Abstract
The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1–2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.
Highlights
The coronavirus disease 2019 (COVID-19) has spread, infecting over 115 million people worldwide and approaching 2.6 million deaths globally by March 4, 2021
The mother of the patient did not report any additional diseases related to the patient or that any members of the family had tested positive for COVID-19
COVID-19 reinfections appear to be rare with very few cases confirmed by wholegenome sequencing reported globally to date [17]
Summary
The coronavirus disease 2019 (COVID-19) has spread, infecting over 115 million people worldwide and approaching 2.6 million deaths globally by March 4, 2021. Despite the arrival of several candidate vaccines, which have effectively started to tackle the ongoing pandemic, several questions remain unanswered regarding the dynamics of COVID-19 infection and most importantly the continuing evolution and ever-changing mutational landscape of SARS-CoV-2 genomes [1]. A sustained number of mutations of the viral genome have led to the emergence of “Variants of epidemiological concern”. Amongst these are the British variant (B.1.1.7), Brazilian variant (P.1.) and South. Reinfections and few studies have documented suchsuch events. Reinfectionsare arerare rareininCOVID-19, COVID-19, and few studies have documented events African variant (B.1.1.32), the latter two with a key repertoire of mutations in the spike gene linked to the potential occurrence of reinfections [2,3,4].
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