1
|
Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic surveillance of SARS-CoV-2 using long-range PCR primers. Front Microbiol 2024; 15:1272972. [PMID: 38440140 PMCID: PMC10910555 DOI: 10.3389/fmicb.2024.1272972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). Methods In this study we used a set of seven long-range PCR primer pairs to sequence clinical isolates of SARS-CoV-2 on Oxford Nanopore sequencer. These long-range primers generate seven amplicons approximately 4500 bp that covered whole genome of SARS-CoV-2. One of these regions includes the full-length S-gene by using a set of flanking primers. We also evaluated the performance of these long-range primers with Midnight primers by sequencing 94 clinical isolates in a Nanopore flow cell. Results and discussion Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias. The key finding of this study is that long range primers can be used in single-molecule sequencing of RNA viruses in surveillance of emerging variants. We also show that by designing primers flanking the S-gene, we can obtain reliable identification of SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Sangam Kandel
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - Ashton K. Ingold
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Grace A. Turner
- Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Joshua L. Kennedy
- Arkansas Children's Research Institute, Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David W. Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| |
Collapse
|
2
|
Curini V, Ancora M, Jurisic L, Di Lollo V, Secondini B, Mincarelli LF, Caporale M, Puglia I, Di Gialleonardo L, Mangone I, Di Domenico M, Di Pasquale A, Lorusso A, Marcacci M, Cammà C. Evaluation of next generation sequencing approaches for SARS-CoV-2. Heliyon 2023; 9:e21101. [PMID: 38027571 PMCID: PMC10643093 DOI: 10.1016/j.heliyon.2023.e21101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.
Collapse
Affiliation(s)
- Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | | | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| |
Collapse
|
3
|
Misra G, Manzoor A, Chopra M, Upadhyay A, Katiyar A, Bhushan B, Anvikar A. Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India. Sci Rep 2023; 13:14847. [PMID: 37684328 PMCID: PMC10491582 DOI: 10.1038/s41598-023-42065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
The various strains and mutations of SARS-CoV-2 have been tracked using several forms of genomic classification systems. The present study reports high-throughput sequencing and analysis of 99 SARS-CoV-2 specimens from Western Uttar Pradesh using sequences obtained from the GISAID database, followed by phylogeny and clade classification. Phylogenetic analysis revealed that Omicron lineages BA-2-like (55.55%) followed by Delta lineage-B.1.617.2 (45.5%) were predominantly circulating in this area Signature substitution at positions S: N501Y, S: D614G, S: T478K, S: K417N, S: E484A, S: P681H, and S: S477N were commonly detected in the Omicron variant-BA-2-like, however S: D614G, S: L452R, S: P681R and S: D950N were confined to Delta variant-B.1.617.2. We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. Based on the phylogenetic diversification studies and similar changes in other lineages, our analysis revealed indications of convergent evolution as the virus adjusts to the shifting immunological profile of its human host. To the best of our knowledge, this study is an approach to comprehensively map the circulating SARS-CoV-2 strains from Western Uttar Pradesh using an integrated approach of whole genome sequencing and phylogenetic analysis. These findings will be extremely valuable in developing a structured approach toward pandemic preparedness and evidence-based intervention plans in the future.
Collapse
Affiliation(s)
- Gauri Misra
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India.
| | - Ashrat Manzoor
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Meenu Chopra
- National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Upadhyay
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Amit Katiyar
- Bioinformatics Facility, Centralized Core Research Facility, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Brij Bhushan
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| | - Anup Anvikar
- Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), A-32, Sector-62, Institutional Area, Noida, UP, 201309, India
| |
Collapse
|
4
|
Dhanasooraj D, Viswanathan P, Saphia S, Jose BP, Parambath FC, Sivadas S, Akash NP, Vimisha TV, Nair PR, Mohan A, Hafeez N, Poovullathi JK, Vadekkandiyil S, Govindan SKK, Khobragade R, Aravindan KP, Radhakrishnan C. Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala. Front Public Health 2022; 10:974667. [PMID: 36091505 PMCID: PMC9454329 DOI: 10.3389/fpubh.2022.974667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 01/21/2023] Open
Abstract
Next Generation Sequencing (NGS) is the gold standard for the detection of new variants of SARS-CoV-2 including those which have immune escape properties, high infectivity, and variable severity. This test is helpful in genomic surveillance, for planning appropriate and timely public health interventions. But labs with NGS facilities are not available in small or medium research settings due to the high cost of setting up such a facility. Transportation of samples from many places to few centers for NGS testing also produces delays due to transportation and sample overload leading in turn to delays in patient management and community interventions. This becomes more important for patients traveling from hotspot regions or those suspected of harboring a new variant. Another major issue is the high cost of NGS-based tests. Thus, it may not be a good option for an economically viable surveillance program requiring immediate result generation and patient follow-up. The current study used a cost-effective facility which can be set up in a common research lab and which is replicable in similar centers with expertise in Sanger nucleotide sequencing. More samples can be processed at a time and can generate the results in a maximum of 2 days (1 day for a 24 h working lab). We analyzed the nucleotide sequence of the Receptor Binding Domain (RBD) region of SARS-CoV-2 by the Sanger sequencing using in-house developed methods. The SARS-CoV-2 variant surveillance was done during the period of March 2021 to May 2022 in the Northern region of Kerala, a state in India with a population of 36.4 million, for implementing appropriate timely interventions. Our findings broadly agree with those from elsewhere in India and other countries during the period.
Collapse
Affiliation(s)
- Dhananjayan Dhanasooraj
- Multidisciplinary Research Unit, Government Medical College, Kozhikode, Kerala, India,Dhananjayan Dhanasooraj
| | - Prasanth Viswanathan
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - Shammy Saphia
- Multidisciplinary Research Unit, Government Medical College, Kozhikode, Kerala, India
| | - Beena Philomina Jose
- Department of Microbiology, Government Medical College, Kozhikode, Kerala, India
| | | | - Saritha Sivadas
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - N. P. Akash
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - T. V. Vimisha
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | | | - Anuja Mohan
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | - Nimin Hafeez
- Virus Research and Diagnostic Laboratory, Government Medical College, Kozhikode, Kerala, India
| | | | - Shameer Vadekkandiyil
- Department of General Medicine, Government Medical College, Kozhikode, Kerala, India
| | | | - Rajan Khobragade
- Department of Health and Family Welfare, Government of Kerala, Thiruvananthapuram, India
| | | | - Chandni Radhakrishnan
- Department of Emergency Medicine, Government Medical College, Kozhikode, Kerala, India,*Correspondence: Chandni Radhakrishnan
| |
Collapse
|
5
|
Cao J, Liu Y, Zhou M, Dong S, Hou Y, Jia X, Lan X, Zhang Y, Guo J, Xiao G, Wang W. Screening of Botanical Drugs against SARS-CoV-2 Entry Reveals Novel Therapeutic Agents to Treat COVID-19. Viruses 2022; 14:v14020353. [PMID: 35215943 PMCID: PMC8877376 DOI: 10.3390/v14020353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 01/27/2023] Open
Abstract
An escalating pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely impacted global health. There is a severe lack of specific treatment options for diseases caused by SARS-CoV-2. In this study, we used a pseudotype virus (pv) containing the SARS-CoV-2 S glycoprotein to screen a botanical drug library containing 1037 botanical drugs to identify agents that prevent SARS-CoV-2 entry into the cell. Our study identified four hits, including angeloylgomisin O, schisandrin B, procyanidin, and oleanonic acid, as effective SARS-CoV-2 S pv entry inhibitors in the micromolar range. A mechanistic study revealed that these four agents inhibited SARS-CoV-2 S pv entry by blocking spike (S) protein-mediated membrane fusion. Furthermore, angeloylgomisin O and schisandrin B inhibited authentic SARS-CoV-2 with a high selective index (SI; 50% cytotoxic concentration/50% inhibition concentration). Our drug combination studies performed in cellular antiviral assays revealed that angeloylgomisin O has synergistic effects in combination with remdesivir, a drug widely used to treat SARS-CoV-2-mediated infections. We also showed that two hits could inhibit the newly emerged alpha (B.1.1.7) and beta (B.1.351) variants. Our findings collectively indicate that angeloylgomisin O and schisandrin B could inhibit SARS-CoV-2 efficiently, thereby making them potential therapeutic agents to treat the coronavirus disease of 2019.
Collapse
Affiliation(s)
- Junyuan Cao
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
| | - Minmin Zhou
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Dong
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxia Hou
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoying Jia
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohao Lan
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Yueli Zhang
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jiao Guo
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-87198232
| |
Collapse
|
6
|
Deval H, Nyayanit DA, Mishra SK, Yadav PD, Zaman K, Shankar P, Misra BR, Behera SP, Kumar N, Kumar A, Bhardwaj P, Dwivedi GR, Singh R, Shete AM, Pandit P, Pandey AK, Yadav GK, Gupta S, Kumar M, Kavathekar A, Singh RS, Prajapati S, Kant R. Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Front Med (Lausanne) 2022; 8:781287. [PMID: 35071267 PMCID: PMC8777020 DOI: 10.3389/fmed.2021.781287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Hirawati Deval
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Pragya D. Yadav
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Prem Shankar
- All India Institute of Medical Sciences, Gorakhpur, India
| | - Brij R. Misra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Niraj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Abhinendra Kumar
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Pooja Bhardwaj
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Gaurav Raj Dwivedi
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Anita M. Shete
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Priyanka Pandit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Ashok K. Pandey
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Girijesh Kumar Yadav
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Shashi Gupta
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Manoj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Asif Kavathekar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Ravi Shankar Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sanjay Prajapati
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| |
Collapse
|
7
|
Jha N, Hall D, Kanakan A, Mehta P, Maurya R, Mir Q, Gill HM, Janga SC, Pandey R. Geographical Landscape and Transmission Dynamics of SARS-CoV-2 Variants Across India: A Longitudinal Perspective. Front Genet 2022; 12:753648. [PMID: 34976008 PMCID: PMC8719586 DOI: 10.3389/fgene.2021.753648] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/17/2021] [Indexed: 12/21/2022] Open
Abstract
Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020–Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January–February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.
Collapse
Affiliation(s)
- Neha Jha
- Integrative Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Dwight Hall
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States
| | - Akshay Kanakan
- Integrative Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Priyanka Mehta
- Integrative Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Ranjeet Maurya
- Integrative Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Quoseena Mir
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States
| | - Hunter Mathias Gill
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Indianapolis, IN, United States
| | - Rajesh Pandey
- Integrative Genomics of Host-Pathogen (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
8
|
Limaye S, Kasibhatla SM, Ramtirthkar M, Kinikar M, Kale MM, Kulkarni-Kale U. Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak. Viruses 2021; 13:2238. [PMID: 34835044 PMCID: PMC8619538 DOI: 10.3390/v13112238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as 'Others' in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus-host interactions, differential glycosylation, immune evasion, and escape from neutralization.
Collapse
Affiliation(s)
- Sanket Limaye
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
| | - Sunitha M. Kasibhatla
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune 411008, India
| | - Mukund Ramtirthkar
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (M.R.); (M.M.K.)
| | - Meenal Kinikar
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
| | - Mohan M. Kale
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (M.R.); (M.M.K.)
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
| |
Collapse
|
9
|
Insights from genomes and genetic epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh. Epidemiol Infect 2021. [PMCID: PMC8367868 DOI: 10.1017/s0950268821001424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with a limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13324X. We identified 564 high-quality SARS-CoV-2 variants. A total of 18 variants mapped to reverse transcription polymerase chain reaction primer/probe sites, and four variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (20A, 20B and 20C) (94%), whereas 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Collapse
|
10
|
Srivastava S, Banu S, Singh P, Sowpati DT, Mishra RK. SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants. J Biosci 2021; 46:22. [PMID: 33737495 PMCID: PMC7895735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 04/01/2024]
Abstract
Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.
Collapse
Affiliation(s)
- Surabhi Srivastava
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Sofia Banu
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Priya Singh
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Divya Tej Sowpati
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Rakesh K. Mishra
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| |
Collapse
|