Recently, Australian and Southern California physician-researchers involved in a new microbiome venture in Ventura, California further probed a finding involving stool detections. Specifically, the research group identified SARS-CoV-2 not only in respiratory secretions but also in stool collections. The study team enriched next-generation sequencing (NGS) from fecal samples but also conducted a whole-genome analysis to better understand the impact of the novel coronavirus on patients’ microbiome. To the surprise of at least some, the researchers found SARS-CoV-2 in fecal samples. They suggest the possible role of SARS-CoV-2 in fecal-oral transmission. The recent study also showcased the advantages of  SARS-CoV-2 enrichment NGS, a potential methodology to document complete viral eradication. This study indicates the SARS-CoV-2 spreads in the gut. What can be done with this knowledge to fight the pandemic?

As reported recently in the peer-review journal Gut Pathogens, the study team was led by the corresponding author Andreas Papoutsis, Ph.D., joined by his research partner and Principal Investigator Dr. Sabine Hazan from Progenabiome as well as Australia’s Dr. Thomas Borody. Dr. Borody was most famous for his groundbreaking work in developing the triple therapy cure for peptic ulcers in 1987.

An expert in oversight and execution of molecular clinical trial testing under international guidelines including GxP, GmP, GLP standards, Papoutsis, and team sought to better connect SARS-CoV-2 diagnosis and stool samples.

The Study

Led by Principal Investigator Sabine Hazan, MS, the study was titled, “A Study to Explore the Role of Gut Flora in COVID-19 Infection.” (NCT04359836). Targeting up to 250 participants, the study’s primary endpoint centered on the correlation of microbiome to disease via relative abundance found in microbiome sequencing over the first year.

At the Progenabiome lab in Ventura, California, the researchers tested the fecal samples of SARS-CoV-2 patients via whole-genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). They found that the “Concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal was 100%.”

Moreover, the team identified distinctive variants in four subjects, while they identified a total of 33 different mutations among the positive samples identified by genome enrichment NGS.

The authors concluded that there is in fact a significant probability that SARS-CoV-2 can be detected by feces, but larger studies must be accomplished. Moreover, the study also clarifies some of the advantages of SARS-Cov-2 enrichment NGS, which could represent a fundamental approach to document complete viral eradication.

The study team at Progenabiome recruited patients that had to be 18 or up (male or female), with signed informed consent, and who were diagnosed with COVID-19 infection by RT-PCR within one (1) week of study screening.

Some patients could not be included per the exclusion criteria. For example, if they refused to sign informed consent or had a history of bariatric surgery, total colectomy with ileorectal anastomosis, or proctectomy, they couldn’t participate. Neither could they if an individual had a history of postoperative stoma, ostomy or ileoanal pouch, or treatment with total parenteral nutrition.


The team found that this sequencing technology pinpointed the SARS-CoV-2 whole genome sequence in 100% of patients with positive nasopharyngeal RT-PCR and failed to detect it in asymptomatic post-treatment patients, or those with negative RT-PCR. 

Of significant interest, the investigators found that one patient tested positive for the novel coronavirus via NGS from stool 38 days after the initial primary nasopharyngeal RT-PCR test. Dr. Hazan and the team believe that this may indicate that the virus may remain in people’s GI tract for longer than anticipated. 

The results herein include the primary value of metagenomic analysis of the SARS-CoV-2 viral genome and may present an alternative diagnostic methodology that could possibly help with viral identification, diagnosis, and surveillance of its evolutionary progression through the human population on to its termination.


Hazan and her team found copies of the full genome of the SARS-CoV-2 virus in just one tiny stool sample. That finding was the same for each person with the virus. According to Dr. Hazan, “This means that the virus is setting up shop in the gut and relies on favorable conditions in that environment to replicate. ” Hazan continued, “To understand what this means you have to understand what happens in the gut.”

Dr. Hazan further noted, “What does this mean for the prevention and treatments associated with COVID-19?

About Progenabiome

Ventura, California-based Progenabiome is on a mission to crack the genetic code of a trillion bacteria, fungi, and viruses that live in the human gut (the microbiome). Set up as a genetic sequencing research laboratory dedicated to continuing the research of the late Dr. Sydney Finegold, who many consider being one of the fathers of the microbiome—that is a person who recognized the power of anaerobic bacteria. 

Lead Research/Investigator

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