Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis

Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico; Kisielius, Jonas José; Ueda-Ito, M.; Brandão, Paulo Eduardo; Curti, Suely Pires

doi:10.1016/j.virusres.2013.09.018

Cited by 17 publications

(20 citation statements)

References 67 publications

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“… 29 In addition, a virus detected in fecal samples or respiratory tract secretions may have been inhaled or ingested and may have passed through the lumen of the respiratory or digestive tract without replicating into that host. 3 , 12 The human bocavirus exemplifies the difficulty in evaluating the causal association between a newly discovered virus in the respiratory tract and the clinical manifestations. Bocaviruses were discovered in 2005 using a metagenomic approach in a pool of randomly selected samples of nasopharyngeal aspirates 1 and have been a topic of intense research since then.…”

Section: Discovery Of Viruses Through Viral Metagenomicsmentioning

confidence: 99%

“… 29 Além disso, um vírus detectado em fezes e amostras de secreção de vias respiratórias pode apenas ter sido inalado ou ingerido e ser um passageiro através do lúmen dos dutos do trato respiratório ou digestivo, sem se replicar naquele hospedeiro. 3 , 12 O bocavírus humano exemplifica essa dificuldade em avaliar a associação de um vírus novo descoberto no trato respiratório a um quadro clínico. Descoberto em 2005 por abordagem metagenômica em um pool de amostras selecionadas aleatoriamente de aspirado nasofaríngeo, 1 o bocavírus tem sido alvo de inúmeras pesquisas desde então.…”

Section: Descoberta De Vírus Através Da Metagenômica Viralunclassified

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The metagenomic approach and causality in virology

Castrignano

Nagasse-Sugahara

2015

Rev. Saúde Pública

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Section: Discovery Of Viruses Through Viral Metagenomicsmentioning

confidence: 99%

Section: Descoberta De Vírus Através Da Metagenômica Viralunclassified

The metagenomic approach and causality in virology

Castrignano

Nagasse-Sugahara

2015

Rev. Saúde Pública

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“…Sequence-Independent Single-Primer Amplification (SISPA) has been used in viral genomics and metagenomics to obtain whole genome sequences (Castrignano et al, 2013; Depew et al, 2013; Djikeng et al, 2008; Rosseel et al, 2013), but its use in bacterial genomics has not been explored. The method uses a barcoded amplification primer with 3′-end random nucleotides that anneal to template DNA and a second round of single primer PCR amplification.…”

Section: Introductionmentioning

confidence: 99%

SISPA-Seq for rapid whole genome surveys of bacterial isolates

Wright

Stockwell

Beck

et al. 2015

Infection, Genetics and Evolution

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Whole genome sequencing (WGS) of large isolate collections has many applications, yet sequencing costs are still significant. We sought to develop a rapid and cost efficient WGS method to address fundamental questions in clinical microbiology. We evaluated the performance of SISPA (Sequence-Independent, Single-Primer Amplification) combined with next-generation sequencing (SISPA-Seq) of 75 clinical isolates of Acinetobacter baumannii to establish whether SISPA-Seq resulted in sufficient coverage and quality to 1) determine strain phylogenetic placement and 2) and carriage of known antibiotic resistance (AbR) genes. Strains for which whole genome sequences were available were included for validation. Two libraries for each strain were constructed from separate SISPA reactions with different barcoded primers, using genomic DNA prepared from either high quality or rapid heat-lysis preparations. SISPA-Seq resulted in a median of 65x genome coverage when reads from both primer sets were combined. Coverage and quality were sufficient for detection of AbR genes by comparison of reads to the ARG-ANNOT database and were often sufficient to distinguish between different allelic variants of the same gene. kSNP and RAxML were used to construct a robust phylogeny based on single-nucleotide variants (SNVs) that showed that the SISPA-seq data was sufficient for sensitive and accurate phylogenetic placement. Advantages of the SISPA-Seq method include inexpensive and rapid DNA preparation and a typical total cost less than one-half that of standard genome sequencing. In summary, SISPA-Seq can be used to survey whole genomes of a large strain collection and identify strains that should be targeted for additional sequencing.

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“…In addition to six recognized CRESS DNA viral families, a large number of novel CRESS DNA viruses, waiting to be classified by ICTV, have been rapidly discovered in faeces of humans and animals through viral metagenomics in recent years. The hosts include chimpanzees (Blinkova et al, 2010), pigs Zhang et al, 2014), rodents (Phan et al, 2011), bats (Ge et al, 2011), humans (Castrignano et al, 2013), dromedaries (Woo et al, 2014), duck (Steel et al, 2016), deer (Steel et al, 2016), llama (Steel et al, 2016), chamois (Steel et al, 2016), bovine (Steel et al, 2016), flying fox (Male et al, 2016), chickens (Lima et al, 2017) and macaques (Kapusinszky et al, 2017).…”

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confidence: 99%

Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China

Guo

Tang

et al. 2018

Virus Research

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In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The virus, named Bo-Circo-like virus CH, has a circular genome with 3909 nucleotides (nt). Six putative open reading frames (ORFs) were identified, including Rep, capsid (Cap) and four proteins of unknown function. Both the genome size and the number as well as the organization of encoded ORFs, Bo-Circo-like virus CH is most closely related to Po-Circo-like virus 21 detected in pig faeces. A preliminary survey using specific primers for the Rep region showed that 5.3% (4/75) of diarrheic samples were positive for Bo-Circo-like virus, and all 42 healthy samples were negative. In conclusion, our results indicate that Bo-Circo-like virus CH may represent a new virus in bovine. Further investigation is needed to determine the relationship between the virus infection and diarrhea.

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Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis

Cited by 17 publications

References 67 publications

The metagenomic approach and causality in virology

The metagenomic approach and causality in virology

SISPA-Seq for rapid whole genome surveys of bacterial isolates

Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China

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