**Background:** Ventilator-associated pneumonia (VAP) is a frequent complication in COVID-19 patients with acute respiratory distress syndrome (ARDS), with reported incidences as high as 50-60%. While bacterial superinfection rates may be influenced by the nature of the infecting viral variant and widespread corticosteroid use, the relationship between specific SARS-CoV-2 mutations and VAP occurrence had not been systematically investigated. The authors hypothesized that specific SARS-CoV-2 mutations, either in the spike protein or other viral proteins, could impact VAP prevalence through alterations in the upper respiratory tract microbiome or virus-host interactions.
**Methods:** This prospective multicenter observational cohort study included patients from 11 ICUs in the Greater Paris area (ANTICOV study, NCT04733105) admitted between October 1, 2020 and May 30, 2021. Inclusion criteria were age ≥18 years, confirmed SARS-CoV-2 infection by RT-PCR, ICU admission requiring mechanical ventilation for >48 hours for acute respiratory failure. Patients with low viral load (PCR Ct >32) were excluded. Full-length SARS-CoV-2 genome sequencing was performed using next-generation sequencing (Illumina COVIDSeq Test). Lineages were determined using Pangolin and NextClade. The primary endpoint was the difference in prevalence of first VAP according to SARS-CoV-2 variants. VAP was defined per current guidelines requiring: new/progressive pulmonary infiltrates, purulent tracheal secretions, fever/hypothermia or leukocytosis/leukopenia, and positive quantitative lower respiratory tract sample (ETA ≥10⁵ CFU/mL, BAL ≥10⁴ CFU/mL, or PTC ≥10³ CFU/mL). Statistical analysis used a competing risk model (Fine and Gray model) with death and ventilator weaning as competing events.
**Key Results:** Of 845 patients admitted to participating ICUs, 413 had Ct ≤32 and available samples for sequencing; 267 were mechanically ventilated >48 hours, and 259 were included in the final analysis. Patient characteristics: median age 65 years [IQR 58-71], 71.4% male, 88.8% had ARDS, 93.4% received corticosteroids, 92.7% required prone positioning, 20.1% required ECMO, and 44% died in ICU. Among the 259 patients, 122 (47%) were infected with pre-existing ancestral variants, 116 (45%) with variant α (B.1.1.7), and 21 (8%) with other variants (β [B.1.351]: n=19, 4.6%; γ [P.1]: n=2, 0.5%; other variants of interest: n=12, 2.9%). VAP occurred in 153 patients (59%). The Fine and Gray model showed no significant difference in VAP probability between patients infected with variant α versus others [sub-hazard ratio = 1.26 (0.62-2.54), p = 0.53] after adjusting for competing events. Analysis of 17 pre-selected spike protein mutations (substitutions and deletions) found no significant association with VAP occurrence, except for A67V which was present in only 1 patient (p<0.05), considered too small for clinically relevant conclusions. Multivariable analysis adjusting for age, sex, antibiotic at admission, and SAPS II confirmed no significant association between variant α [SHR 0.76, 95% CI 0.54-1.07] or other variants [SHR 1.07, 95% CI 0.62-1.87] and VAP risk.
**Clinical Implications:** This study provides strong evidence that VAP occurrence in critically ill COVID-19 patients is not related to the specific SARS-CoV-2 variant or mutational pattern, but rather to non-virological factors such as prolonged mechanical ventilation, ARDS severity, and immunosuppressive treatments. These findings suggest that VAP prevention strategies should focus on standard infection control measures and ventilator management protocols rather than variant-specific approaches. The study's limitations include the predominance of pre-existing and α variants (pre-dating δ and ο variants), limited statistical power, and the single-region design. Strengths include the prospective multicenter design, well-phenotyped cohort, and full-length genome sequencing in a large number of patients.