Metagenomic analysis identified co-infection with human rhinovirus C and bocavirus 1 in an adult suffering from severe pneumonia

Li, Yanpeng; Deng, Xilong; Hu, Fengyu; Wang, Jian; Liu, Ying; Huang, Huang; Ma, Jinmin; Zhang, Jianhui; Zhang, Fuchun; Zhang, Chiyu

doi:10.1016/j.jinf.2017.10.012

Cited by 16 publications

(17 citation statements)

References 10 publications

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“…For rapidly emerging infectious diseases, metagenomic next-generation sequencing (mNGS) offers an opportunity to both recover whole viral genomes for epidemiological purposes and to agnostically determine co-infections that may be associated with increased morbidity and mortality in emerging infectious diseases (8).…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization

et al. 2020

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Abstract Background More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. Methods To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. Results Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients’ respiratory symptoms. Conclusion Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.

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Section: Introductionmentioning

confidence: 99%

Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization

et al. 2020

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“…[147,151] The sensitivity of mNGS is further highlighted in mixed pulmonary infection diagnosis and severe nonresponding pneumonia. [153][154][155] In fact, the detection accuracy rate of mNGS may even reach 100% in the analysis of immunocompromised patients. [156] Additionally, mNGS provides more strain-specific information and helps to identify new pathogens.…”

Section: Respiratory Infectionsmentioning

confidence: 99%

“…NGS is currently the preferred methodology for virus discovery, particularly for emerging pneumonia-causing viruses (i.e., SARS-CoV, MERS-CoV, and H7N9), and could potentially help to trace and control outbreaks. [154] Interestingly, the specificity of mNGS is reportedly higher for transbronchial lung biopsy (TBLB) tissue than for BALF; however, detection in BALF has been shown to have a higher sensitivity in the diagnosis of peripheral pulmonary infectious lesions. [152] However, in our experience, the overall sensitivity of mNGS does not differ among respiratory tract sample types and is not superior to that of culture for recognizing common bacteria.…”

Section: Respiratory Infectionsmentioning

confidence: 99%

High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

et al. 2020

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The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next‐generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third‐generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS‐related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.

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“…To further exclude the possibility of laboratory contamination, we searched for any sequences similar to GkV_CN-GZ1 from the metagenomic sequencing data generated from more than 200 human swab samples (including another patient with severe pneumonia who was admitted to the same hospital during the same period [8]) with the same protocol and reagents in our laboratory. No GkV sequences were found.…”

Section: Confirmation and Prevalence Screeningmentioning

confidence: 99%

Gemykibivirus Genome in Lower Respiratory Tract of Elderly Woman With Unexplained Acute Respiratory Distress Syndrome

Wang

et al. 2019

Clinical Infectious Diseases

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Metagenomic analysis identified co-infection with human rhinovirus C and bocavirus 1 in an adult suffering from severe pneumonia

Cited by 16 publications

References 10 publications

Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization

Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization

High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

Gemykibivirus Genome in Lower Respiratory Tract of Elderly Woman With Unexplained Acute Respiratory Distress Syndrome

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