Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

• DOI: 10.3201/eid2906.221696
• Publication Date: 2023-05-16T17:40:36Z
• Authors: Cristina Rodrígue...; Agustín Estévez; Rosalía Palomino-...; Andrea Molero-Sal...; Daniel Peñas-Utrilla; Marta Herranz; Amadeo Sanz-Pérez; Luis Alcalá; Cristina Veintimilla; Pilar Catalán; Carolina Martínez...; Roberto Alonso; Patricia Muñoz; Laura Pérez-Lago; Darío García de V...
• Keywords: SARS; SARS-CoV-2; Research; R; COVID-19; Infectious and parasitic diseases; RC109-216; Genomics; United States; respiratory infections; coronavirus disease; Spain; Risk Factors; Reinfection; Medicine; Humans; severe acute respiratory syndrome coronavirus 2

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.