We have identified both links and discrepancies between the course of SARS-CoV-2 in chronic infection and VOCs, and our findings underscore the importance of continuously monitoring chronic SARS-CoV infection. -2 in immunocompromised patients. Indeed, a negative PCR result might not indicate virus clearance, and viral rebound might suggest that a fitter virus has emerged and constant patient monitoring is needed. Moreover, genomic analysis of chronic infection is a key avenue to understand how VOCs emerge. As immunocompromised patients are at high risk for complications from COVID-19 and could serve as the foundation for the virus to thrive and evolve, these individuals must be protected against SARS-CoV-2 infection.

This study has several limitations, including a relatively small sample size, and may have biases related to age, gender, and medical history. It should also be noted that all sequencing data analyzed in this study were obtained before the emergence of most VOCs. Additionally, much of the global community is now vaccinated against and/or recovered from SARS-CoV-2, and new treatments are available. These developments could generate a new set of selective pressures for the virus. We intend to continue our investigations by examining a new cohort of patients with a weakened immune system and chronic infection with the current VOC, Omicron. The results of this research could allow us to predict and prepare for new VOCs.

Sheri Harari and Maayan Tahor, Tel Aviv University, Tel Aviv, Israel.