Bronchoalveolar lavage is the best method to obtain SAR-Cov2 samples compared to throat swab, feces and sputum - a 10 patient RNA-seq data analysis, along with bacterial metagenome.

False negatives [1] using RT-PCR are a huge problem in detecting SARS-Cov2 [2], making doctors depend on CT [3] to properly diagnose patients. Identifying the best method to collect samples is critical to avoid false negatives, as often there is not enough viral load to constitute on full genome [4,5]. Here, I analyze the viral (and bacterial) load from RNA-seq data submitted for 10 patients from China (Wuhan, Tiananmen and Jingzhou) - covering bronchoalveolar lavage, throat swab, feces and sputum (Accid:PRJNA616446).Bronchoalveolar lavage is the best method to obtain SAR-Cov2 samplesBronchoalveolar lavage (BAL) is clearly the best region to obtain SAR-Cov2 samples, while sputum is the worst (Table 1). That BAL is good has been reported earlier - ‘bronchoalveolar lavage fluid specimens showed the highest positive rates (14 of 15; 93%)’ [6]. This is contrary to previous reports, which stated that sputum was better than throat swabs (BAL was not done) [7,8]. Note, there is only one sputum sample, so the sample size may be a confounding factor. Another paper has compared BAL to peripheral blood mononuclear cells [9]. These are reads per million. The metagenomic analysis of each samples will be done shortly to identify bacterial species in these different regions.