Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

Juliet R C Pulliam, Cari van Schalkwyk, Nevashan Govender, Anne von Gottberg, Cheryl Cohen, Michelle J Groome, Jonathan Dushoff, Koleka Mlisana, Harry Moultrie, Juliet R C Pulliam, Cari van Schalkwyk, Nevashan Govender, Anne von Gottberg, Cheryl Cohen, Michelle J Groome, Jonathan Dushoff, Koleka Mlisana, Harry Moultrie

Abstract

We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.

Figures

Fig. 1.. Daily numbers of detected primary…
Fig. 1.. Daily numbers of detected primary infections, individuals eligible to be considered for reinfection, and suspected reinfections in South Africa.
(A) Time series of detected primary infections. Black line indicates 7-day moving average; black points are daily values. Colored bands represent wave periods, defined as the period for which the 7-day moving average of cases (detected infections and reinfections) was at least 15% of the corresponding wave peak (purple = wave 1, pink = wave 2, orange = wave 3, turquoise = wave 4). (B) Population at risk for reinfection (individuals who tested positive at least 90 days ago and have not yet had a suspected reinfection). (C) Time series of suspected second infections. Blue line indicates 7-day moving average; blue points are daily values.
Fig. 2.. Time between consecutive infections, based…
Fig. 2.. Time between consecutive infections, based on the time between successive positive tests.
Note that the time since the previous positive test must be at least 90 days to be considered a reinfection. (A) Time in days between the last positive test of the putative first infection and the first positive test of the suspected second infection. (B) Time in days between the last positive test of the putative second infection and the first positive tests of the suspected third infection. Colors represent suspected reinfections diagnosed on or after 01 November 2021. In both panels, bars for these individuals are colored by the wave during which the previous infection occurred (purple = wave 1, pink = wave 2, orange = wave 3, light grey = inter-wave).
Fig. 3.. Timing of infections for individuals…
Fig. 3.. Timing of infections for individuals with multiple suspected reinfections.
Circles represent the first positive test of the first detected infection; triangles represent the first positive test of the suspected second infection; squares represent the first positive test of the suspected third infection; crosses represent the first positive test of the suspected fourth infection. Colored bands represent wave periods, defined as the period for which the 7-day moving average of cases was at least 15% of the corresponding wave peak (purple = wave 1, pink = wave 2, orange = wave 3, turquoise = wave 4).
Fig. 4.. Observed and expected temporal trends…
Fig. 4.. Observed and expected temporal trends in reinfection numbers.
Blue lines (points) represent the 7-day moving average (daily values) of suspected reinfections. Grey lines (bands) represent median predictions (95% projection intervals) from the null model. (A and C) The null model was fit to data on suspected reinfections through 28 February 2021. (B and D) Comparison of data to projections from the null model over the projection period. The divergence observed reinfections from the projection interval in November suggests immune escape. (A) and (B): National. (C) and (D) Gauteng.
Fig. 5.. Estimates of infection and reinfection…
Fig. 5.. Estimates of infection and reinfection hazards.
(A) Estimated time-varying hazard coefficients for primary infection (black) and second infections (blue). Colored bands represent wave periods, defined as the period for which the 7-day moving average of cases was at least 15% of the corresponding wave peak (purple = wave 1, pink = wave 2, orange = wave 3, turquoise = wave 4). (B) Ratio of the estimated hazard for reinfections to the estimated hazard for primary infections.

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