Viral genome sequencing for Defining Re-infection with COVID-19

Dear Editor,

I read with great interest the article “COVID-19 reinfection: Linked Possibilities and future Outlook” published in the December edition of your esteemed journal.[1] The article was eye-opening and aroused great interest in me. The need of symptom-free period and a negative test between the two positive RT-PCR tests was well stressed. But the role of Whole viral genome sequencing in defining COVID-19 Re-infection has not been stated. COVID-19 Re-infection can be defined only by establishing that the number of differing nucleotides in viral genome sequencing between the first and second episode of infection is significant enough to rule out mutation changes.[2] There is increasing concern that patients who recover from Coronavirus disease 2019 (COVID-19) may be at risk of reinfection. But, the virus has been reported to be detected again in recovered patients. RT-PCR does not have the capacity to define Re-infection. Persistent fragments or delayed viral clearance may give positive RT-PCR after recovery. Whole viral genome sequencing is essential to confirm re-infection in COVID-19.[3] The aim of this article is to update the need of Whole Viral genome sequencing for defining COVID-19 Re-infection. Cases of Re-infection established by viral genome sequencing have been reported in several countries. First case was reported in Hong kong.[4] In India alone, 2 cases have been reported.[5] Most have reported the lineage of SARS-CoV-2 by whole genome sequencing. Several other cases have also been reported from the USA, Ecuador, Belgium, Qatar and Netherlands. Some have not reported the strain while in some only partial genome sequencing has been done. Evidence about Re-infection and risk factors for re-infection in COVID-19 are lacking. Only case reports have been published. There is no global registry to validate these case reports or future studies on epidemiology of Re-infection and include them for evidence synthesis. There is no data on risk of re-infection or incidence rate of re-infection in COVID-19 established purely by viral genome sequencing.

It is the need of the hour as many countries are facing up/gearing up for second wave of pandemic which may be hugely influenced by Re-infection. Emphasis should also be kept on whole-genome sequencing instead of partial sequencing, storage of adequate samples for genome sequencing at the time of collection and establishment of well-equipped centres for the same. The need of boosters or need of vaccination every year like influenza or seasonal vaccination also depends upon the data on Re-infection in COVID-19. There is a need to establish a global registry for Re-infection in COVID-19.

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Conflicts of interest

There are no conflicts of interest.