Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India
Background: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection.Methods: Nasophary...
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Frontiers Media S.A.
2021-03-01
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| Series: | Frontiers in Medicine |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmed.2021.631769/full |
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| author | Jayanthi Shastri Swapneil Parikh Sachee Agrawal Nirjhar Chatterjee Manish Pathak Sakshi Chaudhary Chetan Sharma Akshay Kanakan Vivekanand A Janani Srinivasa Vasudevan Ranjeet Maurya Saman Fatihi Lipi Thukral Anurag Agrawal Lancelot Pinto Rajesh Pandey Sujatha Sunil |
| author_facet | Jayanthi Shastri Swapneil Parikh Sachee Agrawal Nirjhar Chatterjee Manish Pathak Sakshi Chaudhary Chetan Sharma Akshay Kanakan Vivekanand A Janani Srinivasa Vasudevan Ranjeet Maurya Saman Fatihi Lipi Thukral Anurag Agrawal Lancelot Pinto Rajesh Pandey Sujatha Sunil |
| author_sort | Jayanthi Shastri |
| collection | DOAJ |
| description | Background: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection.Methods: Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (WB) samples were collected from paired samples of four individuals who were suspected of SARS-CoV-2 reinfection based on distinct clinical episodes and RT-PCR tests. Details from their case record files and investigations were documented. RNA was extracted from the NP and OP samples and subjected to WGS, and the nucleotide and amino acid sequences were subjected to genome and protein-based functional annotation analyses. Serial serology was performed for Anti-N IgG, Anti- S1 RBD IgG, and sVNT (surrogate virus neutralizing test).Findings: Three patients were more symptomatic with lower Ct values and longer duration of illness. Seroconversion was detected soon after the second episode in three patients. WGS generated a genome coverage ranging from 80.07 to 99.7%. Phylogenetic analysis revealed sequences belonged to G, GR and “Other” clades. A total of 42mutations were identified in all the samples, consisting of 22 non-synonymous, 17 synonymous, two in upstream, and one in downstream regions of the SARS-CoV-2 genome. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the two episodes in all four paired samples.Interpretation: Based on the criteria of genome variations identified by whole genome sequencing and supported by clinical presentation, molecular and serological tests, we were able to confirm reinfections in two patients, provide weak evidence of reinfection in the third patient and unable to rule out a prolonged infection in the fourth. This study emphasizes the importance of detailed analyses of clinical and serological information as well as the virus's genomic variations while assessing cases of SARS-CoV-2 reinfection. |
| first_indexed | 2024-12-14T18:06:37Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2296-858X |
| language | English |
| last_indexed | 2024-12-14T18:06:37Z |
| publishDate | 2021-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Medicine |
| spelling | doaj.art-78e238a2ae6a46eb80aad0569362f3222022-12-21T22:52:22ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2021-03-01810.3389/fmed.2021.631769631769Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, IndiaJayanthi Shastri0Swapneil Parikh1Sachee Agrawal2Nirjhar Chatterjee3Manish Pathak4Sakshi Chaudhary5Chetan Sharma6Akshay Kanakan7Vivekanand A8Janani Srinivasa Vasudevan9Ranjeet Maurya10Saman Fatihi11Lipi Thukral12Anurag Agrawal13Lancelot Pinto14Rajesh Pandey15Sujatha Sunil16Kasturba Hospital for Infectious Disease, Mumbai, IndiaKasturba Hospital for Infectious Disease, Mumbai, IndiaKasturba Hospital for Infectious Disease, Mumbai, IndiaKasturba Hospital for Infectious Disease, Mumbai, IndiaKasturba Hospital for Infectious Disease, Mumbai, IndiaKasturba Hospital for Infectious Disease, Mumbai, IndiaInternational Centre for Genetic Engineering and Biotechnology, New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaP. D. Hinduja Hospital, Mumbai, IndiaCouncil of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, IndiaInternational Centre for Genetic Engineering and Biotechnology, New Delhi, IndiaBackground: SARS-CoV-2 infection may not provide long lasting post-infection immunity. While hundreds of reinfections have reported only a few have been confirmed. Whole genome sequencing (WGS) of the viral isolates from the different episodes is mandatory to establish reinfection.Methods: Nasopharyngeal (NP), oropharyngeal (OP) and whole blood (WB) samples were collected from paired samples of four individuals who were suspected of SARS-CoV-2 reinfection based on distinct clinical episodes and RT-PCR tests. Details from their case record files and investigations were documented. RNA was extracted from the NP and OP samples and subjected to WGS, and the nucleotide and amino acid sequences were subjected to genome and protein-based functional annotation analyses. Serial serology was performed for Anti-N IgG, Anti- S1 RBD IgG, and sVNT (surrogate virus neutralizing test).Findings: Three patients were more symptomatic with lower Ct values and longer duration of illness. Seroconversion was detected soon after the second episode in three patients. WGS generated a genome coverage ranging from 80.07 to 99.7%. Phylogenetic analysis revealed sequences belonged to G, GR and “Other” clades. A total of 42mutations were identified in all the samples, consisting of 22 non-synonymous, 17 synonymous, two in upstream, and one in downstream regions of the SARS-CoV-2 genome. Comparative genomic and protein-based annotation analyses revealed differences in the presence and absence of specific mutations in the virus sequences from the two episodes in all four paired samples.Interpretation: Based on the criteria of genome variations identified by whole genome sequencing and supported by clinical presentation, molecular and serological tests, we were able to confirm reinfections in two patients, provide weak evidence of reinfection in the third patient and unable to rule out a prolonged infection in the fourth. This study emphasizes the importance of detailed analyses of clinical and serological information as well as the virus's genomic variations while assessing cases of SARS-CoV-2 reinfection.https://www.frontiersin.org/articles/10.3389/fmed.2021.631769/fullSARS-CoV-2COVID-19reinfectionwhole genome sequencingseroconversion |
| spellingShingle | Jayanthi Shastri Swapneil Parikh Sachee Agrawal Nirjhar Chatterjee Manish Pathak Sakshi Chaudhary Chetan Sharma Akshay Kanakan Vivekanand A Janani Srinivasa Vasudevan Ranjeet Maurya Saman Fatihi Lipi Thukral Anurag Agrawal Lancelot Pinto Rajesh Pandey Sujatha Sunil Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India Frontiers in Medicine SARS-CoV-2 COVID-19 reinfection whole genome sequencing seroconversion |
| title | Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India |
| title_full | Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India |
| title_fullStr | Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India |
| title_full_unstemmed | Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India |
| title_short | Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India |
| title_sort | clinical serological whole genome sequence analyses to confirm sars cov 2 reinfection in patients from mumbai india |
| topic | SARS-CoV-2 COVID-19 reinfection whole genome sequencing seroconversion |
| url | https://www.frontiersin.org/articles/10.3389/fmed.2021.631769/full |
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