Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers

Abstract

SARS-CoV-2 infection was monitored in 1898 health care workers (HCWs) after receiving full vaccination with BNT162b2. Untill 30 June 2021, 10 HCWs tested positive for SARS-CoV-2 using real time RT-PCR, resulting in a 4-month cumulative incidence of 0.005%. The infection was mildly symptomatic in six (60%) and asymptomatic in four (40%) individuals. Among the infected HCWs, eight consenting individuals provided paired NPS and saliva during the course of infection, for the purpose of the analysis performed in the present study. Genomic and subgenomic viral RNAs were investigated using real-time RT-PCR in both biological specimens. The temporal profile of viral load was measured using ddPCR. Viral mutations were also analysed. Subgenomic viral RNA was detected in 8/8 (100%) NPS and in 6/8 (75%) saliva specimens at the baseline. The expression of subgenomic RNA was observed for up to 7 days in 3/8 (38%) symptomatic cases. Moreover, concordance was observed between NPS and saliva in the detection of viral mutations, and both N501Y and 69/70del (associated with the B.1.1.7 variant) were detected in the majority 6/8 (75%) of subjects, while the K417T mutation (associated with the P.1-type variants) was detected in 2/8 (25%) individuals. Overall, our findings report a low frequency of infected HCWs after full vaccination. It is, therefore, important to monitor the vaccinees in order to identify asymptomatic infected individuals. Saliva can be a surrogate for SARS-CoV-2 surveillance, particularly in social settings such as hospitals.

Lower probability and shorter duration of infections after COVID-19 vaccine correlate with anti-SARS-CoV-2 circulating IgGs

“…In our study we observed the occurrence of infection in vaccinated individuals with high viral titers suggestive of efficient viral replication. This is supported by previous studies that detected active viral replication in SARS-CoV-2-positive vaccinated individuals by analysis of subgenomic viral RNA [ 20 , 21 ]. Nonetheless, similarly to our results, the frequency of infection post-vaccination was low, the symptomatology was really mild and, importantly, the viral load rapidly declined [ 20 , 21 ].…”

“…This is supported by previous studies that detected active viral replication in SARS-CoV-2-positive vaccinated individuals by analysis of subgenomic viral RNA [ 20 , 21 ]. Nonetheless, similarly to our results, the frequency of infection post-vaccination was low, the symptomatology was really mild and, importantly, the viral load rapidly declined [ 20 , 21 ]. In particular, in agreement with our data, in the one case report, the speed of viral decay was significantly faster compared to a reference group of non-vaccinated individuals [ 21 ].…”

Subgenomic and negative sense RNAs are not markers of active replication of SARS-CoV-2 in nasopharyngeal swabs

“…However this is not practical in most diagnostic laboratories, and importantly, may not be sensitive enough to detect low levels of potential infectivity [7,11] . This has led to a number of other molecular indicators such as detection of subgenomic RNAs or negative sense RNA being proposed as possible markers of whether an individual is likely to be infectious or not to aid in the control of SARS-CoV-2 [7,12-14] . The rationale being that these molecules are generated intracellularly by the virus during virus replication.…”

“…Several studies have proposed using subgenomic RNA or negative sense SARS-CoV-2 RNA as a marker of active replication of the virus within an individual [7,11,13,14,24] . However, we recently reported that we were able to detect subgenomic RNA and negative sense RNA in samples up to 17 days post infection, and that subgenomic RNAs are relatively stable and likely persist in samples protected by the double membrane structures created during the replication of the virus in the cytoplasm of SARS-CoV-2 infected cells [23] .…”

“…Given that there is ongoing interest in subgenomic RNAs as a potential marker of active replication and a dichotomy of conclusions being drawn within the scientific community as to the utility of subgenomic RNA as a marker of infectivity [7,9,11,13,14,23,24] , we decided to further examine the presence of subgenomic RNAs in a larger number of routine diagnostic SARS-CoV-2 positive nasopharyngeal swab samples. These swabs were collected subsequent to our last study during the second SARS-CoV-2 epidemic wave in Victoria, Australia in mid-to late 2020 [23,26] .…”