PRJNA768603
Genomic evidence of reinfection and persistence in asympto-matic patients with SARS-CoV-2
The identification and follow-up of SARS-CoV-2 infected patients is essential to have lights re-garding the progression of the pandemic in the population. This is especially relevant for two reasons: first, because of the appearance of more and more variants of the virus in the world; second, because of the findings about people with more than one infectious event or people in-fected during months.in the face of the appearance of more and more variants of the virus in the world. The possibility of determining the similarity or difference between viral genomes through genomic sequencing of surveillance pro-grams in people who have been reinfected or infected for a long time, will make possible to suggest a recurrent infection with another variant of the virus or a persistent infection with the same variant. We collected individual-level data on patients who had been tested for SARS-CoV-2 diagnosis in our laboratory (Santiago, Chile) in 2020. We ana-lyzed by genomic sequencing the viral genome of those reinfected asymptomatic individuals. During the screenings, 58.177 people were tested, of whom a 22.1% were positive. From May-2020 until July-2020, the positive cases reached 33.3%; in this period, 3338 samples were analyzed twice, and 1561 of them were analyzed within a time interval of over 30 days. Samples were re-analyzed after a time interval of around 45 days, of which 633 tested negatives in both analyzes, 67 samples were positive and turned negative in the second testing, 115 tested negatives in the first analysis and positive in the second testing, and seven samples were positive in both ana-lyzes. Asymptomatic individuals reported positive twice within a time frame of 55 (CMM-55d) and 58 days (named JTF-58d). CMM-55d (60-years old health care worker female) showed a high similarity between the samples compared to the reference genome, registering a difference, alt-hough reduced, in the evolution of both samples over time. On the other hand, JTF-58 (54-years old homeless female) showed the viral genomes belong to different clades (clades 20B and 19A) with a divergence of 9 and 4 SNVs compared to the reference genome, respectively. Collectively, the molecular and clinical data of these PCR-positive individuals demonstrate persistence and reinfection of the virus. Our study reports the persistence and reinfection by SARS-CoV-2 in asymptomatic patients coming from two different social niches. The identification of a reinfection process in less than two months in a person in a homeless situation could increases the viral spreading and contribute to the augment of the infection rates and the loss of traceability asso-ciated with the infection.