SARS-CoV-2 and co-infections detection in nasopharyngeal throat swabs of COVID-19 patients by metagenomics
Fecha
2020Autor
Tan Le, Van
Hong Nguyen, Thi Thu
Ngoc, Nghiem My
Thwaites, Guy
Chau Nguyen, Van Vinh
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Resumen
e read with interest a recent article in this journal regarding
co-infections in people with COVID-19.1 Rapid and simultaneous
detection of SARS-CoV-2, the cause of COVID-19, and co-infections
is essential for clinical management of COVID-19 patients. However, the diversity of possible co-infecting pathogens (bacteria and
viruses) challenges conventional diagnostics approaches (bacterial
culture and PCR). Metagenomics is a sensitive pan-pathogen assay for infectious disease diagnosis and the discovery of novel
pathogens.2 However, there have been only three studies reporting the application of metagenomics to detect SARS-CoV-2 and coinfections, with a combined sample size of nine patients.3–5
Since the beginning of March 2020 an observational study have
been conducted at the Hospital for Tropical Diseases (HTD) in Ho
Chi Minh City, Vietnam and another one at one of its two designated centers for receiving and treating COVI-19 patients from
southern Vietnam with a population of over 40 million (Supplementary Figure 1). We enrolled patients with a confirmed SARSCoV-2 diagnosis by a WHO recommended assay admitted to the
study settings within 48 h. We collected nasopharyngeal throat
swabs (NTS), clinical and laboratory data, and travel and contact
history from each study participant. The collected NTS was stored
at 4 °C at the study sites within four hours and was then transferred to the clinical laboratory of HTD for analysis. The clinical
studies received approvals from the Institutional Review Board of
the HTD and the Oxford Tropical Research Ethics Committee of
the University of Oxford. Study participants gave their written informed consent.
Palabras clave
SARS-CoV-2; COVID-19; Patients by metagenomicsEnlace al recurso
https://doi.org/10.1016/j.jinf.2020.06.033Colecciones
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