Posted on May 09, 2019, 4 p.m.
A previously unknown family of DNA viruses has been identified by the University of Pennsylvania which is suggested to represent the second most abundant DNA virus in human lungs and mouths; it was named Redondoviridae as published in Cell Host Microbe.
Elevated levels of redondovirus DNA was found in lung specimens from critically ill patients who were in intensive care units, and in mouths of patients with untreated gum disease; viral levels declined in the patients with gum disease after receiving treatment for periodontitis.
Viruses are the most abundant biological entities on Earth, but it can be hard to identify new types in the human virome if their sequences are not similar to those in reference databases. “New sequencing techniques have helped us uncover a world of new viruses. However, the majority of the sequence data we have so far remains unclassified, leaving us much work to do in order to better understand the human virome and how these new species may be associated with illness.” says Frederic D. Bushman, Phd.
The researchers concluded “These results suggest that redondoviruses colonize human oro-respiratory sites and can bloom in several human disorders.”
Previous analyses of bronchoalveolar lavage samples from 2 organ donors identified short stretches of DNA similar to those of an uncharacterized pig virus. This study queried metagenomic datasets from multiple bronchoalveolar lavage samples, and the team was able to construct additional complete redondovirus genomes. “Assembly of shotgun metagenomic reads yielded complete circular genomes, which were then used to interrogate our collection of lung virome samples, allowing us to identify seven genomes. These genomes were then used as alignment targets to interrogate publicly available datasets. Twelve more samples had sufficient coverage of redondovirus sequences to allow assembly, yielding 19 complete genomes.”
The newly identified viruses were verified not to have originated from environmental contamination of clinical samples or reagents used in the lab, and that they were not bacteriophages. Analysis of metagenomic sequence datasets from over 7,500 samples held in 173 datasets covering 51 different organisms and environments indicates the redondovirus family is found exclusively in humans, being localized to the lungs and oral cavity, and rarely found in gut samples.
“Redondoviruses were not found in other animals, fresh water, marine, or soil samples (1,087 non-human biological samples) nor in laboratory reagents (144 contamination control sample),” the researchers stated. “We thus conclude that redondoviruses are authentically present in the human oro-respiratory tract… We cannot rule out that redondoviruses colonize other animal species, although thus far we only identified hits in human samples.”
“...redondoviruses are associated with periodontitis in multiple studies and that levels are reduced with effective treatment. The role of redondoviruses in periodontitis warrants further study. Interestingly, direct qPCR analysis of lung samples from 60 healthy adults and 69 critically ill individuals indicated that although redondoviruses were present in healthy people, viral levels were also elevated in the critically ill patients.”
“Here, we introduce Redondoviridae, a family of small, circular DNA viruses discovered in metagenomic sequence data, which is found selectively in human lung and oro-pharyngeal samples. Of the DNA viruses we surveyed in 20 human virome datasets, redondoviruses were the second most abundant, exceeded only by anelloviruses.”
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