In this study, we evaluated SARS-CoV-2 genomes of individuals who tested positive at least 90 days after an initial positive test to determine the frequency of reinfections. We previously reported infrequent cases of sequence-validated reinfections and a few instances in which positivity over 90 days was consistent with persistence of the genome from the initial infection ( 15, 16) using data prior to the Omicron surge. It is, therefore, unclear in these cases whether the positive result could be due to prolonged shedding, repeat infection, or erroneous PCR results. There are potential issues with this approach, as prolonged shedding of RNA and prolonged active infection are both well documented ( 13, 14) and can last longer than 90 days ( 15). Thus, reinfections have generally been suspected in cases with a positive PCR test more than 90 days after the original positive PCR test in asymptomatic individuals or 45 days after initial infection in symptomatic individuals ( 12). In most cases of reinfections, sequencing data was not available to validate these findings. Additionally, large increases in the rates of breakthrough cases and reinfection with the Omicron variant were reported ( 10, 11). Some reports showed a decrease in antibody neutralization to Omicron in both vaccinated and previously infected individuals ( 8, 9). The factors that contributed to the unprecedented success of Omicron are not completely understood, but immune evasion is the most likely ( 2– 7). The Omicron variant of SARS-CoV-2 quickly displaced Delta to become the most predominant variant by the end of December 2021 ( 1). Funding was provided by the Johns Hopkins Center of Excellence in Influenza Research and Surveillance (HHSN272201400007C), CDC (75D30121C11061), Johns Hopkins University President’s Fund Research Response, Johns Hopkins Department of Pathology, and the Maryland Department of Health. Sequence-validated reinfections increased with the Omicron surge but were generally associated with mild infections.įUNDING. Of the 45 patients with sequence-validated reinfections, 43 (96%) had reinfections that were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%) were vaccinated prior to the second infection, 6 (13%) were immunosuppressed, and only 2 (4%) were hospitalized.ĬONCLUSION. A total of 122 (98%) patients showed evidence of reinfection 45 of these patients had sequence-validated reinfection and 77 had inferred reinfections (later sequencing showed a clade that was not circulating when the patient was initially infected). Rates of successful sequencing spiked during the Omicron surge there was a higher median number of days from initial infection in these cases compared with those with failed sequences. Sequencing was attempted on 231 samples and was successful in 127. A total of 755 patients (920 samples) had a positive test at least 90 days after the initial test, with a median time between tests of 377 days. SARS-CoV-2 genomes of patients’ initial and later samples were compared. Patients who had 2 or more positive SARS-CoV-2 tests in our system, with samples sequenced as a part of our surveillance efforts, were identified as the cohort for our study. In this study, we used Johns Hopkins SARS-CoV-2 genomic surveillance data to evaluate the frequency of sequencing-validated, confirmed, and inferred reinfections between March 2020 and July 2022. Increased SARS-CoV-2 reinfection rates have been reported recently, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection.
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