Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota [version 2; peer review: 1 approved, 1 approved with reservations]

• Published in: F1000 research Vol. 11; p. 292
• Main Authors: Petrillo, Mauro, Querci, Maddalena, Brogna, Carlo, Ponti, Jessica, Cristoni, Simone, Markov, Peter V, Valsesia, Andrea, Leoni, Gabriele, Benedetti, Alessandro, Wiss, Thierry, Van den Eede, Guy
• Format: Journal Article
• Language: English
• Published: England Faculty of 1000 Ltd 2022; F1000 Research Limited; F1000 Research Ltd
• Subjects: Antibiotics; Antibodies; Bacteria; Bacteriophages - isolation & purification; Bacteriophages - physiology; Coronaviruses; COVID-19; COVID-19 - virology; Disease transmission; eng; Experiments; Feces; Feces - microbiology; Gastrointestinal Microbiome; Genomes; Gut microbiota; Humans; Inoculation; Intestinal microflora; Laboratories; Mass spectrometry; Microbiota; Microscopy; Nucleocapsids; Peptides; Phages; Plaques; Protein biosynthesis; Proteins; Reference materials; Replication; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; SARS-CoV-2 - physiology; Scientific imaging; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - biosynthesis; Spike Glycoprotein, Coronavirus - genetics; Spike Glycoprotein, Coronavirus - metabolism; Spike protein; United States > US; Italy; COVID-19; SARS-CoV-2; gut microbiota
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.109236.2

Background In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a 'bacteriophage-like' behaviour of SARS-CoV-2. Methods We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of a subject positive to SARS-CoV-2; (2) mass spectrometric analysis of these cultures to assess the eventual de novo synthesis of SARS-CoV-2 spike protein; (3) sequencing of SARS-CoV-2 collected from plaques obtained from two different gut microbial bacteria inoculated with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Results Immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirmed presence of SARS-CoV-2 both outside and inside bacteria. De novo synthesis of SARS-CoV-2 spike protein was observed, as evidence that SARS-CoV-2 RNA is translated in the bacterial cultures. In addition, phage-like plaques were spotted on faecal bacteria cultures after inoculation with supernatant from faecal microbiota of an individual positive to SARS-CoV-2. Bioinformatic analyses on the reads obtained by sequencing RNA extracted from the plaques revealed nucleic acid polymorphisms, suggesting different replication environment in the two bacterial cultures. Conclusions Based on these results we conclude that, in addition to its well-documented interactions with eukaryotic cells, SARS-CoV-2 may act as a bacteriophage when interacting with at least two bacterial species known to be present in the human microbiota. If the hypothesis proposed, i.e., that under certain conditions SARS-CoV-2 may multiply at the expense of human gut bacteria, is further substantiated, it would drastically change the model of acting and infecting of SARS-CoV-2, and most likely that of other human pathogenic viruses.