Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota

Mauro Petrillo,Peter V Markov,Carlo Brogna,Andrea Valsesia,Simone Cristoni,Guy Van Den Eede,Thierry Wiss,Gabriele Leoni,Maddalena Querci,Jessica Ponti,Alessandro Benedetti

doi:10.12688/f1000research.109236.1

Abstract

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.

Highlights

In a recent study, we reported a series of observations suggesting unexpected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – bacteria interactions
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
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

Summary

Introduction

We reported a series of observations suggesting unexpected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – bacteria interactions. Increase of viral loads was influenced by the administration of specific antibiotics The observations reported in Ref. 1 are in line with additional ones reported more recently, like evidence that gut virome is affected by the SARS-CoV-2 infection and may play an important role in the disease progression of coronavirus disease 2019 (COVID-19),[2] the presence of SARS-CoV-2 nucleoprotein (N) in intestinal epithelial cells of approximately 35% of patients with COVID-19 even several weeks or months after initial diagnosis,[3] the high rate of positive polymerase chain reaction (PCR) findings in more than one type of clinical specimen collected up to 43 days after COVID-19 patients had presented the first symptom.[4] To investigate these observations in more detail, we designed and carried out three different experiments, which make use of electron microscopy (EM), mass spectrometry and next-generation sequencing (NGS). 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

Methods

Results

Discussion

Conclusion