Redondovirus DNA in human respiratory samples

Spezia, Pietro Giorgio; Macera, Lisa; Mazzetti, Paola; Curcio, M. Joan; Biagini, C.; Sciandra, Ilaria; Turriziani, Ombretta; Lai, Michele; Antonelli, Guido; Pistello, Mauro; Maggi, Fabrizio

doi:10.1016/j.jcv.2020.104586

Cited by 22 publications

(20 citation statements)

References 20 publications

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“…The prevalence (56.9%) of redondoviruses detected in our study participants was higher than the reported prevalence of 15% in the oropharynx of healthy Americans [8], 11% among Italians [10], and 2% among Spanish subjects [11]. However, phylogenetic analysis found no large-scale geographical clustering between viruses detected in Vietnam, the US, Spain, and China, indicating the wide geographic distribution and genetic diversity of redondoviruses.…”

Section: Discussioncontrasting

confidence: 83%

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Deng

Hong

et al. 2021

Viruses

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Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined.

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Section: Discussioncontrasting

confidence: 83%

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Deng

Hong

et al. 2021

Viruses

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“…Anelloviridae levels are typically elevated in immunocompromised states ( 13 , 14 ). Redondoviridae are a recently-described family of viruses that appear restricted to the human oral and respiratory tract and have a prevalence of up to 15% ( 15 , 33 ). Redondoviridae levels are elevated in the airway of intubated patients and in oral samples of periodontitis patients ( 15 , 33 ), suggesting that they may be barometers for disease activity in some conditions.…”

Section: Discussionmentioning

confidence: 99%

Signatures of COVID-19 severity and immune response in the respiratory tract microbiome

Merenstein

Liang

Whiteside

et al. 2021

Preprint

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Rationale: Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Objective: To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes. Methods and Measurements: We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC). Main Results: COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Conclusions: The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.

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“…As with Anelloviridae , whether Redondoviridae can cause disease is unknown. Preliminary studies show increased levels of redondoviruses in humans with periodontitis, patients who are critically ill in a medical intensive care unit and individuals with severe respiratory diseases 32 , 33 , although to date there is no evidence that redondoviruses are contributing to the disease states. Thus, both anelloviruses and redondoviruses appear to be common commensal viruses that might be undetected if not for developments in viral metagenomic sequencing methods.…”

Section: Virome Of Different Body Sitesmentioning

confidence: 99%

“…Greater abundance of Anelloviridae has been found in indi viduals who are immunocompromised, including the recipients of lung transplants, individuals who are HIV positive and individuals on immuno suppressive medi cations owing to inflammatory bowel disease, indicat ing that Anelloviridae are normally under host immune control 12,14,[29][30][31] . The newly discovered Redondoviridae are another family of small circular DNA viruses that appear to be widespread commensals commonly found in the respiratory tract [32][33][34] .…”

Section: Human Virome Diversitymentioning

confidence: 99%

“…However, it should be noted that prevalence meas ures are expected to be dependent on the sampling meth ods used, and the multiple displacement amplification steps typically used to amplify virome samples likely favour amplification of small DNA circles, potentially boosting detection of Anelloviridae and Redondoviridae. Reports so far put the prevalence of Redondoviridae at 2-15% in different populations [32][33][34] . As with Anelloviridae, whether Redondoviridae can cause disease is unknown.…”

Section: Viral Contigsmentioning

confidence: 99%

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The human virome: assembly, composition and host interactions

2021

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The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the ‘virome’. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 10 31 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 10 13 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral ‘dark matter’. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host–virome interactions in health and disease.

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Redondovirus DNA in human respiratory samples

Abstract: Highlights ReDoV infection may not be systemic or the presence of circulating virus can be only intermittent. ReDoV infection is mainly present in the respiratory tract.

Cited by 22 publications

References 20 publications

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

Signatures of COVID-19 severity and immune response in the respiratory tract microbiome

The human virome: assembly, composition and host interactions

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