Using SARS-CoV-2 Sequencing Data to Identify Reinfection Cases in the Global Emerging Infections Surveillance...

Area of Science:

• Infectious Diseases
• Virology
• Genomics

Background:

• Reinfection with SARS-CoV-2 is defined by positive tests >90 days apart or genomic sequencing confirming a different lineage.
• Previous studies examined reinfection dynamics using PCR or antigen surveillance data.
• Understanding reinfection is crucial for public health and military readiness.

Purpose of the Study:

• To identify and characterize SARS-CoV-2 reinfections within the US Military Health System.
• To analyze the impact of variants, patient demographics, symptoms, and vaccination status on reinfection.
• To investigate intrahost mutation rates in persistent infections.

Main Methods:

• Utilized whole-genome sequencing data from the US Military Health System (March 2020-July 2022).
• Identified patients with multiple positive SARS-CoV-2 tests to detect reinfection cases.
• Compared reinfection data with patient demographics, symptoms, and vaccination status.

Main Results:

• Identified 267 reinfections, with 90% attributed to the SARS-CoV-2 Omicron variant.
• Found that reinfection symptom severity correlated with initial infection severity and time elapsed since the first infection.
• Observed significant variation in intrahost mutation rates among 72 cases of ongoing infection with the same variant.

Conclusions:

• The Omicron variant was the predominant cause of SARS-CoV-2 reinfections in the studied population.
• Symptom severity in reinfections is influenced by prior infection history and time.
• Further research on reinfections by emerging SARS-CoV-2 variants is essential for maintaining military readiness.