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Rophina M, Sinha A, Biswas D, Basu D, Datta SS, Scaria V. Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases. Transfus Apher Sci 2024; 63:103872. [PMID: 38272782 DOI: 10.1016/j.transci.2024.103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
The DEL phenotype represents an intriguing and challenging aspect of blood group serology. This condition is characterized by an extremely weak expression of the D antigen on red blood cells, to the extent that it often eludes detection through routine serological methods. Identifying the DEL phenotype necessitates more specialized techniques, such as adsorption and elution tests, to reveal the presence of the D antigen. This distinctive phenotype underscores the complexity and subtlety of blood group genetics and highlights the importance of using advanced methods to accurately classify individuals with this condition, as their ability to form anti-D antibodies can have clinical implications during transfusion and pregnancy scenarios. There is a paucity of data for the DEL phenotype in the Indian population, and the molecular basis has not been elucidated yet. Our investigation delves into the genetic underpinnings of two distinct DEL phenotype cases that pose challenges for resolution through conventional serological techniques. We employ next-generation amplicon sequencing to unravel the intricate genetic landscape underlying these cases. In the D-negative donor, the DEL phenotype was first identified serologically, which was subsequently confirmed by molecular analysis. In the second case, it was associated with an anti-D antibody in a D-positive patient. Initial data analysis unveiled a substantial reduction in coverage across the exonic segments of the RHD gene in both samples, suggesting the potential presence of RHD exon deletions. On both occasions, we identified a homozygous intronic RHD polymorphism that is well established to be linked to the RHD* 01EL.32/RHD*DEL32 variant.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Ayesha Sinha
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Durba Biswas
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Debapriya Basu
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India
| | - Suvro Sankha Datta
- Department of Transfusion Medicine, Tata Medical Center, Newtown, Rajarhat, 700160, Kolkata, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India; Vishwanath Cancer Care Foundation, B 702, Neelkanth Business Park Kirol Village, Mumbai, 400 086, India
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2
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Datta SS, Rophina M, Scaria V. Molecular analysis and transfusion management in a rare case of cis-AB blood group: A report from India. Transfus Clin Biol 2024; 31:31-35. [PMID: 37805160 DOI: 10.1016/j.tracli.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Molecular characterization of a rare cis-AB blood group has not been done in the Indian subcontinent. Herein, we report a case of A2B3 blood group in an Indian patient which was subsequently confirmed to be a case of cis-AB phenotype. Blood grouping was performed by the column agglutination technique (CAT), conventional tube technique (CTT) and subsequently, whole exome sequencing for molecular analysis. The patient was initially typed as AB, RhD positive in forward grouping. However, serum grouping showed agglutination (2+) with the B red cells in CAT. In CTT, an extra reaction was observed with A1 red cells and a strong agglutination was seen with Anti-H lectin. Thus, the blood group was identified serologically as A2B3. During the next-generation sequencing, a total of 10 exonic variants in the ABO gene were filtered, of which 2 (rs8176747 and rs7853989) were found to be non-synonymous and occurring on the same allele. The other allele was found to be ABO*A1.01. The sample analyzed in the study was found to carry two previously reported nucleotide changes of cis-AB (c.803G > C and c.526C > G) on the same allele which had not been reported before. Transfusion requirement was managed with type O red cells and type AB plasma.
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Affiliation(s)
- Suvro Sankha Datta
- Department of Transfusion Medicine, Tata Medical Center, Kolkata, India.
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, India; Vishwanath Cancer Care Foundation, B 702, Neelkanth Business Park Kirol Village, Mumbai, 400 086, India.
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3
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Mirza S, Arvinden VR, Rophina M, Bhawalkar J, Khan U, Chothani B, Singh S, Sharma T, Dwivedi A, Pandey E, Garg S, Mukhida SS, Sange ZSA, Bhaumik S, Varughese J, Devkar VY, Singh J, V K A, K V, Mandviwala HSH, Scaria V, Gupta A. Impact of COVID-19 outbreak on healthcare workers in a Tertiary Healthcare Center in India: a cross sectional study. Sci Rep 2024; 14:1504. [PMID: 38233495 PMCID: PMC10794462 DOI: 10.1038/s41598-023-50317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
Numerous speculations have continually emerged, trying to explore the association between COVID-19 infection and a varied range of demographic and clinical factors. Frontline healthcare workers have been the primary group exposed to this infection, and there have been limited global research that examine this cohort. However, while there are a few large studies conducted on Indian healthcare professionals to investigate their potential risk and predisposing factors to COVID-19 infection, to our knowledge there are no studies evaluating the development of long COVID in this population. This cross-sectional study systematically utilized the demographic and clinical data of 3329 healthcare workers (HCW) from a tertiary hospital in India to gain significant insights into the associations between disease prevalence, severity of SARS-Cov-2 infection and long COVID. Most of the study population was found to be vaccinated (2,615, 78.5%), while 654 (19.65%) HCWs were found to be SARS-CoV-2 positive at least once. Of the infected HCWs, 75.1% (491) did not require hospitalization, whereas the rest were hospitalized for an average duration of 9 days. A total of 206 (6.19%) individuals were found to be suffering from long COVID. Persistent weakness/tiredness was the most experienced long-COVID symptom, while females (1.79, 1.25-2.57), individuals who consumed alcohol (1.85, 1.3-2.64) or had blood group B (1.9, 1.33-2.7) were at a significantly higher risk for developing long COVID.
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Affiliation(s)
- Shahzad Mirza
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - V R Arvinden
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Jitendra Bhawalkar
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Uzair Khan
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Bhavin Chothani
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Shivankur Singh
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Tanya Sharma
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Aryan Dwivedi
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Ellora Pandey
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Shivam Garg
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Sahjid Sadrudin Mukhida
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Zeeshan Shabbir Ahmed Sange
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Shalini Bhaumik
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Jessin Varughese
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Vishwamohini Yallappa Devkar
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Jyoti Singh
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - AnjuMol V K
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Veena K
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Husen Shabbir Husen Mandviwala
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aayush Gupta
- Dr. D.Y. Patil Medical College, Hospital and Research Centre, Dr. D.Y. Patil Vidyapeeth, Pimpri, Pune, Maharashtra, 411018, India.
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4
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Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Vatsyayan A, Jolly B, Sivasubbu S, Scaria V. Genetic landscape of human platelet antigen variants in the Indian population analysed from 1029 whole genomes. Int J Immunogenet 2023; 50:134-143. [PMID: 37160415 DOI: 10.1111/iji.12622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Genetic variants in human platelet antigens (HPAs) considered allo- or auto antigens are associated with various disorders, including neonatal alloimmune thrombocytopenia, platelet transfusion refractoriness and post-transfusion purpura. Although global differences in genotype frequencies were observed, the distributions of HPA variants in the Indian population are largely unknown. This study aims to explore the landscape of HPA variants in India to provide a basis for risk assessment and management of related complications. Population-specific frequencies of genetic variants associated with the 35 classes of HPAs (HPA-1 to HPA-35) were estimated by systematically analysing genomic variations of 1029 healthy Indian individuals as well as from global population genome datasets. Allele frequencies of the most clinically relevant HPA systems in the Indian population were found as follows, HPA-1a - 0.884, HPA-1b - 0.117, HPA-2a - 0.941, HPA-2b - 0.059, HPA-3a - 0.653, HPA-3b - 0.347, HPA-4a - 0.999, HPA-4b - 0.0010, HPA-5a - 0.923, HPA-5b - 0.077, HPA-6a - 0.998, HPA-6b - 0.002, HPA-15a - 0.582 and HPA-15b - 0.418. This study provides the first comprehensive analysis of HPA allele and genotype frequencies using large scale representative whole genome sequencing data of the Indian population.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aastha Vatsyayan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Roy SS, Sharma S, Rizvi ZA, Sinha D, Gupta D, Rophina M, Sehgal P, Sadhu S, Tripathy MR, Samal S, Maiti S, Scaria V, Sivasubbu S, Awasthi A, Harshan KH, Jain S, Chowdhury S. G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters. Front Mol Biosci 2023; 10:1133123. [PMID: 37006620 PMCID: PMC10061221 DOI: 10.3389/fmolb.2023.1133123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across >5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.
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Affiliation(s)
- Shuvra Shekhar Roy
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shalu Sharma
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Zaigham Abbas Rizvi
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Dipanjali Sinha
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Divya Gupta
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Mercy Rophina
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Paras Sehgal
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srikanth Sadhu
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Manas Ranjan Tripathy
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Sweety Samal
- Translational Health Science and Technology Institute, Faridabad, 411008, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-National Chemical Laboratory, Pune, 121001, India
| | - Vinod Scaria
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amit Awasthi
- Immuno-biology Laboratory, Infection and Immunology Centre, Translational Health Science and Technology Institute, Faridabad, 121001, India
| | - Krishnan H. Harshan
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, 560029, India
| | - Shantanu Chowdhury
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
- *Correspondence: Shantanu Chowdhury,
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6
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Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Jolly B, Sivasubbu S, Scaria V. Genetic landscape of human neutrophil antigen variants in India from population-scale genomes. HLA 2023; 101:262-269. [PMID: 36502377 DOI: 10.1111/tan.14938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Antibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia, transfusion-related acute lung injury, and other nonhemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. Ten genetic variants in four human genes encoding alleles of HNAs class I-V approved by the International Society of Blood Transfusion-Granulocyte Immunobiology Working Party were used in the analysis. Genetic variants from whole genome sequences of 1029 healthy Indian individuals corresponding to HNA alleles were analyzed. The frequencies of the variants were compared with global population datasets using an in-house computational pipeline. In HNA class I, allele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 encoding HNA-1a, HNA-1b, and HNA-1c were 0.07, 0.8, and 0.13, respectively. HNA class 3 alleles namely SLC44A2*01 (encoding HNA-3a) and SLC44A2*02 (encoding HNA-3b) were found at allele frequencies of 0.78 and 0.22, respectively. The frequencies of ITGAM*01 encoding HNA-4a and ITGAM*02 encoding HNA-4a were 0.95 and 0.05, respectively. Furthermore, allele frequencies of HNA class 5 alleles were 0.32 for ITGAL*01 (encoding HNA-5a) and 0.68 for ITGAL*02 (encoding HNA-5b). Interestingly, it was also found that rs2230433 variant deciding the HNA class 5 alleles, was highly prevalent (78.2%) in the Indian population compared with other global populations. This study presents the first comprehensive report of HNA allele and genotype frequencies in the Indian population using population genome datasets of 1029 individuals. Significant difference was observed in the prevalence of HNA5a and HNA5b in India in comparison to other global populations.
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Affiliation(s)
- Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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7
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Rophina M, Kek TL, Sivasubbu S, Scaria V, Salleh MZ. In silico genotyping of blood group alleles using WGS data: a comparative study of the Orang Asli in Peninsular Malaysia. J Genet 2023; 102:42. [PMID: 37697701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Differences in the distribution of RBC antigens defining the blood group types among different populations have been well established. Fewer studies exist that have explored the blood group profiles of indigenous populations worldwide. With the availability of population-scale genomic datasets, we have explored the blood group profiles of theOrang Aslis, who are the indigenous population in Peninsular Malaysia and provide a systematic comparison of the same with major global population datasets. Variant call files fromwhole genome sequence data (hg19) of 114 Orang Asli were retrieved from The Orang Asli Genome Project. Systematic variant annotations were performed using ANNOVAR and only those variants mapping back to genes associated with 43 blood group systems and transcription factors KLF1 and GATA1 were filtered. Blood group-associated allele and phenotype frequencies were determined and were duly compared with other datasets including Singapore SequencingMalay Project, aboriginal western desert Australians and global population datasets including The 1000 Genomes Project and gnomAD. This study reports four alleles (rs12075, rs7683365, rs586178 and rs2298720) of DUFFY, MNS, RH and KIDD blood group systems which were significantly distinct between indigenous Orang Asli and cosmopolitanMalaysians. Eighteen alleles that belong to 14 blood group systems were found statistically distinct in comparison to global population datasets. Although not much significant differences were observed in phenotypes of most blood group systems, major insights were observed when comparing Orang Asli with aboriginal Australians and cosmopolitanMalaysians.This study serves as the first of its kind to utilize genomic data to interpret blood group antigen profiles of the OrangAsli population. In addition, a systematic comparison of blood group profiles with related populations was also analysed and documented.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 025,
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8
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Rophina M, Scaria V. Genetic epidemiology of human neutrophil antigen variants suggests significant global variability. Int J Immunogenet 2022; 49:345-352. [PMID: 36029282 DOI: 10.1111/iji.12597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/28/2022]
Abstract
Human neutrophil antigens possess significant clinical implications especially in the fields of transfusion and transplantation medicine. Efforts to estimate the prevalence of genetic variations underpinning the antigenic expression are emerging. However, there lacks a precise capture of the global frequency profiles. Our article emphasizes the potential utility of maintaining an organized online repository of evidence on neutrophil antigen-associated genetic variants from published literature and reports. This, in our opinion, is an emerging area and would significantly benefit from the awareness and understanding of population-level diversities.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research-Human Resource Development Centre, Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research-Human Resource Development Centre, Ghaziabad, Uttar Pradesh, India
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9
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Bajaj A, Senthivel V, Bhoyar R, Jain A, Imran M, Rophina M, Divakar MK, Jolly B, Verma A, Mishra A, Sharma D, Deepti S, Sharma G, Bansal R, Yadav R, Scaria V, Naik N, Sivasubbu S. 1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants. Hum Genomics 2022; 16:30. [PMID: 35932045 PMCID: PMC9354277 DOI: 10.1186/s40246-022-00402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/11/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The prevalence and genetic spectrum of cardiac channelopathies exhibit population-specific differences. We aimed to understand the spectrum of cardiac channelopathy-associated variations in India, which is characterised by a genetically diverse population and is largely understudied in the context of these disorders. RESULTS We utilised the IndiGenomes dataset comprising 1029 whole genomes from self-declared healthy individuals as a template to filter variants in 36 genes known to cause cardiac channelopathies. Our analysis revealed 186,782 variants, of which we filtered 470 variants that were identified as possibly pathogenic (440 nonsynonymous, 30 high-confidence predicted loss of function ). About 26% (124 out of 470) of these variants were unique to the Indian population as they were not reported in the global population datasets and published literature. Classification of 470 variants by ACMG/AMP guidelines unveiled 13 pathogenic/likely pathogenic (P/LP) variants mapping to 19 out of the 1029 individuals. Further query of 53 probands in an independent cohort of cardiac channelopathy, using exome sequencing, revealed the presence of 3 out of the 13 P/LP variants. The identification of p.G179Sfs*62, p.R823W and c.420 + 2 T > C variants in KCNQ1, KCNH2 and CASQ2 genes, respectively, validate the significance of the P/LP variants in the context of clinical applicability as well as for large-scale population analysis. CONCLUSION A compendium of ACMG/AMP classified cardiac channelopathy variants in 1029 self-declared healthy Indian population was created. A conservative genotypic prevalence was estimated to be 0.9-1.8% which poses a huge public health burden for a country with large population size like India. In the majority of cases, these disorders are manageable and the risk of sudden cardiac death can be alleviated by appropriate lifestyle modifications as well as treatment regimens/clinical interventions. Clinical utility of the obtained variants was demonstrated using a cardiac channelopathy patient cohort. Our study emphasises the need for large-scale population screening to identify at-risk individuals and take preventive measures. However, we suggest cautious clinical interpretation to be exercised by taking other cardiac channelopathy risk factors into account.
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Affiliation(s)
- Anjali Bajaj
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Vigneshwar Senthivel
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Rahul Bhoyar
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India
| | - Abhinav Jain
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mohamed Imran
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mercy Rophina
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mohit Kumar Divakar
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Bani Jolly
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Ankit Verma
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India
| | - Anushree Mishra
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India
| | - Disha Sharma
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Siddharthan Deepti
- grid.413618.90000 0004 1767 6103Department of Cardiology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029 India
| | - Gautam Sharma
- grid.413618.90000 0004 1767 6103Department of Cardiology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029 India
| | - Raghav Bansal
- grid.413618.90000 0004 1767 6103Department of Cardiology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029 India
| | - Rakesh Yadav
- grid.413618.90000 0004 1767 6103Department of Cardiology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029 India
| | - Vinod Scaria
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Nitish Naik
- grid.413618.90000 0004 1767 6103Department of Cardiology, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029 India
| | - Sridhar Sivasubbu
- grid.417639.eCSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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10
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Sahana S, Bhoyar RC, Sivadas A, Jain A, Imran M, Rophina M, Senthivel V, Kumar Diwakar M, Sharma D, Mishra A, Sivasubbu S, Scaria V. Pharmacogenomic landscape of Indian population using whole genomes. Clin Transl Sci 2022; 15:866-877. [PMID: 35338580 PMCID: PMC9010271 DOI: 10.1111/cts.13153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Ethnic differences in pharmacogenomic (PGx) variants have been well documented in literature and could significantly impact variability in response and adverse events to therapeutics. India is a large country with diverse ethnic populations of distinct genetic architecture. India's national genome sequencing initiative (IndiGen) provides a unique opportunity to explore the landscape of PGx variants using population-scale whole genome sequences. We have analyzed the IndiGen variation dataset (N = 1029 genomes) along with global population scale databases to map the most prevalent clinically actionable and potentially deleterious PGx variants among Indians. Differential frequencies for the known and novel variants were studied and interaction of the disrupted PGx genes affecting drug responses were analyzed by performing a pathway analysis. We have highlighted significant differences in the allele frequencies of clinically actionable PGx variants in Indians when compared to the global populations. We identified 134 mostly common (allele frequency [AF] > 0.1) potentially deleterious PGx variants that could alter or inhibit the function of 102 pharmacogenes in Indians. We also estimate that on, an average, each Indian individual carried eight PGx variants (single nucleotide variants) that have a direct impact on the choice of treatment or drug dosing. We have also highlighted clinically actionable PGx variants and genes for which preemptive genotyping is most recommended for the Indian population. The study has put forward the most comprehensive PGx landscape of the Indian population from whole genomes that could enable optimized drug selection and genotype-guided prescriptions for improved therapeutic outcomes and minimizing adverse events.
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Affiliation(s)
- S Sahana
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohit Kumar Diwakar
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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11
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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, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, Ramya J E, Devi P N, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, Meyakumla, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S. Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes. J Genet Eng Biotechnol 2021; 19:183. [PMID: 34905135 PMCID: PMC8671593 DOI: 10.1186/s43141-021-00268-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022]
Abstract
Background Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient’s ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood. However, India has a limited number of genetic studies reported for autoinflammatory disorders till date. The whole genome sequencing and analysis of 1029 Indian individuals performed under the IndiGen project persuaded us to perform the genetic epidemiology of the autoinflammatory disorders in India. Results We have systematically annotated the genetic variants of 56 genes implicated in autoinflammatory disorder. These genetic variants were reclassified into five categories (i.e., pathogenic, likely pathogenic, benign, likely benign, and variant of uncertain significance (VUS)) according to the American College of Medical Genetics and Association of Molecular pathology (ACMG-AMP) guidelines. Our analysis revealed 20 pathogenic and likely pathogenic variants with significant differences in the allele frequency compared with the global population. We also found six causal founder variants in the IndiGen dataset belonging to different ancestry. We have performed haplotype prediction analysis for founder mutations haplotype that reveals the admixture of the South Asian population with other populations. The cumulative carrier frequency of the autoinflammatory disorder in India was found to be 3.5% which is much higher than reported. Conclusion With such frequency in the Indian population, there is a great need for awareness among clinicians as well as the general public regarding the autoinflammatory disorder. To the best of our knowledge, this is the first and most comprehensive population scale genetic epidemiological study being reported from India. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00268-2.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Vidhya A K
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha B M
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - Ezhil Ramya J
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Nirmala Devi P
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Meyakumla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India
| | - Sreedevi S
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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12
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Rophina M, Pandhare K, Jadhao S, Nagaraj SH, Scaria V. BGvar: A comprehensive resource for blood group immunogenetics. Transfus Med 2021; 32:229-236. [PMID: 34897852 DOI: 10.1111/tme.12844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Blood groups form the basis of effective and safe blood transfusion. There are about 43 well-recognised human blood group systems presently known. Blood groups are molecularly determined by the presence of specific antigens on the red blood cells and are genetically determined and inherited following Mendelian principles. The lack of a comprehensive, relevant, manually compiled and genome-ready dataset of red cell antigens limited the widespread application of genomic technologies to characterise and interpret the blood group complement of an individual from genomic datasets. MATERIALS AND METHODS A range of public datasets was used to systematically annotate the variation compendium for its functionality and allele frequencies across global populations. Details on phenotype or relevant clinical importance were collated from reported literature evidence. RESULTS We have compiled the Blood Group Associated Genomic Variant Resource (BGvar), a manually curated online resource comprising all known human blood group related allelic variants including a total of 1700 International Society of Blood Transfusion approved alleles and 1706 alleles predicted and curated from literature reports. This repository includes 1682 single nucleotide variations (SNVs), 310 Insertions, Deletions (InDels) and Duplications (Copy Number Variations) and about 1360 combination mutations corresponding to 43 human blood group systems and 2 transcription factors. This compendium also encompasses gene fusion and rearrangement events occurring in human blood group genes. CONCLUSION To the best of our knowledge, BGvar is a comprehensive and a user-friendly resource with most relevant collation of blood group alleles in humans. BGvar is accessible online at URL: http://clingen.igib.res.in/bgvar/.
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Affiliation(s)
- Mercy Rophina
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Kavita Pandhare
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Sudhir Jadhao
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Shivashankar H Nagaraj
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,Translational Research Institute, Brisbane, Australia
| | - Vinod Scaria
- Genome Informatics and Big Data, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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13
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Dhar MS, Marwal R, VS R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, VR A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 PMCID: PMC7612010 DOI: 10.1126/science.abj9932] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/06/2021] [Indexed: 01/16/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A. Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden VR
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - The Indian SARS-CoV-2 Genomics Consortium (INSACOG)‡
- National Centre for Disease Control, Delhi, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Ravindra K. Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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14
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Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V, Naushin S, Rophina M, Mellan TA, Mishra S, Whittaker C, Fatihi S, Datta M, Singh P, Sharma U, Ujjainiya R, Bhatheja N, Divakar MK, Singh MK, Imran M, Senthivel V, Maurya R, Jha N, Mehta P, A V, Sharma P, Vr A, Chaudhary U, Soni N, Thukral L, Flaxman S, Bhatt S, Pandey R, Dash D, Faruq M, Lall H, Gogia H, Madan P, Kulkarni S, Chauhan H, Sengupta S, Kabra S, Gupta RK, Singh SK, Agrawal A, Rakshit P, Nandicoori V, Tallapaka KB, Sowpati DT, Thangaraj K, Bashyam MD, Dalal A, Sivasubbu S, Scaria V, Parida A, Raghav SK, Prasad P, Sarin A, Mayor S, Ramakrishnan U, Palakodeti D, Seshasayee ASN, Bhat M, Shouche Y, Pillai A, Dikid T, Das S, Maitra A, Chinnaswamy S, Biswas NK, Desai AS, Pattabiraman C, Manjunatha MV, Mani RS, Arunachal Udupi G, Abraham P, Atul PV, Cherian SS. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science 2021; 374:995-999. [PMID: 34648303 DOI: 10.1101/2021.06.02.21258076] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.
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Affiliation(s)
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | | | | | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Viren Sardana
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Salwa Naushin
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Thomas A Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | - Uma Sharma
- National Centre for Disease Control, Delhi, India
| | - Rajat Ujjainiya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Nitin Bhatheja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Ranjeet Maurya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Neha Jha
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyanka Mehta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Vivekanand A
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Pooja Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Arvinden Vr
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Namita Soni
- National Centre for Disease Control, Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | - Hemlata Lall
- National Centre for Disease Control, Delhi, India
| | - Hema Gogia
- National Centre for Disease Control, Delhi, India
| | - Preeti Madan
- National Centre for Disease Control, Delhi, India
| | | | | | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
| | | | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | | | - Anurag Agrawal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy for Scientific and Innovative Research, Ghaziabad, India
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15
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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, Scaria V, Sivasubbu S, Guleria R. Variants of concern responsible for SARS-CoV-2 vaccine breakthrough infections from India. J Med Virol 2021; 94:1696-1700. [PMID: 34786733 PMCID: PMC8662202 DOI: 10.1002/jmv.27461] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/08/2022]
Abstract
Emerging reports of SARS‐CoV‐2 breakthrough infections entail methodical genomic surveillance for determining the efficacy of vaccines. This study elaborates genomic analysis of isolates from breakthrough infections following vaccination with AZD1222/Covishield and BBV152/Covaxin. Variants of concern B.1.617.2 and B.1.1.7 responsible for cases surge in April–May 2021 in Delhi, were the predominant lineages among breakthrough infections.
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Affiliation(s)
- Urvashi B Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Kiran Bala
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Nayer Jamshed
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Ritu Gupta
- Department of Laboratory Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Mohit K Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Subrata Sinha
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - V R Arvinden
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Anjali Bajaj
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Afra Shamnath
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | | | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, India
| | - Randeep Guleria
- Department of Pulmonary Critical Care & Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
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16
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Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B, Scaria V. ESC: a comprehensive resource for SARS-CoV-2 immune escape variants. Nucleic Acids Res 2021; 50:D771-D776. [PMID: 34643704 PMCID: PMC8728294 DOI: 10.1093/nar/gkab895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/13/2022] Open
Abstract
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have built a database with precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 5258 variants accounting for 2068 unique variants tested against 230 antibodies, patient convalescent plasma and vaccine breakthrough events. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape variants which would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.
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Affiliation(s)
- Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Afra Shamnath
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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17
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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; 22:603-618. [PMID: 34142560 PMCID: PMC8216321 DOI: 10.2217/pgs-2021-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. Materials & methods: We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug–gene (pharmacogenetic), drug–drug and drug–drug–gene interactions associated with COVID-19 therapy in the Indian population. Results: We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants. COVID-19-associated pharmacogenes were substantially overlapped with those of metabolic disorder therapeutics. CYP3A4, ABCB1 and ALB are the most shared pharmacogenes. Fifteen COVID-19 therapeutics were predicted as likely drug–drug interaction candidates when used with four CYP inhibitor drugs. Conclusion: Our findings provide actionable insights for future validation studies and improved clinical decisions for COVID-19 therapy in Indians.
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Affiliation(s)
- S Sahana
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Mohit Mangla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Abhinav Jain
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kavita Pandhare
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Anushree Mishra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Disha Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthivel
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mercy Rophina
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Arushi Batra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sumit Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Sanjay Siwach
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra, 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra, 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand, 825301, India
| | - A K Vidhya
- Department of Biochemistry, Dr. Kongu Science & Art College, Erode, Tamil Nadu, 638107, India
| | - Suman Jain
- Thalassemia & Sickle cell Society, Hyderabad, Telangana, 500052, India
| | - Debasis Dash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Pabitha Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | | | - J Ezhil Ramya
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - P Nirmala Devi
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu, 627011, India
| | - Anjali Bajaj
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vishu Gupta
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Samatha Mathew
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sangam Goswami
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Savinitha Prakash
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Kandarp Joshi
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Meya Kumla
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - S Sreedevi
- Department of Microbiology, St. Pious X Degree & PG College for Women, Hyderabad, Telangana, 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology & Leprology, Regional Institute of Medical Sciences, Imphal, Manipur, 795004, India
| | - Rohit Yadav
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science & Technology, Jorhat, Assam, 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra, 411018, India
| | - Mitali Mukerji
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sivaprakash Ramalingam
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - B K Binukumar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
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18
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Radhakrishnan C, Divakar MK, Jain A, Viswanathan P, Bhoyar RC, Jolly B, Imran M, Sharma D, Rophina M, Ranjan G, Sehgal P, Jose BP, Raman RV, Kesavan TN, George K, Mathew S, Poovullathil JK, Keeriyatt Govindan SK, Nair PR, Vadekkandiyil S, Gladson V, Mohan M, Parambath FC, Mangla M, Shamnath A, Sivasubbu S, Scaria V. Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions. Front Genet 2021; 12:630542. [PMID: 33815467 PMCID: PMC8010186 DOI: 10.3389/fgene.2021.630542] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/12/2021] [Indexed: 12/04/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.
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Affiliation(s)
| | - Mohit Kumar Divakar
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Abhinav Jain
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Rahul C. Bhoyar
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Bani Jolly
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Mohamed Imran
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Disha Sharma
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mercy Rophina
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Gyan Ranjan
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Paras Sehgal
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | | | | | | | | | | | | | | | | | | | | | | | - Mohit Mangla
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Afra Shamnath
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Sridhar Sivasubbu
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Vinod Scaria
- Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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19
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Bhoyar RC, Jain A, Sehgal P, Divakar MK, Sharma D, Imran M, Jolly B, Ranjan G, Rophina M, Sharma S, Siwach S, Pandhare K, Sahoo S, Sahoo M, Nayak A, Mohanty JN, Das J, Bhandari S, Mathur SK, Kumar A, Sahlot R, Rojarani P, Lakshmi JV, Surekha A, Sekhar PC, Mahajan S, Masih S, Singh P, Kumar V, Jose B, Mahajan V, Gupta V, Gupta R, Arumugam P, Singh A, Nandy A, P. V. R, Jha RM, Kumari A, Gandotra S, Rao V, Faruq M, Kumar S, Reshma G. B, Varma G. N, Roy SS, Sengupta A, Chattopadhyay S, Singhal K, Pradhan S, Jha D, Naushin S, Wadhwa S, Tyagi N, Poojary M, Scaria V, Sivasubbu S. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLoS One 2021; 16:e0247115. [PMID: 33596239 PMCID: PMC7888613 DOI: 10.1371/journal.pone.0247115] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023] Open
Abstract
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.
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Affiliation(s)
- Rahul C. Bhoyar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Paras Sehgal
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sumit Sharma
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sanjay Siwach
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Kavita Pandhare
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Swayamprabha Sahoo
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Maheswata Sahoo
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Ananya Nayak
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Jatindra Nath Mohanty
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Jayashankar Das
- Institute of Medical Sciences and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | | | | | - Anshul Kumar
- Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | - Rahul Sahlot
- Sawai Man Singh Medical College, Jaipur, Rajasthan, India
| | | | | | | | | | - Shelly Mahajan
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Shet Masih
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Pawan Singh
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vipin Kumar
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Blessy Jose
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vidur Mahajan
- Center for Advanced Research in Imaging, Neuroscience & Genomics, New Delhi, Delhi, India
| | - Vivek Gupta
- Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India
| | - Rakesh Gupta
- Government Institute of Medical Sciences, NOIDA, Uttar Pradesh, India
| | - Prabhakar Arumugam
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Anjali Singh
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Ananya Nandy
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Ragavendran P. V.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Rakesh Mohan Jha
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Anupama Kumari
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sheetal Gandotra
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Vivek Rao
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mohammed Faruq
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sanjeev Kumar
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Betsy Reshma G.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Narendra Varma G.
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Shuvra Shekhar Roy
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Antara Sengupta
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sabyasachi Chattopadhyay
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Shalini Pradhan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Diksha Jha
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Salwa Naushin
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Saruchi Wadhwa
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Nishu Tyagi
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Mukta Poojary
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy for Scientific and Innovative Research, Human Resource Development Centre Campus, Ghaziabad, Uttar Pradesh, India
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20
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Rophina M, Sharma D, Poojary M, Scaria V. Circad: a comprehensive manually curated resource of circular RNA associated with diseases. Database (Oxford) 2021; 2020:5812714. [PMID: 32219412 PMCID: PMC7100626 DOI: 10.1093/database/baaa019] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/22/2020] [Accepted: 02/17/2020] [Indexed: 01/17/2023]
Abstract
Circular RNAs (circRNAs) are unique transcript isoforms characterized by back splicing of exon ends to form a covalently closed loop or circular conformation. These transcript isoforms are now known to be expressed in a variety of organisms across the kingdoms of life. Recent studies have shown the role of circRNAs in a number of diseases and increasing evidence points to their potential application as biomarkers in these diseases. We have created a comprehensive manually curated database of circular RNAs associated with diseases. This database is available at URL http://clingen.igib.res.in/circad/. The Database lists more than 1300 circRNAs associated with 150 diseases and mapping to 113 International Statistical Classification of Diseases (ICD) codes with evidence of association linked to published literature. The database is unique in many ways. Firstly, it provides ready-to-use primers to work with, in order to use circRNAs as biomarkers or to perform functional studies. It additionally lists the assay and PCR primer details including experimentally validated ones as a ready reference to researchers along with fold change and statistical significance. It also provides standard disease nomenclature as per the ICD codes. To the best of our knowledge, circad is the most comprehensive and updated database of disease associated circular RNAs. Availability: http://clingen.igib.res.in/circad/
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Affiliation(s)
- Mercy Rophina
- Genome Informatics Department, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, District-South Delhi, New Delhi-110025, India
| | - Disha Sharma
- Genome Informatics Department, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, District-South Delhi, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), AcSIR headquarters, CSIR-HRDC campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh -201002, India
| | - Mukta Poojary
- Genome Informatics Department, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, District-South Delhi, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), AcSIR headquarters, CSIR-HRDC campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh -201002, India
| | - Vinod Scaria
- Genome Informatics Department, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, District-South Delhi, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), AcSIR headquarters, CSIR-HRDC campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh -201002, India
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21
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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 N, Jha GN, Ashrafi N, Mishra PK, A. K. V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma R, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B. M. P, Rajagopal RE, J. ER, P. ND, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, S. S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B. K. B, Scaria V, Sivasubbu S. IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. Nucleic Acids Res 2021; 49:D1225-D1232. [PMID: 33095885 PMCID: PMC7778947 DOI: 10.1093/nar/gkaa923] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 10/22/2020] [Indexed: 12/15/2022] Open
Abstract
With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as 'IndiGenomes' http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.
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Affiliation(s)
- Abhinav Jain
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kavita Pandhare
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Disha Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Mohamed Imran
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vigneshwar Senthivel
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mohit Kumar Divakar
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mercy Rophina
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Bani Jolly
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Arushi Batra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sumit Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sanjay Siwach
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Arun G Jadhao
- Department of Zoology, RTM Nagpur University, Nagpur, Maharashtra 440033, India
| | - Nikhil V Palande
- Department of Zoology, Shri Mathuradas Mohota College of Science, Nagpur, Maharashtra 440009, India
| | - Ganga Nath Jha
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Nishat Ashrafi
- Department of Anthropology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Prashant Kumar Mishra
- Department of Biotechnology, Vinoba Bhave University, Hazaribag, Jharkhand 825301, India
| | - Vidhya A. K.
- Department of Biochemistry, Dr. Kongu Science and Art College, Erode, Tamil Nadu 638107, India
| | - Suman Jain
- Thalassemia and Sickle cell Society, Hyderabad, Telangana 500052, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | | | - Andrew Vanlallawma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram 796004, India
| | - Ranjan Jyoti Sarma
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram 796004, India
| | | | | | - Radha Mahadevan
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Sunitha Kandasamy
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Pabitha B. M.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | | | - Ezhil Ramya J.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Nirmala Devi P.
- TVMC, Tirunelveli Medical College, Tirunelveli, Tamil Nadu 627011, India
| | - Anjali Bajaj
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vishu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sangam Goswami
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mohit Mangla
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Savinitha Prakash
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kandarp Joshi
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Sreedevi S.
- Department of Microbiology, St.Pious X Degree & PG College for Women, Hyderabad, Telangana 500076, India
| | - Devarshi Gajjar
- Department of Microbiology, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Ronibala Soraisham
- Department of Dermatology, Venereology and Leprology, Regional Institute of Medical Sciences, Imphal, Manipur 795004, India
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Yumnam Silla Devi
- CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Pune, Maharashtra 411018, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sivaprakash Ramalingam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Binukumar B. K.
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Jain A, Rophina M, Mahajan S, Krishnan BB, Sharma M, Mandal S, Fernandez T, Sultanji S, Jolly B, Mathew S, Sivasubbu S, Scaria V. Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays. Int J Infect Dis 2020; 102:460-462. [PMID: 33181329 PMCID: PMC7834429 DOI: 10.1016/j.ijid.2020.10.086] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/26/2022] Open
Abstract
An epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus diseases (C0VID-19) initially reported in Wuhan, China has rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of the disease. Since the virus evolves by accumulating base substitutions, mutations in the viral genome could possibly affect the accuracy of RT-PCR-based detection assays. The recent availability of genomes of SARS-CoV-2 isolates motivated us to assess the presence and potential impact of variations in target sites of the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primer or probe sequences from literature and data available in the public domain. Our analysis revealed that a total of 5862 unique genetic variants mapped to at least one of the 132 primer or probe binding sites in the genome. A total of 29 unique variants were present in ≥ 1% of genomes from at least one of the continents (Asia, Africa, Australia, Europe, North America, and South America) that mapped to 36 unique primers or probes binding sites. Similarly, a total of 27 primer or probe binding sites had cumulative variants frequency of ≥ 1% in the global SARS-CoV-2 genomes. These included primers or probes sites which are used worldwide for molecular diagnosis as well as approved by national and international agencies. We also found 286 SARS-CoV-2 genomic regions with low variability at a continuous stretch of ≥ 20bps that could be potentially used for primer designing. This highlights the need for sequencing genomes of emerging pathogens to enable evidence-based policies for development and approval of diagnostics.
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Affiliation(s)
- Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Mercy Rophina
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Saurabh Mahajan
- St. Joseph's College, Langford Gardens, Bengaluru, Karnataka 560027 India
| | | | - Manasa Sharma
- Ramaiah University of Applied Sciences, Bengaluru, Karnataka 560054, India
| | - Sreya Mandal
- St. Joseph's College, Langford Gardens, Bengaluru, Karnataka 560027 India
| | - Teresa Fernandez
- St. Joseph's College, Langford Gardens, Bengaluru, Karnataka 560027 India
| | - Sumayra Sultanji
- St. Joseph's College, Langford Gardens, Bengaluru, Karnataka 560027 India
| | - Bani Jolly
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Samatha Mathew
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India.
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