Clinical, Serological, Whole Genome Sequence Analyses to Confirm SARS-CoV-2 Reinfection in Patients From Mumbai, India

Frontiers in Medicine

article

Jayanthi Shastri¹  Janani Srinivasa Vasudevan²  Ranjeet Maurya²  Saman Fatihi²  Lipi Thukral²  Anurag Agrawal²  Lancelot Pinto³  Rajesh Pandey²  Sujatha Sunil⁴  Swapneil Parikh¹  Sachee Agrawal¹  Nirjhar Chatterjee¹  Manish Pathak¹  Sakshi Chaudhary¹  Chetan Sharma⁴  Akshay Kanakan²  Vivekanand A² 

[1] Kasturba Hospital for Infectious Disease;Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB);P. D. Hinduja Hospital;International Centre for Genetic Engineering and Biotechnology

关键词: SARS-CoV-2;    COVID-19;    reinfection;    whole genome sequencing;    seroconversion;   

DOI  :  10.3389/fmed.2021.631769

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

CC BY