Shastri Jayanthi, Parikh Swapneil, Agrawal Sachee, Chatterjee Nirjhar, Pathak Manish, Chaudhary Sakshi, Sharma Chetan, Kanakan Akshay, A Vivekanand, Srinivasa Vasudevan Janani, Maurya Ranjeet, Fatihi Saman, Thukral Lipi, Agrawal Anurag, Pinto Lancelot, Pandey Rajesh, Sunil Sujatha
Kasturba Hospital for Infectious Disease, Mumbai, India.
International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
Front Med (Lausanne). 2021 Mar 9;8:631769. doi: 10.3389/fmed.2021.631769. eCollection 2021.
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. 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). 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. 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.
新型冠状病毒2型（SARS-CoV-2）感染可能无法提供持久的感染后免疫力。虽然已报告数百例再次感染病例，但仅有少数得到确诊。对不同感染事件中分离出的病毒进行全基因组测序（WGS）对于确定再次感染至关重要。从四名基于不同临床症状和逆转录聚合酶链反应（RT-PCR）检测怀疑再次感染SARS-CoV-2的个体的配对样本中采集了鼻咽（NP）、口咽（OP）和全血（WB）样本。记录了他们病例档案和调查的详细信息。从NP和OP样本中提取RNA并进行WGS，对核苷酸和氨基酸序列进行基于基因组和蛋白质的功能注释分析。对抗N IgG、抗S1 RBD IgG和替代病毒中和试验（sVNT）进行了系列血清学检测。三名患者症状更明显，病毒载量值（Ct值）更低，病程更长。三名患者在第二次发病后不久检测到血清转化。WGS产生的基因组覆盖率在80.07%至99.7%之间。系统发育分析显示序列属于G、GR和“其他”分支。在所有样本中总共鉴定出42个突变，包括22个非同义突变、17个同义突变、SARS-CoV-2基因组上游的两个突变和下游的一个突变。基于全基因组测序确定的基因组变异标准，并得到临床表现、分子和血清学检测的支持，我们能够确认两名患者再次感染，为第三名患者提供了再次感染的微弱证据，并且无法排除第四名患者存在持续性感染。这项研究强调了在评估SARS-CoV-2再次感染病例时详细分析临床和血清学信息以及病毒基因组变异的重要性。
