Occurrence of SARS-CoV-2 reinfections at regular intervals in Ecuador

Abstract

SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their incidence has fluctuated with specific SARS-CoV-2 variant waves. Initially, reinfections were estimated to represent less than 1% of total COVID-19 infections. With the advent of the Omicron variant, reinfections became more frequent, representing up to 10% of cases (based on data from developed countries). The frequency of reinfections in Latin America has been scarcely reported. The current study shows that in Ecuador, the frequency of reinfections has increased 10-fold following the introduction of Omicron, after 22 months of surveillance in a single center of COVID-19 diagnostics. Suspected reinfections were identified retrospectively from a database of RT-qPCR-positive patients. Cases were confirmed by sequencing viral genomes from the first and second infections using the ONT MinION platform. Monthly surveillance showed that the main incidence peaks of reinfections were reached within four to five months, coinciding with the increase of COVID-19 cases in the country, suggesting that the emergence of reinfections is related to higher exposure to the virus during outbreaks. This study performed the longest monitoring of SARS-CoV-2 reinfections, showing an occurrence at regular intervals of 4-5 months and confirming a greater propensity of Omicron to cause reinfections.

Keywords: COVID-19; SARS-CoV-2; genomic epidemiology; reinfection; sequencing.

Figure 1

Flow chart for the selection of suspected reinfections. The database includes tests performed at IM-USFQ from May 2020 to February 2022. Suspected cases were identified retrospectively, first by patients who reported more than one positive test, and then by the compliance with inclusion criteria: at least 45 days between infections, or less if the Ct revealed a higher viral load in the reinfection. From the 44 patients who accomplished inclusion criteria, 22 were considered for sequencing.

Figure 2

Monthly surveillance of reinfections. Suspected cases identified each month within the 22 months period (A) and the corresponding incidence regarding the total SARS-CoV-2 positive tests (B).

Figure 3

Timing of reinfections and variants identified. Plot of the first and second infection detected for each patient (y-axis) over the 22-month surveillance period (x-axis). Each identified variant is represented in different colors.

Figure 4

Phylogram of paired sequences. Only paired consensus sequences were used and rooted to the Wuhan-Hu’s SARS-CoV-2 reference genome. Each pair is represented in different colors. Bootstraps equal to or above 70 are shown.