The study measured SARS-CoV-2 subgenomic RNA (sgRNA) and E-gene genomic sequences in samples collected from 265 clinically confirmed COVID-19 cases with an aim to retrospectively assess the association between the disease severity and the active viral load. The study also attempted to define the clearance of the active SARS-CoV-2 virus. A viral load of > 10³ was defined as clinically relevant. The duration of the active virus was assessed in individuals who continued to test positive for E-gene or E-gene-derived sgRNA after 10 days, 11–20 days, 21–30 days and 31+ days. These nasopharyngeal swab samples  were collected during the first wave of COVID-19 infection in the South West of the UK between March 2020 and November 2020 and included viral genomes strains circulating in the UK population at the time of testing. Age, sex, initial viral load, severity of infection, presence of comorbidities, immunocompromised state or use of immunosuppressants were the clinical features evaluated.

According to the results reported in the International Journal of Infectious Diseases, samples obtained from 176 patients were positive for SARS-CoV-2 E-gene. Of these, 72 were also positive for E-sgRNA. Persons who had had symptoms of Covid-19 showed higher viral loads for both E-gene and E-sgRNA fragments compared to those who were asymptomatic. A significantly higher E-gene viral load was seen in those who had two or more underlying comorbid conditions compared to those with less than two comorbidities; however, no such association was seen for E-sgRNA.

In a small subset analysis, in seven out of 17 serially available samples, E-sgRNA was not detected, even though these samples had tested positive for E-gene, while five out of the 17 samples were positive for E-sgRNA in subsequent samples for up to 68 days from day of confirmation of infection by RT PCR test. Sixteen of the 17 samples were positive for E-gene sequences in subsequent samples. The higher the initial E-sgRNA viral load, the more likely was its detection in subsequent samples.

Twenty-six percent of samples were positive for E-gene between day 11 and day 31+; of these, 22% had levels of < 103 copies/mL. While 28% of samples were positive for E-sgRNA between day 11 and day 31+ and 13% of the sgRNA-positive cases had levels of > 103 copies/mL. What is of significance was the observation that none of these patients had any clinical features suggestive of continued infectivity.

Detection of persons infected with SARS-CoV-2 and their subsequent isolation is key to break the chain of transmission. The CDC has recently shortened the recommended time for isolation for the public to 5 days and “if they are asymptomatic or their symptoms are resolving (without fever for 24 hours), follow that by 5 days of wearing a mask when around others”. Similarly, the UK has also reduced the self-isolation period from 7 days to five days if the test is negative on both day five and day six and patients do not have fever.

This study has suggested E-sgRNA as a marker for the active virus and therefore of infectivity in place of the conventional RT-qPCR. It has shown that the potentially active virus persisted at clinically relevant levels for more than 10 days in more than 10% of patients. While in some, these levels remained for up to 68 days. Patients who were positive for E-sgRNA beyond 10 days did not have any clinical features suggestive of persistence of the virus. Such patients can be a potential source of infection and may cause further spread of the virus. Hence, it is important to identify patients who may continue to be infectious for prolonged duration. The study authors conclude by stating that “in situations such as hospital inpatient care or patients returning to long-term care facilities following hospital discharge, where onward transmission would be especially problematic, it may be prudent to obtain molecular evidence of remission to protect vulnerable populations”.

Reference

1. Merlin Davies, et al. Persistence of clinically relevant levels of SARS-CoV2 envelope gene s9712(21)01206-6. doi: 10.1016/j.ijid.2021.12.312.