Shedding of infectious SARS-CoV-2 despite vaccination

Abstract

The SARS-CoV-2 Delta Variant of Concern is highly transmissible and contains mutations that confer partial immune escape. The emergence of Delta in North America caused the first surge in COVID-19 cases after SARS-CoV-2 vaccines became widely available. To determine whether individuals infected despite vaccination might be capable of transmitting SARS-CoV-2, we compared RT-PCR cycle threshold (Ct) data from 20,431 test-positive anterior nasal swab specimens from fully vaccinated (n = 9,347) or unvaccinated (n = 11,084) individuals tested at a single commercial laboratory during the interval 28 June- 1 December 2021 when Delta variants were predominant. We observed no significant effect of vaccine status alone on Ct value, nor when controlling for vaccine product or sex. Testing a subset of low-Ct (<25) samples, we detected infectious virus at similar rates, and at similar titers, in specimens from vaccinated and unvaccinated individuals. These data indicate that vaccinated individuals infected with Delta variants are capable of shedding infectious SARS-CoV-2 and could play a role in spreading COVID-19.

Fig 1. Individuals infected with SARS-CoV-2 despite full vaccination have low Ct values and shed similar amounts of infectious virus as unvaccinated individuals.

A. N1 Ct values for SARS-CoV-2-positive specimens were grouped by vaccination status. RT-PCR was performed by Exact Sciences Corporation, responsible for over 10% of all PCR tests in Wisconsin during this period, using a qualitative diagnostic assay targeting the SARS-CoV-2 N gene (oligonucleotides identical to CDC’s N1 primer and probe set) that has been authorized for emergency use by FDA (https://www.fda.gov/media/138328/download)). See also Table 1. An effect size of d< 0.2 is negligible. The number of samples in each group is listed under the dot plot. B. N1 Ct values for SARS-CoV-2-positive specimens grouped by vaccination status for individuals who were symptomatic or either asymptomatic or did not have any information, at the time of testing. Light yellow box indicates Ct values <25. C. We performed plaque assays on Vero E6 TMPRSS2 cells on a subset of specimens. Specimens were selected by N1 Ct-matching between fully vaccinated and unvaccinated persons. Specimens from individuals with unknown vaccination status were excluded from the analysis. Infectious titers are expressed as plaque-forming units (PFU) per milliliter of specimen. Specimens underwent a freeze-thaw cycle prior to virus titration.