Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19

Lu, Zhenhua; Zhou, Hao-Wei; Wu, Wei-Kang; Fu, Ting; Yan, Min; He, Zhen; Sun, Shiwei; Ji, Zhenyu; Shao, Zhongjun

doi:10.3389/fcimb.2021.790422

Cited by 20 publications

(19 citation statements)

References 49 publications

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“…1 Furthermore, 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).…”

Section: Introductionsupporting

confidence: 76%

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

Petrillo¹,

Querci

Brogna³

et al. 2022

F1000Res

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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.

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Section: Introductionsupporting

confidence: 76%

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

Petrillo¹,

Querci

Brogna³

et al. 2022

F1000Res

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“…In a recent study involving COVID‐19 patients, Myoviridae, Siphoviridae, Microviridae, Podoviridae , and crass‐like phages were detected in the virome of fecal DNA of patients. 23 The results from the study correlate with our findings. In addition, the study reported that the virome composition in the gut changed significantly in the COVID‐19 patients when compared with healthy controls and the significant changes might be related to the changes in the bacteriome composition.…”

Section: Resultssupporting

confidence: 89%

“…The phage abundance drastically reduces from the severe cases to the nonsevere cases. In a recent study involving COVID‐19 patients, Myoviridae, Siphoviridae, Microviridae, Podoviridae , and crass‐like phages were detected in the virome of fecal DNA of patients 23 . The results from the study correlate with our findings.…”

Section: Resultssupporting

confidence: 89%

Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Ferravante

Arslan-Gatz

Dell’Annunziata

et al. 2022

Journal of Medical Virology

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In December 2019, several patients were hospitalized and diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, which subsequently led to a global pandemic. To date, there are no studies evaluating the relationship between the respiratory phageome and the SARS‐CoV‐2 infection. The current study investigated the phageome profiles in the nasopharyngeal swabs collected from 55 patients during the three different waves of coronavirus disease 2019 (COVID‐19) in the Campania Region (Southern Italy). Data obtained from the taxonomic profiling show that phage families belonging to the order Caudovirales have a high abundance in the patient samples. Moreover, the severity of the COVID‐19 infection seems to be correlated with the phage abundance.

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“…Upon viral clearance, prior hyperinflammatory state and microbiome imbalance may damage gastrointestinal integrity and function [47]. Current findings have emphasized changes in the gut microbiota in patients following COVID-19 infection [48][49][50].…”

Section: Symptoms Of Long Covidmentioning

confidence: 99%

“…SARS-CoV-2 RNA can be detected from fecal samples during acute stage, indicating gastrointestinal (GI) involvement in COVID-19 pathology [46,76]. Recent studies reveal that gut microbiome diversity and composition are changed post COVID-19 infection [48][49][50]. Increase in viral-induced cytokines may compromise intestinal integrity, facilitating the entry of bacteria and metabolites into circulation.…”

Section: Gut Microbiotamentioning

confidence: 99%

Long COVID and its Management

Koc¹,

Xiao²,

Liu³

et al. 2022

Int. J. Biol. Sci.

139

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The pandemic of COVID-19 is the biggest public health crisis in 21 st Century. Besides the acute symptoms after infection, patients and society are also being challenged by the long-term health complications associated with COVID-19, commonly known as long COVID. While health professionals work hard to find proper treatments, large amount of knowledge has been accumulated in recent years. In order to deal with long COVID efficiently, it is important for people to keep up with current progresses and take proactive actions on long COVID. For this purpose, this review will first introduce the general background of long COVID, and then discuss its risk factors, diagnostic indicators and management strategies. This review will serve as a useful resource for people to understand and prepare for long COVID that will be with us in the foreseeable future.

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Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19

Cited by 20 publications

References 49 publications

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

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

Dynamics of nasopharyngeal tract phageome and association with disease severity and age of patients during three waves of COVID‐19

Long COVID and its Management

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