COVID-19

ABOUT THE COVID-19 OPEN INITIATIVE

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.

IN MEDIA

Research at the COVID-19 Open

featured in News and Media

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

COVID-19 Genome Analysis Summaries

The Genome Analysis Summaries provides systematic analysis summaries of genetic sequence variants in SARS-nCoV-2 genomes from across the world to understand whether the efficiency of diagnostics could be impacted by genetic variants. [COVID-19 GENOME WATCHPOST]
Genomic variants in SARS-CoV-2 isolates from India and its impact on diagnostic assays - what we need to know We catalogued a total of 132 primers or probes sequences from the literature and the public domain. Our analysis revealed a total of 125 unique genetic variants in 80 either ...
Posted Aug 20, 2020, 11:34 PM by Vinod Scaria
GENETIC DIVERSITY OF INDIAN SARS-NCOV-2 ISOLATES 15/05/2020 Credits: Inforgraphics: Bani Jolly Data Source: GISAID Acknowledge data submitted from NIMHANS Bengaluru, NCDC Delhi, ICMR NIV Pune, NIBMG Kalyani, GBRC Gandhinagar and Gandhi Medical College, Secunderabad Methods and Resources ...
Posted May 14, 2020, 8:20 AM by Vinod Scaria

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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

Poojary M, Shantaraman A, Jolly B, Scaria V Computational Protocol for Assembly and Analysis of SARS-nCoV-2 Genomes Research Reports (2020) Accepted

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

bioRxiv 2020.08.10.242677; doi: https://doi.org/10.1101/2020.08.10.242677 [Preprint]

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 bioRxiv 2020.09.09.289892; doi: https://doi.org/10.1101/2020.09.09.289892 [Preprint]

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 V Asymptomatic reactivation of SARS-CoV-2 in a child with neuroblastoma characterised by whole genome sequencing, IDCases (2020), e01018, https://doi.org/10.1016/j.idcr.2020.e01018.

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 V Genetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomes bioRxiv 2020.12.24.424332; doi: https://doi.org/10.1101/2020.12.24.424332 [Preprint]

PROJECTS

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

Genomics of COVID-19 Re-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. [Project Data and Details]

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.

[Project Data and Details]

Modeling SARS-nCoV2 Epidemic in India

The aim of the project is to develop methods and approaches to accurately model the epidemic in India and also assess the impact of early interventions. [Project Data and Details]

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. [Blog Post] [Questionnaire]

KERALA INITIATIVE ON ANALYTICS, AI AND OPEN SCIENCE FOR RESPONDING TO EPIDEMICS (KAISER)

KERALA INITIATIVE ON ANALYTICS, AI AND OPEN SCIENCE FOR RESPONDING TO EPIDEMICS (KAISER) is a citizen science initiative relying on open science to be able to prepare, understand and respond to epidemics. This initiative also endeavours to build the much required skill base, resources, data and technologies to be able to help and cater to similar requirements nationally and globally.

Join us