COVID-19 Re-Infection by a Phylogenetically Distinct SARS-CoV-2 Variant, First Confirmed Event in South America.

Abstract

The permanence of rt-PCR positivity after a long time in COVID-19 patients has prompted the question of whether SARS-CoV-2 could cause a persistent infection or patients can become re-infected by this virus. Both possibilities could have critical implications for the management and control of COVID-19. Here we present the first confirmed case of SARS-CoV-2 reinfection in Ecuador and South America. Materials and methods: Our diagnostic laboratory detected a potential re-infection in one patient who was SARS-COv2 rt-PCR positive twice (in May and July 2020). The first laboratory-confirmed infection presented with mild symptoms and full recovery, reaffirmed by a negative RT-PCR test result obtained two weeks after symptom onset. More severe COVID-19-like symptoms presented again four weeks after the first event, and a third RT-PCR test was performed which resulted positive. The total RNA extraction (from the samples collected on both occasions) was sequenced in an Oxford Nanopore MinION using a tilling PCR protocol developed by the ARTIC-Network, and the reads were analyzed using the artic-medaka consensus generation tool. Anti SARS-CoV-2 IgM and IgG antibodies were investigated. Results: different SARS-CoV-2 variants were identified in each infection event. For the first infection, the genome was assigned to the B1.p9 GISAID clade while the variant associated with the second episode was assigned to the A.1.1 GISAID clade. High levels of both SARS-CoV-2 specific IgM and IgG were observed during the second event.Discussion: a patient with two COVID-19 events presented two different SARS-CoV-2 variants on each event, confirming reinfection. This phenomenon is still considered rare.