SARS-CoV-2 RNA load in nasopharyngeal specimens from outpatients with breakthrough COVID-19 due to Omicron BA.1 and BA.2

This retrospective observational study compared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA load in nasopharyngeal specimens (NPs) from patients with breakthrough coronavirus disease 2019 (COVID-19) caused by the Omicron BA.1 or BA.2 sublineages. The convenience sample was composed of 277 outpatients (176 female/112 male; median age, 48 years; range, 12-97) with breakthrough COVID-19 (n = 130 due to BA.1 and n = 147 due to BA.2). All participants had completed a full vaccination schedule and 56% had received a booster vaccine dose at the time of COVID-19 breakthrough microbiological diagnosis. NPs were collected within 7 days (median 2 days) after symptom onset. The TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific) was used to estimate viral loads in NPs. Overall, viral RNA loads in NPs were comparable (p = 0.31) for BA.1 (median, 7.1 log₁₀ copies/ml; range, 2.7-10.6) and BA.2 (median, 7.5 log₁₀ copies/ml; range, 2.7-10.6), yet peak viral load appeared to be reached sooner for BA.2 than for BA.1 (Day 1 vs. Days 3-5; p = 0.002). Time elapsed since last vaccine dose had no significant impact on SARS-CoV-2 RNA loads in the upper respiratory tract (URT) for either BA.1 or BA.2. The data presented do not support that the transmissibility advantage of BA.2 over BA.1 is related to generation of higher viral loads in the URT early after infection.