Metagenome of SARS-Cov2 from a patient in Brazil shows a wide range of bacterial species - Lautropia, Prevotella, Haemophilus - overshadowing viral reads, which does not even add up to a full genome, explaining false negatives
Sandeep Chakraborty
Abstract
LetterHere, I analyze the metagenome from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil (Accid:PRJNA613951).Very little viral load, not covering the entire genomeThere are just 152 reads matching to SARS-Cov2 [1] (SIbrazil/SARS-Cov2.reads.fa), which adds up a total of 21190 bp, much lesser than the 30000bp SARS-Cov2 genome. This is a very plausible cause for false negatives, there is just not enough virus to detect.For eg, if the RT-PCR test was looking for a genomic fragment in the spike protein (3879bp) from 369– 1174, it would not find a match. Thus, it is important to use multiple primers spread across the genome, something which the CDC test does not do.Much more bacterial load - Lautropia, Prevotella, Haemophilus dominatingThere are a wide range of bacteria (SIbrazil/allbact.list.txt,n=117) - Lautropia, Prevotella, Haemophilus dominating (Table 1). These are the same bacteria found in China [2] and San Diego county [3]. There are 10851 reads matching to bacteria (SIbrazil/allbactsequences.fa). These bacterial co-infections form the basis of hydroxychloroquine and azithromycin working in clinical trials [4].