COVID-19 Research

COVID-19 Open Research

The recent declaration of COVID-19 as a global pandemic by the World Health Organisation has prompted us to make the relevant Data, Research and Resources at the Vinod Scaria Lab at CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) in an open format to ensure that they are widely accessible as well as relevant. The programme would embrace the concepts of open-source and open access.

Protocols

Jolly B, Scaria VComputational Analysis and Phylogenetic clustering of SARS-Cov-2 GenomesBio-protocol (2021) Vol 11, Iss 8, April 20, 2021 https://doi.org/10.21769/BioProtoc.3999
Bhoyar, Rahul C., et al. An Amplicon-based Approach for Sequencing of SARS-CoV-2 Using CovidSeq Assay on Illumina Miseq Sequencing Platforms.STAR Protocols (2021)
Poojary M, Shantaraman A, Jolly B, Scaria V Computational Protocol for Assembly and Analysis of SARS-nCoV-2 Genomes Research Reports (2020)
Samatha MathewStandard Operating Protocol for Capillary sequencing based screening of SARS-CoV-2 S-gene variants (SpikeSeq v1.0)

Publications and Preprints

Publications

Gupta, V., Bhoyar, R. C., Jain, A., Srivastava, et al, Asymptomatic reinfection in two healthcare workers from India with genetically distinct SARS-CoV-2. Clinical Infectious Diseases (2020) ciaa1451, https://doi.org/10.1093/cid/ciaa1451
Govindaraj GM, Krishnakumar P, Scaria V, Athulya E, Ajithkumar VT, Dongre AR. Building on an Ad Hoc Covid-19 Response to Enhance Community-based Care for Vulnerable Children in Kerala, India. NEJM Catal Innov Care Deliv. (2020) doi: 10.1056/CAT.20.0543.
Banu S, Jolly B, Mukherjee M, Singh P, Khan S, Zaveri L, Shambhavi S, Gaur N, Mishra RK, Scaria V, Sowpati DT A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates Open Forum Infectious Diseases, (2020), ofaa434, https://doi.org/10.1093/ofid/ofaa434
Jain A, Rophina M, Mahajan S, Krishnan BB, Sharma M, Mandal S, Fernandez T, Sultanji S, Mathew S, Sivasubbu S, Scaria V Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays International Journal of Infectious Diseases https://doi.org/10.1016/j.ijid.2020.10.086
Bhoyar RC, et al, High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing PLoS ONE (2021) Accepted
Radhakrishnan C, Divakar MK, Jain A et al, Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions Frontiers in Genetics (2021) Accepted
Yadav SP, Thakkar D, Bhoyar RC, Jain A, Wadhwa T, Imran M, Jolly B, Divakar MK, Kapoor R, Rastogi N, Sharma D, Sehgal P, Ranjan G, Sivasubbu S, Sarma S, Scaria VAsymptomatic reactivation of SARS-CoV-2 in a child with neuroblastoma characterised by whole genome sequencing,IDCases (2021), e01018, https://doi.org/10.1016/j.idcr.2020.e01018.
Rani, PR., Imran M, Lakshmi J, Jolly B, Jain A, Surekha A, Senthivel V, et al.Symptomatic Reinfection of Sars-cov-2 with Spike Protein Variant N440K Associated with Immune Escape. J Med Virol . 2021 Apr 5. doi: 10.1002/jmv.26997
J, Beena P., Bani Jolly, Neethu John, Rahul C. Bhoyar, Nisha Majeed, Vigneshwar Senthivel, Fairoz C. P, et al. 2021. Genomic Survey of Sars-Cov-2 Vaccine Breakthrough Infections in Healthcare Workers from Kerala, India.Journal of Infection (2021) Accepted
Cotsapas C, Saarela J, Farmer JR, Scaria V, Abraham RS. Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19? J Clin Invest. 2021 Jun 1:149459. doi: 10.1172/JCI149459
Sahana S, Sivadas A, Mangla M, Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, Vidhya AK, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, Devi P, Rajagopal RE, Ramya JE, Devi PN, Bajaj A, Gupta V, Mathew S, Goswami S, Prakash S, Joshi K, Kumla M, Sreedevi S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Sivasubbu S, Scaria V. Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes. Pharmacogenomics. 2021 Jun 18. doi: 10.2217/pgs-2021-0028. Epub ahead of print. PMID: 34142560.
Roja Rani P, Imran M, Vijaya Lakshmi J, Jolly B, Afsar S, Jain A, Divakar MK, Suresh P, Sharma D, Rajesh N, Bhoyar RC, Ankaiah D, Shanthi Kumari S, Ranjan G, Anitha Lavanya V, Rophina M, Umadevi S, Sehgal P, Renuka Devi A, Surekha A, Chandra Sekhar P, Hymavathy R, Vanaja PR, Scaria V, Sivasubbu S. Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh. Epidemiology and Infection. 2021;:1–11.
Devassikutty, FM, Jain A, Edavazhippurath A, Joseph MC, Peedikayil MNT, Scaria V, Sandhya P, and Govindaraj GM.X-Linked Agammaglobulinemia and COVID-19: Two Case Reports and Review of LiteraturePediatric Allergy, Immunology, and Pulmonology.Sep 2021.115-118.http://doi.org/10.1089/ped.2021.0002
Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B and Scaria VESC - a comprehensive resource for SARS-CoV-2 immune escape variants. Nucleic Acids Research (2021) Accepted
Gupta A; Bhoyar RC; Mirza S; Jolly B; Senthivel V; Shamnath A; Divakar MK; Imran M; Gupta V; Agrawal SJ; Mukhida S; Sivasubbu S; Scaria VSARS-CoV-2 vaccine breakthrough infection following a previous infection in a healthcare workerJournal of Infection (2021) https://doi.org/10.1016/j.jinf.2021.10.008
Singh UB, Rophina M, Chaudhry R, Senthivel V, Bala K, Bhoyar RC, Jolly B, Jamshed N, Imran M, Gupta R, Aggarwal P, Divakar MK, Sinha S , Arvinden VR, Bajaj A, Shamnath A, Jain A, COVID CBNAAT CORE GROUP, Scaria V, Sivasubbu S, Guleria RVariants of Concern responsible for SARS-CoV-2 vaccine breakthrough infections from IndiaJ Med Virol . 2021 (Accepted)
Thiruvengadam R, Awasthi A, Medigeshi G, Bhattacharya S, Mani S, Sivasubbu S, Shrivastava T, Samal S, Rathna Murugesan D, Koundinya Desiraju B, Kshetrapal P, Pandey R, Scaria V, Kumar Malik P, Taneja J, Binayke A, Vohra T, Zaheer A, Rathore D, Ahmad Khan N, Shaman H, Ahmed S, Kumar R, Deshpande S, Subramani C, Wadhwa N, Gupta N, Pandey AK, Bhattacharya J, Agrawal A, Vrati S, Bhatnagar S, Garg PK; Department of Biotechnology India Consortium for COVID-19 research. Effectiveness of ChAdOx1 nCoV-19 vaccine against SARS-CoV-2 infection during the delta (B.1.617.2) variant surge in India: a test-negative, case-control study and a mechanistic study of post-vaccination immune responses. Lancet Infect Dis. 2021 Nov 25:S1473-3099(21)00680-0. doi: 10.1016/S1473-3099(21)00680-0.

Preprints

Rophina, M., Pandhare, K., Mangla, M., Shamnath, A., Jolly, B., Sethi, M., & Scaria, V. FaviCoV -a comprehensive manually curated resource for functional genetic variants in SARS-CoV-2.OSF Preprints (2020, November 17). https://doi.org/10.31219/osf.io/wp5tx [Preprint]
Jolly B, Rophina M, Shamnath A, Imran M, Bhoyar RC, Divakar M, Rani PR, Ranjan G, Sehgal P, Chandrasekhar P, Afsar S, Vijaya Lakshmi J, Surekha A, Sivasubbu S, Scaria VGenetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomesbioRxiv 2020.12.24.424332; doi: https://doi.org/10.1101/2020.12.24.424332 [Preprint]
Niyas, V. K. M., Shamnath, A., KJ, R., Bhoyar, R. C., N, V. A., Jolly, B. et al. Genomic analysis of early SARS-CoV-2 breakthrough infections from the state of Kerala suggest a preponderance of variants of concern.OSF Preprints https://doi.org/10.31219/osf.io/vn3xs

genepi-box

genepi-box is an automated computational resource for assembly, analysis and sharing of pathogen genomic data including for SARS-CoV-2.

The resource is built keeping in mind resource limitations in bioinformatics analysis of pathogen genomes.

GitHub - banijolly/genepi-box

Resources for Genomic Epidemiology

Indian SARS-CoV-2 Genome Surveillance Dashboard maintained at the CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) incorporates data from the INSACOG initiative and state surveillance programmes from Kerala, and Maharashtra

#GENESCoV2

Genetic Epidemiology of SARS-CoV-2 in Kerala

The unique partnership between the Department of Health & Family Welfare, Government of Kerala, National health Mission Kerala, CSIR Institute of Genomics & Integrative Biology (CSIR-IGIB) and various clinical and public health centers in Kerala aimed at providing insights into the genetic epidemiology of COVID-19 in Kerala

The initiative of Public Health relevance involves 12 Govt Medical Colleges, State Public Health & Regional Laboratories, Inter-University Centre for Biomedical Research, Central University of Kerala& 14 District Surveillance Units

Outreach in Malayalam from the Lab

NETWORK SUPPORTRead our article which describes the genetic epidemiology of SARS-CoV-2 in India (The Week May 2020)

In Media

Research at the COVID-19 Open featured in News and Media

India’s Covid-19 Numbers Have Fallen. A Third Wave Still Looms NYT 17/08/2021
‘Delta, lineages can’t fully escape immunity, make vax a priority’ ToI 17/08/2021
COVID Data - Open to all Mid-Day 27/12/2020
21 experts you should follow if you want to make sense of the pandemic ZME Science 28/09/2020
Two asymptomatic healthcare workers reinfected with Covid-19 Deccan Herald 14/08/2020
Coronavirus strain predominant in India originated in Europe Rediff 03/09/2020
Open Minds 2020 : Mind over Matter OPEN 31/07/2020
Slight genetic changes of virus don't change strain, say geneticists Business Standard 14/08/2020
COVID-19 Response: Young Scientists Are Among India’s Unsung Heroes The Wire 23/06/2020
Family portrait of novel coronavirus reveals a new type in India The Federal 7/06/2020
India to have own genome data bank to decode COVID-19 virus The New Indian Express 12/06/2020
New data to understand virus origin, mutation The New Indian Express 27/05/2020
An asset to a pandemic PhDs of India 02/06/2020

Meet the people who warn the world about new covid variants

Researchers in the UK had just set the scientific world ablaze with news that a covid variant called B.1.1.7—soon to be referred to as alpha—was to blame for skyrocketing case counts there. Jolly, a third-year PhD student at the CSIR Institute of Genomics and Integrative Biology in New Delhi, expected to find that it was driving infections in her country too.

Genome meets GitHub: Using tech tools, India’s virus hunters track a shape-shifting killer

The danger of new virus variants highlights the importance of keeping a close watch on them. That’s where genomic surveillance helps. Using scientific and technological tools — from virtual networks to GitHub pages — researchers are sharing their updates and building genomic databanks to gain an upper hand on the virus and sharpen the weapons to fight it.

How one of India’s premier research institutes is tracking new SARS-COV2 variants

Vinod Scaria, principal scientist at Delhi-based CSIR-IGIB, and Bani Jolly, a graduate student at the same institution, are among a score of scientists from various laboratories who have been involved in the genome sequencing effort in India.

OPEN MINDS 2020: MIND OVER MATTER , Open

The Covid-19 pandemic has highlighted the need to share genomic data on a global scale. The genetic variants in the virus genome would allow effective tracing of the origin

The COVID-19 Open Research, Data and Resources is an initiative to make available research and resources at his lab at the CSIR Institute of Genomics and Integrative Biology in an open format to ensure they are widely accessible. Scaria’s genome sequencing of the novel coronavirus is now widely used across the world to understand its characteristics.

Talks of Interest

Projects

The following Projects are open and currently underway. The datasets and results are also listed appropriately.

Genomics of COVID-19 Re-Infections and Breakthrough Infections

The COVID-19 Reinfections observatory aims to compile information on COVID-19 reinfections from across the world as a ready reference. The programme also provides an opportunity to refer potential cases for genomic verification.

Genomics and Biology of Long COVID

The LongCOVID India initiative provides a platform for participatory and collaborative research on LongCOVID in India.

Comparative Genomics and Optimal Diagnostics

The aim of the project would be to compile all primers/probes for screening and diagnosis of SARS CoV-2 infection from across the world.

Genome Analysis and Genetic Epidemiology

The aim of the project is to use public data of SARS CoV-2 genomes for understanding the genetic epidemiology of the epidemic.

COVID19Connect App

COVID19CONNECT is an application integrating recent information, resources and a platform to connect citizens, patients, clinicians and researchers during the COVID19 epidemic in India. [Mobile App for Android] [Web Application]

COVID-19 and RARE DISEASES

The COVID-19 and Rare Diseases initiative aims to quantify the effect of COVID-19 on Rare Disease patients.

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