Key result
Whole genome sequencing combined with clinical and serological data confirmed SARS-CoV-2 reinfection in two patients, provided weak evidence in a third, and could not rule out prolonged infection in a fourth.
Why the study?
SARS-CoV-2 infection may not provide long-lasting immunity, and although many reinfections are reported, few are confirmed using mandatory whole genome sequencing of isolates from different episodes.
Can whole genome sequencing combined with clinical and serological analyses confirm SARS-CoV-2 reinfection?
Case Report (n=4)
No
Can whole genome sequencing combined with clinical and serological analyses confirm SARS-CoV-2 reinfection?
Whole genome sequencing combined with clinical and serological data is crucial for accurately confirming SARS-CoV-2 reinfection versus prolonged infection.
WGS with clinical/serological data may distinguish reinfection from prolonged infection in select cases; leaves open prospective validation before wider use.
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.
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Shastri et al. (2021) conducted a case report in SARS-CoV-2 reinfection (n=4). Whole genome sequencing and serological analysis was evaluated on Confirmation of SARS-CoV-2 reinfection. Whole genome sequencing combined with clinical and serological data confirmed SARS-CoV-2 reinfection in two patients, provided weak evidence in a third, and could not rule out prolonged infection in a fourth.
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