New respiratory viral infections

Jartti, Tuomas; Jartti, Laura; Ruuskanen, Olli; Söderlund‐Venermo, Maria

doi:10.1097/mcp.0b013e328351f8d4

Cited by 90 publications

(80 citation statements)

References 118 publications

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“…One challenge for the control of respiratory diseases is that there are numerous viruses, bacteria, fungi, etc. which can cause acute or incidental illnesses 4. The clinical symptoms are often insufficient for making a clear diagnosis without using clinical microbiology and/or molecular tests 2.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital

Zhou

Fernandez

Yoon

et al. 2016

The American Society of Tropical Medicine and Hygiene

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Numerous pathogens cause respiratory infections with similar symptoms. Routine diagnostics detect only a limited number of pathogens, leaving a gap in respiratory illness etiology surveillance. This study evaluated next-generation sequencing for unbiased pathogen identification. Respiratory samples collected in Thailand, Philippines, Bhutan, and Nepal, that were negative by several molecular and immunofluorescence assays, underwent viral cultivation. Samples which demonstrated cytopathic effect in culture (N = 121) were extracted and tested by Luminex xTAG respiratory viral panel (RVP) assay and deep sequencing by Roche 454 FLX Titanium system. Using RVP assay, 52 (43%) samples were positive for enterovirus or rhinovirus and another three were positive for respiratory syncytial virus B, parainfluenza 4, and adenovirus. Deep sequencing confirmed the Luminex assay results and identified additional viral pathogens. Human enteroviruses, including Enterovirus A type 71 and 12 types of Enterovirus B (EV-B) were identified from a hospital in Bangkok. Phylogenetic and recombination analysis showed high correlation of VP1 gene-based phylogeny with genome-wide phylogeny and the frequent genetic exchange among EV-B viruses. The high number and diversity of enteroviruses in the hospital in Bangkok suggests prevalent existence. The metagenomic approach used in our study enabled comprehensive diagnoses of respiratory viruses.

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Section: Introductionmentioning

confidence: 99%

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital

Zhou

Fernandez

Yoon

et al. 2016

The American Society of Tropical Medicine and Hygiene

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“…Anelloviruses were identified in all but one pool (Table 1). Anelloviruses have been reported previously in human respiratory secretions (Burián et al, 2011;Jartti et al, 2012). Anelloviruses are usually considered commensal viruses (Okamoto, 2009a), although increased prevalence was found in bronchoalveolar lavage of children with acute exacerbation idiopathic pulmonary fibrosis (Wootton et al, 2011) and acute respiratory diseases (Maggi et al, 2003), and in lung tissues of pigs infected with known respiratory pathogens (Rammohan et al, 2012).…”

mentioning

confidence: 99%

Cyclovirus in nasopharyngeal aspirates of Chilean children with respiratory infections

Phan

Luchsinger

Avendaño

et al. 2014

Journal of General Virology

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Some respiratory tract infections remain unexplained despite extensive testing for common pathogens. Nasopharyngeal aspirates (NPAs) from 120 Chilean infants from Santiago with acute lower respiratory tract infections were analysed by viral metagenomics, revealing the presence of nucleic acids from anelloviruses, adenovirus-associated virus and 12 known respiratory viral pathogens. A single sequence read showed translated protein similarity to cycloviruses. We used inverse PCR to amplify the complete circular ssDNA genome of a novel cyclovirus we named CyCV-ChileNPA1. Closely related variants were detected using PCR in the NPAs of three other affected children that also contained anelloviruses. This report increases the current knowledge of the genetic diversity of cycloviruses whose detection in multiple NPAs may reflect a tropism for human respiratory tissues.Cycloviruses, members of a proposed genus within the family Circoviridae, have a circular ssDNA genome of approximately 2 kb (Li et al., 2010). Genetically highly diverse cycloviruses were initially found in the faeces of Pakistani children with and without acute flaccid paralysis (Victoria et al., 2009), in wild chimpanzees (Li et al., 2010) and in tissues of farm animals including cows, goats, bats and chickens (Ge et al., 2011;Li et al., 2010Li et al., , 2011. Unexpectedly, other cyclovirus species have also been detected in insects, namely dragonflies and cockroaches (Dayaram et al., 2013;Padilla-Rodriguez et al., 2013;Rosario et al., 2011). In 2013, a cyclovirus species (CyCV-CN) was found initially using viral metagenomics and then by PCR in 4 % of cerebrospinal fluid (CSF) specimens from Vietnamese children with unexplained central nervous system disorder, but not in CSF from patients with non-neurological problems, as well as in 4.2 % of faeces from healthy Vietnamese children (Tan et al., 2013). CyCV-CN DNA was also detected in a throat swab (Tan et al., 2013). In this study, 58 % of faecal specimens from pigs and poultry in Vietnam were also positive for the same cyclovirus, suggesting possible sources of human infection (Tan et al., 2013). A related cyclovirus was also detected in 10 % of CSF samples and 15 % of serum samples from adult patients with paraplegia (leg paralysis) from Malawi (Smits et al., 2013). Nasopharyngeal aspirates (NPAs) from Chilean children less than 2 years old with acute lower respiratory infections were tested for respiratory syncytial virus (RSV), adenovirus, parainfluenza virus 1-3 and influenza A and B viruses by indirect immunofluorescence assays and virus isolation (Avendaño et al., 2003). From 1998 to 2000, a mean of 29 % of acute lower respiratory infections samples were positive for RSV (Avendaño et al., 2003). To initiate the characterization of the viruses in non-reactive NPA samples, viral particles were enriched by filtration, and unprotected DNA and RNA were digested using a combination of nuclease enzymes (Victoria et al., 2009). The remaining nucleic acids were then extracted using a MagMAX Viral RNA Iso...

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“…Until the 1990s, viral cultures, antigen detection and antibody assays were used to diagnose virus‐specific respiratory infections . The introduction of polymerase chain reaction (PCR) increased the number of viral findings, revealed that multiple viral aetiological findings are common, confirmed that viruses are often found in nonsymptomatic children and even detected new viruses . Rhinoviruses were discovered in 1956, but the slow, nonsensitive viral culture was the only diagnostic method for decades, and the development of antigen or antibody assays did not help, as there are now more than 100 rhinovirus serotypes.…”

Section: Virus‐specific Odds Ratios (Ors) and 95% Confidence Intervalmentioning

confidence: 99%

“…Rhinoviruses were discovered in 1956, but the slow, nonsensitive viral culture was the only diagnostic method for decades, and the development of antigen or antibody assays did not help, as there are now more than 100 rhinovirus serotypes. In the 2000s, PCR highlighted the role of rhinoviruses in paediatric community‐acquired pneumonia (CAP) and identified other agents, such as the metapneumovirus, bocavirus and certain coronaviruses . Multiple viral findings and the presence of viral carriage raised questions about which virus was the real cause of clinical infections in each case .…”

Section: Virus‐specific Odds Ratios (Ors) and 95% Confidence Intervalmentioning

confidence: 99%

The role of rhinoviruses is overestimated in the aetiology of community‐acquired pneumonia in children

Korppi

2017

Acta Paediatrica

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New respiratory viral infections

Cited by 90 publications

References 118 publications

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital

Cyclovirus in nasopharyngeal aspirates of Chilean children with respiratory infections

The role of rhinoviruses is overestimated in the aetiology of community‐acquired pneumonia in children

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