Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation

Abbas, Arwa; Young, J. C.; Clarke, Erik L.; Diamond, Joshua M.; Imai, Ize; Haas, Andrew R.; Cantu, Edward; Lederer, David J.; Meyer, Keith C.; Milewski, Rita K.; Olthoff, Kim M.; Shaked, Abraham; Christie, Jason D.; Bushman, Frederic D.; Collman, Ronald G.

doi:10.1111/ajt.15116

Cited by 33 publications

(44 citation statements)

References 56 publications

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“…The output sam files were process by Samtools 43 , Bedtools 44 and custom code ( https://github.com/guanxiangliang/liang2019 ) to quantify the fraction of the genome covered. We favor use of percent coverage as a metric for genome detection 45 ; amplification during sequence library preparation can yield many copies of single genome regions, yielding many sequence reads but with low genome coverage. Comparisons in several studies thus indicate coverage is a more reliable measure.…”

Section: Methodsmentioning

confidence: 99%

The stepwise assembly of the neonatal virome is modulated by breastfeeding

Liang

Zhao

Zhang

et al. 2020

Nature

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The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, in some cases leading to gastrointestinal disorders 1 – 4 . Here we report that viral community assembly in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium/early stool samples show few or no particles, but by one month of life particle numbers achieve 10 9 per gram, and these numbers appear to persist through life 5 – 7 . We investigated the origin of these viral populations using shotgun metagenomic sequencing of viral-enriched preparations and whole microbial communities, and followed up with targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut, and by one month prophage induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies exclusively fed formula versus those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections 8 – 10 . Phage populations also differed associated with breastfeeding. Evidently colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells, with the second phase modulated by breastfeeding.

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Section: Methodsmentioning

confidence: 99%

The stepwise assembly of the neonatal virome is modulated by breastfeeding

Liang

Zhao

Zhang

et al. 2020

Nature

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204

230

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“…Additional eukaryotic viruses frequently detected include Adenoviridae , Herpesviridae and Papillomaviridae 29 , 58 – 62 . Phages are commonly found, including Caudovirales , Microviridae and Inoviridae 29 , 58 – 62 . Phages, like most of the cellular microbiota, even when found in the lung appear to be derived mainly from the abundant bacterial populations in the mouth and upper respiratory tract.…”

Section: Virome Of Different Body Sitesmentioning

confidence: 99%

“…on respiratory tract samples including sputum, naso pharyngeal swabs and bronchoalveolar lavage, showing that the healthy human lung and respiratory tract can be populated by large viral communities 29,[58][59][60][61][62] . Among human DNA viruses, Anelloviridae has been reported to be the most prevalent family of DNA viruses, followed by Redondoviridae 32 .…”

Section: Respiratory Tract Virome Analyses Have Been Performedmentioning

confidence: 99%

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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“…While attempting to study human virome in bronchoalveolar lavage (BAL) samples of lung transplant patients [ 1 , 2 ], Abbas and colleagues identified sequence reads that aligned with low-coverage to a poorly characterized circovirus, named porcine stool-associated circular virus-5 (PoSCV-5) [ 3 ]. Further genomic characterization of these reads revealed that they belonged to a novel virus having a single, closed molecule of circular DNA approximately 3000 nucleotides (nt) in length called Redondovirus (ReDoV) [ 4 ].…”

Section: Introductionmentioning

confidence: 99%