biswas ◽

Prem Shankar ◽

Leena Lokhande ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Spike Protein ◽

Whole Genome ◽

The Novel ◽

Genome Sequences ◽

Second Wave ◽

Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

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The emergence of SARS-CoV-2 by an unusual genome reconstitution

10.21203/rs.3.rs-33201/v1 ◽

2020 ◽

Author(s):

Seong-Tshool Hong ◽

Md. Mehedi Hassan ◽

Shirina Sharmin ◽

Jinny Hong ◽

Hoi-Seon Lee ◽

...

Keyword(s):

Amino Acids ◽

Phylogenetic Analysis ◽

Pairwise Comparison ◽

Surface Protein ◽

Plasmodium Malariae ◽

Spike Protein ◽

Genome Sequences ◽

The World ◽

The Common ◽

Virus Strains

Abstract SARS-CoV-2 has been spreading remarkedly fast around the world since its emergence while the origin of the virus remains ambiguous. Here, we constructed all of the original prototype genome sequences of SARS-CoV-2 by selecting the common nucleotide among the different virus strains with species. Phylogenetic analysis on the prototype sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pan-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of 7 amino acids within the spike protein of SARS-CoV-2. Database searches showed that the motif originated from a surface protein of Plasmodium malariae, suggesting that the SARS-CoV-2 was emerged after acquiring the motif of the malaria surface protein.

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Omicron strain spreads with the doubling time of 3.2-3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant

10.1101/2021.12.08.21267494 ◽

2021 ◽

Author(s):

Frederic Grabowski ◽

Marek Kochańczyk ◽

Tomasz Lipniacki

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

Linear Regression ◽

Doubling Time ◽

Herd Immunity ◽

The Novel ◽

Gauteng Province ◽

The World ◽

Log Linear ◽

Short Doubling Time

Omicron, the novel, highly mutated SARS-CoV-2 Variant of Concern (belonging to the Pango lineage B.1.1.529), was first collected on November 8, 2021, in Gauteng province of South Africa. By the end of November 2021 it has spread towards fixation in Gauteng and was detected on all continents. Based on data collected till December 7, 2021, we showed the exponential growth of the Omicron variant over the four-week period in Gauteng (November 8-December 5, 2021) with the doubling time equal 3.38 day [CI 95%: 3.18-3.61 day]. Log-linear regression suggests that the spread began around October 10, 2021, however due to stochasticity in the initial spread this estimate is likely inaccurate. Phylogenetic analysis indicates that the Omicron strain started to diverge in between October 28 and November 5, 2021. This implies that the hidden spread of Omicron before October 10, 2021 (which would suggest slower strain growth) is unlikely. The very short doubling time of Omicron in Gauteng, a province that has reached herd immunity to the Delta variant (implied by the decrease of the weekly number of cases between July and October, 2021, at no significant mobility restrictions), suggests that Omicron will cause abrupt outbreaks of COVID-19 epidemics across the world, and will become the (temporarily) dominant strain.

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Genotypes and phylogenetic analysis of adenovirus in children with respiratory infection in Buenos Aires, Argentina (2000–2018)

PLoS ONE ◽

10.1371/journal.pone.0248191 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248191

Author(s):

Débora N. Marcone ◽

Andrés C. A. Culasso ◽

Noelia Reyes ◽

Adriana Kajon ◽

Diana Viale ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Respiratory Infection ◽

Buenos Aires ◽

Respiratory Infections ◽

Severe Disease ◽

Hexon Gene ◽

Genome Sequences ◽

The World ◽

And Shifts ◽

Genomic Variant

Human adenoviruses (HAdV) are one of the most frequent causes of respiratory infections around the world, causing mild to severe disease. In Argentina, many studies focused on the association of HAdV respiratory infection with severe disease and fatal outcomes leading to the discovery in 1984 of a genomic variant 7h associated with high fatality. Although several molecular studies reported the presence of at least 4 HAdV species (B, C, D and E) in Argentina, few sequences were available in the databases. In this study, sequences from the hexon gene region were obtained from 141 patients as a first approach to assess the genetic diversity of HAdVs circulating in Buenos Aires, Argentina. Phylogenetic analysis of these sequences and others recovered from public databases confirmed the circulation of the four above-mentioned species represented by 11 genotypes, with predominance in species B and C and shifts in their proportion in the studied period (2000 to 2018). The variants detected in Argentina, for most of the genotypes, were similar to those already described in other countries. However, uncommon lineages belonging to genotypes C2, C5 and E4 were detected, which might indicate the circulation of local variants and will deserve further studies of whole-genome sequences.

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Analyzing hCov genome sequences: Applying Machine Intelligence and beyond

10.1101/2020.06.03.131987 ◽

2020 ◽

Author(s):

Shashata Sawmya ◽

Arpita Saha ◽

Sadia Tasnim ◽

Naser Anjum ◽

Md. Toufikuzzaman ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Deep Learning ◽

Evolutionary History ◽

Genetic Material ◽

Machine Intelligence ◽

Genome Sequences ◽

Analysis Pipeline ◽

Learning Techniques ◽

The World ◽

Novel Virus

AbstractCovid-19 pandemic, caused by the sars-cov-2 strain of coronavirus, has affected millions of people all over the world and taken thousands of lives. It is of utmost importance that the character of this deadly virus be studied and its nature be analysed. We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. In a nutshell, we have prepared an analysis pipeline for hCov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data.

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ИДЕЈЕ ЕВРОАЗИЈСТВА И „РУСКИ ХРИСТОС“ ДОСТОЈЕВСКОГ IDEAS OF EURASIANISM AND DOSTOEVSKY'S "RUSSIAN CHRIST"

Folia linguistica et litteraria ◽

10.31902/fll.38.2021.4 ◽

2021 ◽

Vol XII (38) ◽

pp. 67-80

Author(s):

Neda Andrić ◽

Jovan Radojević

Keyword(s):

National Culture ◽

Main Part ◽

Special Focus ◽

The Novel ◽

Russian People ◽

The World

In this paper, through a review of the most important ideas of the philosophy of Eurasianism related to concepts of nationality, personality and Orthodoxy, we point out their connection with the world of ideas of F. M. Dostoevsky. The main part of the paper is dedicated to an analysis and observation of the connections between the idea of national culture, nationality, and the idea of Dostoevsky’s "Russian God", as well as Nikolai Trubetzkoy's key ideas about national culture as the only possible one, based on Orthodoxy as the only form of Christianity that preserves the original teaching and tradition. The notion of the "Russian Christ", recognized by Oscar von Schultz in the works of Pushkin, Lermontov, Turgenev, Chekhov and Dostoevsky, is especially present in the novel “The Possessed” through the character of Shatov. The character’s micro-monologue about the "Russian God" is a special focus of our analysis in the light of the phrase “Russian Christ”. This phrase expresses a specific understanding of Christianity that Russia received from Byzantium. Moreover, this specificity has been characteristically reflected, both in the literature and in the character and features of the Russian people, through the dominant kenotic principle.

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UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis

Wellcome Open Research ◽

10.12688/wellcomeopenres.14730.1 ◽

2018 ◽

Vol 3 ◽

pp. 118

Author(s):

Anna Smielewska ◽

Edward Emmott ◽

Kyriaki Ranellou ◽

Ashley Popay ◽

Ian Goodfellow ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Sequence ◽

Sequence Data ◽

Hypervariable Region ◽

Whole Genome Sequence ◽

Whole Genome ◽

Full Genome ◽

Genome Sequences ◽

Genome Data ◽

The Uk

Background:Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts. Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods:Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015. These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3.Results:In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof. We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical.Conclusions:The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.

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Modeling and Simulation: A study on predicting the outbreak of COVID-19 in Saudi Arabia

10.1101/2021.01.17.21249837 ◽

2021 ◽

Author(s):

Ahmed Msmali ◽

Zico Mutum ◽

Idir Mechai ◽

Abdullah Ahmadini

Keyword(s):

Saudi Arabia ◽

Logistic Growth ◽

Special Focus ◽

The Novel ◽

Final Phase ◽

The World ◽

Logistic Growth Model ◽

Novel Coronavirus ◽

Epidemiological Trends

AbstractThe novel coronavirus (Covid-19) infection has resulted in an ongoing pandemic affecting health system and economy of more than 200 countries around the world. Mathematical models are used to predict the biological and epidemiological trends of an epidemic and develop methods for controlling it. In this work, we use mathematical model perspective to study the role of behavior change in slowing the spread of the COVID-19 disease in Saudi Arabia. The real-time updated data from 1st May 2020 to 8th January 2021 is collected from Saudi Ministry of Health, aiming to provide dynamic behaviors of the pandemic in Saudi Arabia. During this period, it has infected 297,205 people, resulting in 6124 deaths with the mortality rate 2.06 %. There is weak positive relationship between the spread of the infection and mortality (R2 =0.412). We use Susceptible-Exposed-Infection-Recovered (SEIR) mode, the logistic growth model and with special focus on the exposed, infection and recovery individuals to simulate the final phase of the outbreak. The results indicate that social distancing, good hygienic conditions, and travel limitation are the crucial measures to prevent further spreading of the epidemic.

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New corona virus: is just a tip of iceberg?

International Journal of Basic & Clinical Pharmacology ◽

10.18203/2319-2003.ijbcp20202957 ◽

2020 ◽

Vol 9 (7) ◽

pp. 1147

Author(s):

Arvind Narwat ◽

Seema Rani ◽

Garima Bhutani ◽

Rahul Saini ◽

Kamaldeep Singh

Keyword(s):

Genome Sequence ◽

Vaccine Development ◽

Antiviral Treatment ◽

Whole Genome Sequence ◽

Whole Genome ◽

The Novel ◽

The Past ◽

Cruise Ships ◽

The World ◽

Novel Coronavirus

The world is again experiencing a global viral epidemic of zoonotic origin. As of March 30, 785807 confirmed cases of coronavirus disease 2019 (COVID-19) and 37820 deaths had been reported in more than 120 countries. Strenuous efforts are being made by various countries of the world to halt transmission through shutting down transport, quarantining entire cities and enforcing the use of face masks. International flights have been cancelled and affected cruise ships quarantined. As in all outbreaks, there is an urgent need to develop effective diagnostics, therapeutics and vaccines. Several experimental diagnostic platforms are already in use in China and elsewhere. The whole-genome sequence of SARS-CoV-2 has been obtained and shared widely. Several potential treatments have been proposed, however, no antiviral treatment has been approved for the novel coronavirus, and despite two outbreaks of novel coronaviruses in the past two decades, vaccine development is still in its infancy.

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