Genomic Evidence Suggests Viral Persistence of SARS-CoV-2 for 386 Days in Health Worker: A Case Report from Santiago of Chile

Abstract

The COVID-19 pandemic continues to affect several countries. One of the best ways to control its spread is the timely identification of infected patients for isolation and quarantine. While an episode of infection lasts an average of 8–10 days from the onset of symptoms, there is literature describing long-lasting viral persistence events. Here, we report a case of persistence of SARS-CoV-2 for 386 days in a health worker from Santiago de Chile. Our study could be one of the longest reported viral persistence events. RNA sequencing analyses indicated that the first positive diagnosis (8 June 2020) corresponded to a SARS-CoV-2 variant belonging to Clade Nextstrain 20A. Three hundred eighty-six days later (23 September 2021), the second positive result reached the same viral variant (Clade 20A) but without presence or circulation in Chile since May 2021. Both sequencing coverages showed an identity of 99.21%, with some mutations related to the severity of the disease (ORF1b:P314L) and more infectivity (S:D614G). This work reinforces the idea of implementing an RT-qPCR or rapid antigen test once the quarantine is fulfilled to ensure viral absence, identify potential persistence, and, consequently, minimize the risk of local outbreaks of SARS-CoV-2 infection.

A retrospective study suggests 55 days of persistence of SARS-CoV-2 during the first wave of the pandemic in Santiago de Chile

“…In the USA, it is posited that patients who remain positive ten days post-symptom onset due to SARS-CoV-2 infection are no longer contagious [ 44 ]. A striking report even cited a 386-day persistence in a health worker, although the patient's infectivity was not assessed [ 45 ]. However, evidence of SARS-CoV-2 infectivity after 30 days [ 9 ], 37 days [ 46 ], and 144 days [ 47 ] from the first infection has been reported.…”

An ecological study on reinfection rates using a large dataset of RT-qPCR tests for SARS-CoV-2 in Santiago of Chile

“…A total of 578,670 tests were analyzed, corresponding to a total of 345,908 patients, of which 43,658 were diagnosed positive for COVID-19, at the laboratory of the University of Santiago de Chile (USACH), between 1 April 2020 and 31 July 2022. Reinfection events were considered >90 days after the first positive diagnosis, although viral persistence events have been reported even after 380 days ( 41 ), which are unusual and isolated cases. At the same time, even some reinfection criteria of ≥40 days have been reported ( 42 ).…”