Repeat testing for SARS-COV-2: Persistence of viral RNA is common, and clearance is slower in older age groups
Authors: Stehlik Paulina , Alcorn Kylie , Jones Anna , Schlebusch Sanmarie , Wattiaux Andre , Henry David 
Published: September 2020

OBJECTIVE

Queensland’s Novel Coronavirus (SARS-CoV-2) suppression program has been relatively successful. Initially, it involved extensive community testing and repeat sampling of positive individuals for release from isolation. This enabled study of several characteristics, including persistence of detectable virus and how apparent viral clearance rates varied by age and sex.

DESIGN

We conducted an exploratory analysis of Queensland Pathology SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) test results. Kaplan Meier analyses were used to estimate median time to apparent viral clearance, and Cox regression to explore the effects of sex and age.

SETTING AND PARTICIPANTS

Individuals tested for presence of SARS-CoV-2 in the upper respiratory tract between January 19 and June 4, 2020.

OUTCOME MEASURES

Presence of viral RNA detected by RT-PCR.

RESULTS

We analyzed 97,476 individuals. Median age was 41y (range <1-105y), and 57.2% (95% CI 57.2, 57.2) were female. In total, 958 (0.98%; 95% CI 0.92,1.05) tested positive for SARS-CoV-2. Positivity rates were lower in regional areas than cities, in females (OR 0.80, 95% CI 0.70, 0.91), and in those aged 16y and below (p<0.01, test for trend).

Of the 958 positive individuals, 243 had two or more (max 17) additional tests, and 92% (95% CI 88.1, 95.2) remained positive after 10 days (max 76 days) after the initial result.

Median time to apparent viral clearance was longer in those 65y and over compared to those under 65y (29 v 43 days, HR 1.85; 95% CI 1.17, 2.90), and was unaffected by sex (HR 0.93; 95% CI 0.66, 1.30).

CONCLUSIONS

Females and those 16y and under were less likely to test positive for SARS-CoV-2. Detectable RNA may persist for long periods, negating the value of repeat testing for declaring individuals free of infection. Viral clearance rates appear lower in those over 65y of age compared with younger individuals.

“The known”

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Early in the COVID-19 pandemic, 2 negative RT-PCR swabs were used to achieve negative status in infected individuals

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There are few published data on the patterns of results seen with repeat testing in Australia.

“The new”

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We analysed data from a large cohort of people tested for viral RNA in Queensland

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We found that females and those 16 y and under were less likely to test positive.

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Viral RNA was detectable for up to 76 days, with >90% testing positive for more than 10 days.

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Viral clearance was slower in those over the age of 65.

“The implications”

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There is likely to be little value in repeat RT-PCR testing to declare individuals free from infection.

The first Australian cases of infection with SARS-CoV-2 were reported in January 2020.1 During the initial phase the peak daily infection rate was in late March 2020 and by the end of June 2020 there had been around 8000 cases and 104 deaths.2 Initially, the majority of cases were acquired outside the country rather than by local transmission.3 The cumulative incidence rates (June 2020) of around 400/million, and mortality of 4/million, were towards the lower end of the rates that have been experienced in other high-income countries, although these are rising quickly with recent outbreaks in Victoria and New South Wales.3 Rates of infection remain relatively low in Queensland.3

In Queensland, the criteria for testing individuals for SARS-CoV-2 changed during the pandemic. Initially, to be tested in Queensland people were required to meet both epidemiological (return from a high-risk country), and clinical criteria (suggestive symptoms). With progression of the pandemic, testing criteria were modified to clinical criteria only (details provided below).

The rollout of a comprehensive testing program and the availability of data from repeated within-subject testing carried out in the initial stages of the Covid-19 pandemic provided an opportunity to conduct an exploratory study to address several questions. We investigated population testing rates and how they varied over time. We estimated the proportions of individuals who returned positive tests and how these varied with location age and sex. We also estimated apparent rates of clearance of viral RNA from the upper respiratory tract of subjects with repeated tests, and the extent to these varied with age and sex.