Stability of human metapneumovirus and human coronavirus NL63 on medical instruments and in the patient environment

ABSTRACTBroad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.

Download Full-text

Deteksi Virus Penyebab Infeksi Saluran Pernafasan Akut di Rumah Sakit (Studi Pendahuluan dengan Uji Fast-Track® Diagnostik)

Media Penelitian dan Pengembangan Kesehatan ◽

10.22435/mpk.v28i4.257 ◽

2018 ◽

Vol 28 (4) ◽

pp. 257-262 ◽

Cited By ~ 1

Author(s):

Vivi Setiawaty ◽

Maretra Anindya Puspaningrum ◽

Arie Ardiansyah Nugraha ◽

Daniel Joko Wahyono

Keyword(s):

Laboratory Testing ◽

Fast Track ◽

Human Adenovirus ◽

Human Metapneumovirus ◽

Human Rhinovirus ◽

Parainfluenza Virus ◽

Influenza B ◽

Rt Pcr ◽

Human Coronavirus ◽

Human Parainfluenza Virus

Abstract Acute respiratory infections (ARI) is the leading cause of morbidity and mortality in the world and Indonesia. Information on the virus that causes ARI is still limited. The aim of this study was to detect the virus that causes ARI hospitalized cases in three sentinel surveillance hospitals of severe ARI. Laboratory testing of 30 nasal and throat swab specimens from ARI hospitalized cases at Deli Serdang Hospital, Wonosari Hospital and Kanudjoso Djati Hospital during August - September 2016. Laboratory testing were carried out at the Virology Laboratory of the Center for Biomedical Research and Development and Basic Health Technology. This research is a preliminary study using Fast-Track Diagnostics multiplex Real-time RT-PCR to detect 21 viruses. The viruses that have been detected are Human Metapneumovirus (21.2%), Human Parainfluenza Virus 1 (12.1%), Influenza B (6.1%), Human Coronavirus-OC43 (6.1%), Human CoronavirusNL63 (6.1%), Human Parainfluenza Virus 2 (3.0%), Human Rhinovirus (3.0%), and Human Adenovirus (3.0%). Of the 17 samples that tested positive for viruses, 14 of them were single cases of infection while the other three were cases of co-infection between Human Coronavirus-NL63 and Human Parainfluenza Virus 1, Human Metapneumovirus with Human Coronavirus-OC43, and Human Adenovirus with Human Rhinovirus. The most detected virus from ARI hospitalized cases are the Human Metapneumovirus. Abstrak Infeksi saluran pernafasan akut (ISPA) merupakan penyakit menular yang menjadi penyebab utama 1 morbiditas dan mortalitas di dunia dan Indonesia. Informasi virus penyebab ISPA masih terbatas. Tujuan dari penelitian ini adalah mendeteksi virus penyebab kasus ISPA rawat inap di tiga rumah sakit sentinel surveilans ISPA berat. Pemeriksaan pada 30 spesimen swab hidung dan tenggorok dari kasus ISPA rawat inap di RSUD Deli Serdang, RSUD Wonosari, dan RS Kanudjoso Djati selama bulan Agustus–September 2016. Pemeriksaan dilakukan di Laboratorium Virologi Pusat Penelitian dan Pengembangan Biomedis dan Teknologi Dasar Kesehatan. Penelitian ini merupakan penelitian pendahuluan menggunakan FastTrack Diagnostics multiplex Real-time RT-PCR untuk mendeteksi 21 virus. Virus-virus yang berhasil dideteksi adalah Human Metapneumovirus (21,2%). Human Parainfluenza Virus 1 (12,1%), Influenza B (6,1%), Human Coronavirus-OC43 (6,1%), Human Coronavirus-NL63 (6,1%), Human Parainfluenza Virus 2 (3,0%), Human Rhinovirus (3,0%), dan Human Adenovirus (3,0%). Dari 17 sampel yang dinyatakan positif mengandung virus, 14 diantaranya merupakan kasus infeksi tunggal sedangkan tiga lainnya merupakan kas us koinfeksi antara Human Coronavirus-NL63 dengan Human Parainfluenza Virus 1, Human Metapneumovirus dengan Human Coronavirus-OC43, dan Human Adenovirus dengan Human Rhinovirus. Virus yang paling banyak terdeteksi dari spesimen kasus ISPA rawat inap adalah Human Metapneumovirus.

Download Full-text