scispace - formally typeset
Search or ask a question
Journal ArticleDOI

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

TL;DR: The data support the idea that viruses with amino acid replacements associated with immune escape are already circulating and importation, spread, and emergence of variants locally of SARS-CoV-2 are spread by travel.
Abstract: Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.136: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%, B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences. Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.

Content maybe subject to copyright    Report

Citations
More filters
Journal ArticleDOI
06 Jan 2022-Science
TL;DR: India’s cumulative COVID deaths by September 2021 were six to seven times higher than reported officially, and this equates to the deaths of more than 3.2 million people, with the majority occurring during April to June of 2021.
Abstract: India’s national COVID death totals remain undetermined. Using an independent nationally representative survey of 0.14 million (M) adults, we compared COVID mortality during the 2020 and 2021 viral waves to expected all-cause mortality. COVID constituted 29% (95% confidence interval, 28 to 31%) of deaths from June 2020 to July 2021, corresponding to 3.2 M (3.1 to 3.4) deaths, of which 2.7 M (2.6 to 2.9) occurred in April to July 2021 (when COVID doubled all-cause mortality). A subsurvey of 57,000 adults showed similar temporal increases in mortality, with COVID and non-COVID deaths peaking similarly. Two government data sources found that, when compared to prepandemic periods, all-cause mortality was 27% (23 to 32%) higher in 0.2 M health facilities and 26% (21 to 31%) higher in civil registration deaths in 10 states; both increases occurred mostly in 2021. The analyses find that India’s cumulative COVID deaths by September 2021 were six to seven times higher than reported officially. Description Uncounted cases in India It is apparent that the official number of COVID-19 cases that have accumulated in India is substantially underestimated, but the question is: by how much? In an independent survey of 137,000 adults, Jha et al. recorded how many people died from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–related causes. Examining the data for all-cause mortality for the year spanning 2020 to 2021 revealed 26 to 29% excess mortality tracking waves of new variant transmission. Extrapolating to the Indian population, this equates to the deaths of more than 3.2 million people, with the majority occurring during April to June of 2021. —CA India’s cumulative COVID deaths by September 2021 were six to seven times higher than reported officially.

85 citations

Posted ContentDOI
30 Jun 2021-medRxiv
TL;DR: In this paper, a two-strain, semi-mechanistic model that synthesizes mortality and genomic data was used to find evidence that altered epidemiological properties of B.1.1617.2 and delayed public health interventions contributed to the resurgence of SARS-CoV-2 in India from February to May 2021.
Abstract: India has seen a surge of SARS-CoV-2 infections and deaths in early part of 2021, despite having controlled the epidemic during 2020. Building on a two-strain, semi-mechanistic model that synthesizes mortality and genomic data, we find evidence that altered epidemiological properties of B.1.617.2 (Delta) variant play an important role in this resurgence in India. Under all scenarios of immune evasion, we find an increased transmissibility advantage for B.1617.2 against all previously circulating strains. Using an extended SIR model accounting for reinfections and wanning immunity, we produce evidence in support of how early public interventions in March 2021 would have helped to control transmission in the country. We argue that enhanced genomic surveillance along with constant assessment of risk associated with increased transmission is critical for pandemic responsiveness. One Sentence Summary Altered epidemiological characteristics of B.1.617.2 and delayed public health interventions contributed to the resurgence of SARS-CoV-2 in India from February to May 2021.

31 citations

Journal ArticleDOI
TL;DR: In this paper, the authors focused on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
Abstract: Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure–function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.

25 citations

Journal ArticleDOI
TL;DR: In this article , the authors compared the spike protein sequence of 91 human SARS CoV2 strains of Iraq to the first reported sequence of SARS-CoV2 isolate from Wuhan Hu-1/China.

12 citations

Journal ArticleDOI
TL;DR: In this article, the authors compared the spike protein sequence of 91 human SARS CoV2 strains of Iraq to the first reported sequence of SARS-CoV2 isolate from Wuhan Hu-1/China.

12 citations

References
More filters
Journal ArticleDOI
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Abstract: We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using treedependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

37,524 citations

Journal ArticleDOI
TL;DR: It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.
Abstract: Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree.

13,668 citations

Journal ArticleDOI
TL;DR: The outbreak of the 2019 novel coronavirus disease (COVID-19) has induced a considerable degree of fear, emotional stress and anxiety among individuals around the world.
Abstract: The outbreak of the 2019 novel coronavirus disease (COVID-19) has induced a considerable degree of fear, emotional stress and anxiety among individuals around t

8,336 citations

Journal ArticleDOI
30 Mar 2020-Nature
TL;DR: This study determines the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 (engineered to facilitate crystallization) in complex with ACE2 and sheds light on the structural features that increase its binding affinity to ACE2.
Abstract: A novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans, causing COVID-191,2. A key to tackling this pandemic is to understand the receptor recognition mechanism of the virus, which regulates its infectivity, pathogenesis and host range. SARS-CoV-2 and SARS-CoV recognize the same receptor—angiotensin-converting enzyme 2 (ACE2)—in humans3,4. Here we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 (engineered to facilitate crystallization) in complex with ACE2. In comparison with the SARS-CoV RBD, an ACE2-binding ridge in SARS-CoV-2 RBD has a more compact conformation; moreover, several residue changes in the SARS-CoV-2 RBD stabilize two virus-binding hotspots at the RBD–ACE2 interface. These structural features of SARS-CoV-2 RBD increase its ACE2-binding affinity. Additionally, we show that RaTG13, a bat coronavirus that is closely related to SARS-CoV-2, also uses human ACE2 as its receptor. The differences among SARS-CoV-2, SARS-CoV and RaTG13 in ACE2 recognition shed light on the potential animal-to-human transmission of SARS-CoV-2. This study provides guidance for intervention strategies that target receptor recognition by SARS-CoV-2. The crystal structure of the receptor-binding domain of the SARS-CoV-2 spike in complex with human ACE2, compared with the receptor-binding domain of SARS-CoV, sheds light on the structural features that increase its binding affinity to ACE2.

3,019 citations

Related Papers (5)