SARS-CoV-2 reinfections during the Delta and Omicron waves
C. Paul Morris, Raghda E. Eldesouki, Amary Fall, David C. Gaston, Julie M. Norton, Nicholas D. Gallagher, Chun Huai Luo, Omar Abdullah, Eili Y. Klein, Heba H. Mostafa
C. Paul Morris, Raghda E. Eldesouki, Amary Fall, David C. Gaston, Julie M. Norton, Nicholas D. Gallagher, Chun Huai Luo, Omar Abdullah, Eili Y. Klein, Heba H. Mostafa
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Clinical Research and Public Health Infectious disease

SARS-CoV-2 reinfections during the Delta and Omicron waves

Abstract

BACKGROUND 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. 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.METHODS 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. SARS-CoV-2 genomes of patients’ initial and later samples were compared.RESULTS 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. Sequencing was attempted on 231 samples and was successful in 127. 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. 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). 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.CONCLUSION Sequence-validated reinfections increased with the Omicron surge but were generally associated with mild infections.FUNDING 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.

Authors

C. Paul Morris, Raghda E. Eldesouki, Amary Fall, David C. Gaston, Julie M. Norton, Nicholas D. Gallagher, Chun Huai Luo, Omar Abdullah, Eili Y. Klein, Heba H. Mostafa

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Figure 1

Repeat positive SARS-CoV-2 tests greater than 90 days apart.

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Repeat positive SARS-CoV-2 tests greater than 90 days apart. (A) Kernel ...
(A) Kernel density estimator (KDE) plot showing the days from initial positive test. Color indicates whether sequencing was attempted or successful (gray, not attempted; blue, pass; red, fail) (n = 920 samples). (B) KDE plot of date of initial positive and post–90-day–positive tests (n of post–90-day positive = 920). (C) Number of tests that failed sequencing or provided high-quality genomes (n = 231). (D) KDE plot showing sample collection dates of sequences that failed or provided high-quality genomes (n = 920). (E) Bar plot showing persistence of initial genomes, inferred reinfection, or sequence-confirmed reinfection (n = 124 patients). (F) Violin plot showing age and reinfection status in individuals with a post–90-day–positive test. (G) Bar plot showing days from initial positive test to post–90-day–positive test. Color represents reinfection status (n = 127 samples). (H) Bar plot showing sample collection date of post–90-day–positive tests. Color represents reinfection status (n = 127 samples). (I) Bar plot showing sex and reinfection status.