Large Scale SARS-CoV-2 Molecular Testing and Genomic Surveillance Reveal Prolonged Infections, Protracted RNA shedding, and Viral Reinfections

Abstract

Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11th 2020 to September 23rd 2021, were used to identify patients with two or more positive results. A total of 3,650 samples collected from 1,529 patients who had between 2 and 20 positive results were identified in a time frame that extended up to 403 days from the first positive. Cycle threshold values (Ct) were available for 1,622 samples, the median of which was over 30 by 11 days after the first positive. Extended recovery of infectious virus on cell culture was notable for up to 70 days after the first positive in immunocompromised patients. Whole genome sequencing data generated as a part of our SARS-CoV-2 genomic surveillance was available for 1,027 samples from patients that had multiple positive tests. Positive samples collected more than 10 days after initial positive with high quality sequences (coverage >90% and mean depth >100), were more likely to be from unvaccinated, or immunosuppressed patients. Reinfections with viral variants of concern were found in 3 patients more than 130 days from prior infections with a different viral clade. In 75 patients that had 2 or more high quality sequences, the acquisition of more substitutions or deletions was associated with lack of vaccination and longer time between the recovered viruses. Our study highlights the value of integrating genomic, laboratory, and clinical data for understanding the biology of SARS-CoV-2 as well as for setting a precedent for future epidemics and pandemics.

Risk of reinfection and disease after SARS‐CoV‐2 primary infection: Meta‐analysis

“…Of the 3282 papers initially retrieved, we included 91 cohort studies evaluating the onset of reinfection, severe and very severe/lethal COVID‐19 among 15,034,624 previously infected subjects (Figure 1), either among health care workers (27 publications; n = 37,598 2,8,9,15,17,24,36,38,42–59 ) or in the general population (67 publications; n = 14,997,026 3–7,10,12,16–23,25–27,43,49,60–106 ).…”

“…As shown in Table S1, most of the included studies ( n = 43) were carried out in Europe, 2,4–10,12,15,17,18,21,24,26,36,38,44,46–51,58,66,69,71,72,75,81,85–88,91–93,95,99,102 24 in the USA, 20,22,23,25,42,43,57,59,63,67,77,79,82–84,89,90,97,98,103,105–107 18 in Asia 3,16,19,27,45,52–54,56,60,62,64,65,70,73,74,100,101 and the remaining six in South America or South Africa 61,68,80,94,96,104 . The mean age of the participants ranged from 15 to 87 years, and the average follow‐up ranged from 29 to 371 days.…”

“…The mean age of the participants ranged from 15 to 87 years, and the average follow‐up ranged from 29 to 371 days. Overall, 38 publications strictly followed the CDC criteria to identify the reinfections and were classified at low risk of misclassification bias 10,16,19,20,22–24,26,36,44,45,48–50,54,56,58,59,68,71,72,75,84,86,89–91,94,99,100,102 . All but five studies ( n = 3,854,961) 66,71,88,91,96 were completed before the emergence of BA.1/B.1.1.529 (Omicron) variant.…”

A rare case of SARS-CoV-2 and influenza A virus super-infection

“…Indeed, recent studies demonstrate that SARS-CoV-2 infection is associated with accelerated replication, high viral RNA titers and isolation of infectious virus during the acute phase, which is followed by a rapid decrease after the first two-three weeks [17] , [18] , [19] , [20] . Nevertheless, the continuous detection of SARS-CoV-2 RNA in clinical specimens for long time could be due to slow replication of a persistent virus [ 16 , 17 ] and this cannot be excluded in the case here reported. Obviously, in this case, it cannot also be excluded that the long COVID observation could be partially affected by the Influenza infection one month later.…”

“…Despite the detection of the RNA alone cannot demonstrate the viability of SARS- CoV-2, and the prolonged RNA shedding could be associated with non-infectious viral recovery, infectious virus from patients with extended RNA shedding has been previously reported in particular for immunocompromised ones [ 15 , 16 ]. Indeed, recent studies demonstrate that SARS-CoV-2 infection is associated with accelerated replication, high viral RNA titers and isolation of infectious virus during the acute phase, which is followed by a rapid decrease after the first two-three weeks [17] , [18] , [19] , [20] .…”