1/ How infectious are various biological samples from COVID-19 patients? And for how long? @Nature pre-print paper out yesterday- what does it actually tell us? See this thread for analysis.
#tweetorial #medthread
nature.com/articles/s4158…
#tweetorial #medthread
nature.com/articles/s4158…
2/ Viral RNA in specimens tells if you are currently SARS-CoV-2 positive. Does not tell you if that is dead or live virus, i.e. actively replicating and infectious. This paper attempts to address the latter- a very important question.
3/ Methods: Nine COVID-19 patients in Munich, Germany infected late Jan. All patients had close contact to a single infected individual, so time of exposure is somewhat controlled. Outbreak cluster described in this report: papers.ssrn.com/sol3/papers.cf…
4/ Methods: Sputum, throat swab, stool, urine, serum collected Day 1 to 26 post-onset of symptoms, BUT not on all patients for all days (see below). So n’s and timepoints for each sample type are variable. 
5/ Valuable data nonetheless, but should be taken into account when interpreting.
6/ Methods: Diagnosis confirmed by RT-PCR of viral RNA. Additionally: Live virus isolation (using Vero E6 cells), confirmation of active viral replication by RT-PCR of sub-genomic mRNA, viral WGS to assess mutations, and seroconversion measured by IgG/IgM.
7/ Findings: While symptoms diminished after first week, viral RNA was detected in swabs through Day 14, and in sputum and stool through Day 21 in 6/9 patients despite full resolution of symptoms.
8/ Findings: (Remember, all data is measured from post-onset of symptoms, not from exposure date). Live virus only isolated from sputum and throat swabs. No live virus isolated after Day 8 despite high viral titers up to 13 days out. (see below).
9/ Findings: No live virus isolated from urine, serum, stool, and all patients seroconverted by Day 10 (50% by Day 7). High viral titers in stool up to 11 days out.
10/ Comment: Stool isolation attempted on only 4/9 patients between days 6-12. No data on days 1-5 or the other 5 patients. We know ACE2 is highly expressed in intestinal epithelial cells- are we missing a critical window of stool infectivity in the early stages?
11/ Findings: 1 of 4 patients from which stool was collected, did show signs of active virus based on course of viral RNA load (see below-grey line = stool).
12/ Next measured sub-genomic mRNA in sputum, swab, stool. A good indicator of live viral replication. SgRNA isn’t packaged into virions and so can be isolated separately. Effective approach, but none detected doesn’t mean small amounts of virus are not there.
13/ Findings: Active replication most evident in sputum and swabs in first 5 days. Little to no sgRNA detected in stool, but not negative. (see below)
14/ Very interesting piece: In 1 patient, different viral genotypes were detected in sputum and throat swab. The mutated virus had been detected earlier (in a separate case report) from a patient in the outbreak cluster.
15/ Authors suggest maybe throat is a site of independent virus replication vs shedding from lung.
16/ Findings: 4/9 patients showed loss of taste and smell akin to what is experienced during a cold, but longer duration than with a cold.
17/ Important to remember that all of these patient symptoms were considered mild. None of this data comes from severe cases.
18/ Take homes: SARS-CoV-2 shedding in sputum, swabs and stool can persist long after symptoms resolve, however this study was unable to isolate live virus beyond Day 8 in any sample post-onset of symptoms.
19/ Take homes: Stool only tested for live virus on Days 6-12 and in 4 patients. We have no data on earlier timepoints nor all patients. Can only conclude no live virus on these days in a small subgroup. Cumulative data suggests 1/4 patient may have active virus in stool.
20/ Opinion: A heroic effort and very valuable data. But very small subset of patients over variable duration. Cannot conclude from this, for example, that stool is not infectious. This study serves as an example of the type of study we need on larger cohorts in more locations.
