Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes−49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.

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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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Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India

10.1101/2021.04.22.440932 ◽

2021 ◽

Author(s):

Sarah Cherian ◽

Varsha Potdar ◽

Santosh Jadhav ◽

Pragya Yadav ◽

Nivedita Gupta ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Natural Infection ◽

Health Impact ◽

Spike Protein ◽

Whole Genome ◽

Furin Cleavage ◽

Genomic Epidemiology ◽

Furin Cleavage Site ◽

Second Wave

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of variants of concern (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains. Phylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, revealed that these may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation against a wider panel of mAbs, sera from vaccinees and those that recovered from natural infection needs to be studied. The emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.

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ASTERACEOUS FLORA OF TERAI REGION OF EASTERN UTTAR PRADESH, INDIA

FLORA AND FAUNA ◽

10.33451/florafauna.v23i1pp105-114 ◽

2017 ◽

Vol 23 (1) ◽

Author(s):

KANCHAN LATA

Keyword(s):

Uttar Pradesh ◽

Eastern Uttar Pradesh ◽

Systematic Identification

The systematic identification of 78 species belonging to 51 genera reported from Terai region of Eastern Uttar Pradesh, India. The present paper provides key to genera, list of plant with their habit, phenology and voucher number of each species.

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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Science ◽

10.1126/science.abh2644 ◽

2021 ◽

pp. eabh2644 ◽

Cited By ~ 2

Author(s):

Nuno R. Faria ◽

Thomas A. Mellan ◽

Charles Whittaker ◽

Ingra M. Claro ◽

Darlan da S. Candido ◽

...

Keyword(s):

Molecular Evolution ◽

Genome Sequencing ◽

Immune Evasion ◽

Molecular Clock ◽

Spike Protein ◽

Dynamical Model ◽

Mortality Data ◽

Clock Analysis ◽

Protection Against Infection ◽

Molecular Clock Analysis

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

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Rotavirus Gastroenteritis in Eastern Uttar Pradesh, India

The Indian Journal of Pediatrics ◽

10.1007/s12098-020-03625-0 ◽

2021 ◽

Cited By ~ 1

Author(s):

Vineeta Gupta ◽

Priyanka Aggarwal ◽

Brajesh Kumar ◽

Nayana P. Nair ◽

Varunkumar Thiyagarajan ◽

...

Keyword(s):

Uttar Pradesh ◽

Rotavirus Gastroenteritis ◽

Eastern Uttar Pradesh

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Cyanophycean Algae from Eastern Uttar Pradesh, India

Ecoprint An International Journal of Ecology ◽

10.3126/eco.v13i0.1627 ◽

2009 ◽

Vol 13 ◽

pp. 35-39 ◽

Cited By ~ 1

Author(s):

P. K. Mishra ◽

R. K. Mehrotra ◽

Madhulika Shukla ◽

Jai Prakash ◽

Purnima Mishra

Keyword(s):

Uttar Pradesh ◽

Eastern Uttar Pradesh ◽

First Time

In the present paper 10 Cyanophycean algae belonging 10 genera have been described from eastern U.P. The genera described are: Chroococcus, Microcystis, Aphanothece, Arthrospira, Spirulina, Lyngbya, Anabaena, Rivularia, and Gloeotrichia. All these forms are being reported for the first time from eastern U.P., India.doi: 10.3126/eco.v13i0.1627Key words: Cyanophycean algaeEcoprint (An International Journal of Ecology) Vol. 13, No. 1, 2006 Page: 35-39

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