COVID: length of positive viral culture

 A recent Letter to the Editor assessed the time-course of culturable, viable SARS-CoV-2 virus in hospitalized patients with Covid-19 in South Korea (see covid culturable virus nejm2021 in dropbox, or DOI: 10.1056/NEJMc2027040 ) 

  

Details: 

--21 patients, representing all patients with PCR-confirmed Covid-19 infections in Chung-Ang University Hospital in Seoul, South Korea between February and June 2020 

--mean age 62, 76% men 

--comorbidities: none 7 (33%), hypertension 10 (48%), diabetes 3 (14%), chronic lung disease 2 (10%), immunocompromise 1 (5%) 

-- 15 (71%) had pneumonia, 8 (38%) on supplemental oxygen, 5 (24%) URI symptoms, 1 (5%) asymptomatic 

--lab findings: all had normal WBC, hemoglobin, platelet, total bilirubin, and CRP 

--treatments: 33% conservative care, 9 (43%) hydroxychloroquine for median 10 days, lopinavir/ritonavir 9 (43%) median 8 days 

--Median SOFA score (Sequential Organ Failure Assessment, range from 0-71) was 0.  (ie: these patients had mild-to-moderate disease) 

--all got PCR testing done about 2 days apart when possible, with viral RNA and cultures done (the latter by plaque assay) 

--all patients were isolated until 2 consecutive PCR tests were negative, at least 24-hours apart 

--165 samples tested at intervals of 1-5 days (median 2), with 89 cultures done 

  

Results: 

-- PCR-positivity after symptom onset: 

    --50% had PCR positivity until 35 days. Lower limit of 95% confidence intervals was 24 days, upper limit was not calculable 

        --all had PCR positivity until 15 days after symptoms 

--29 of the 89 samples (33%) had culturable SAR-CoV-2. 

    --culturable virus by PCR Ct (cycle threshold): 

        --Ct <22: 100% 

        --Ct 22-24: 78% 

        --Ct 24-26: 67% 

        --Ct 26-28: 46% 

        --Ct 28-30: 14% 

        --Ct 30: 0% 

    -culturable virus by time since symptom onset: 

        --within 4 days: 67% 

        --day 5-8: 40% 

        --day 9-12: 23% 

        --day >12: 0% 

    

    -- latest culturable virus was up to 3 days after resolution of fever (in a patient with URI symptoms) 

    -- latest positive culture was 12 days after symptom onset (in a patient with pneumonia). 

 

Commentary: 

-- this study confirms the large discordance between PCR positivity for SARS-CoV-2 and culturable virus:

    -- PCR was positive in all patients until 15 days after symptom onset, and in 50% up until 35 days

        -- prior studies have found PCR positivity up til 100+ days after symptoms onset

    --culturable virus was found until a median of seven days after symptom onset, with one person up to 12 days (and, interestingly, this was a person with very mild disease)

        -- prior studies, though quite small, have found a maximum of eight or nine days. This study suggests we should consider the possibility of a longer time than that

-- this study also found that the actual quantitative PCR was very helpful in determining viral culturability, with the cycle threshold (Ct) of >30 not being associated with viable virus on culture. (The Ct is inversely associated with the viral load). Unfortunately, at this point we do not receive quantitative Ct’s when we test patients, just a binary qualitative: positive or negative. The quantitative one might prove helpful in distinguishing the likelihood of viral transmissibility (though the Ct>30 threshold would need to be verified by other, larger studies)

 

Limitations of the study:

-- viral culture is a laboratory technique and may not correlate well with clinical transmissibility of virus. At this point, it seems to me to be the most likely surrogate marker of transmissibility. However, this needs to be shown in actual clinical studies. for example, there may be a minimal viral load necessary for transmission from one person to another (as per other infections), though the viral culture might still be positive even with much lower viral loads

    --for further discussion on neutralizing antibodies and others, see http://gmodestmedblogs.blogspot.com/2021/02/covid-single-dose-vaccine-post.html

-- this was a small study in a single location, and the results may not be replicable in a larger study in a more diverse population. But, the finding of culturable virus up to 12 days after symptom onset does suggest that be minimal new lower limit for potentially transmissible virus

-- the data are from 8 months ago. would there be these same findings if the newer, more transmissible SARS-CoV-2 variants were included?? would the Ct cutpoint of 30 still hold? are the newer bad actors transmissible for a longer time period? Lots of potential moving targets here....

 

So, an important study for the above reasons:

-- we should not assume that PCR positivity necessarily implies transmissibility of the virus, since PCR positivity can extend for a long period of time after we cannot find culturable virus, perhaps reflecting residual fragments of dead virus, or conceivably very low viral loads that may not be culturable and perhaps not transmissible, or artifacts that the PCR test detects (since there’s a higher possibility of contaminants causing a positive PCR when there is a higher cycle threshold)??

    --though i expect most clinicians understand this PCR/viable virus discordance from several prior studies, this has been a difficult concept for many of my patients. it is hard to reconcile a positive PCR with lack of transmissibility (even though it can remain positive 3+ months), or the (unproven) possibility that a negative PCR test really eliminates transmissibility (though pretty likely so, esp if negative on repeat in 24 hours)

    -- and there is the pretty common scenario i find where employers will not allow an infected employee to return to work until they are PCR-negative, unnecessarily depriving them of income in some cases. and potentially for quite a while.

-- we should extend the potential for a positive culture from 8 to 9 days after symptom onset until at least 12 days (??longer; we need larger and more diverse studies, taking into account the known variants)

--it would be great if more studies did viral cultures at different points of SARS-CoV-2 infection, so we could have a better handle on viral dynamics....

geoff

 

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