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

2018 ◽  
Vol 28 (4) ◽  
pp. 257-262 ◽  
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.

scholarly journals Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

2020 ◽  
Vol 59 (1) ◽  
pp. e02142-20
Author(s):  
Ahmed Babiker ◽  
Heath L. Bradley ◽  
Victoria D. Stittleburg ◽  
Jessica M. Ingersoll ◽  
Autum Key ◽  
...  
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Human Metapneumovirus ◽  
Molecular Testing ◽  
Metagenomic Sequencing ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
Testing Algorithms ◽  
Syncytial Virus

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.

scholarly journals Global hospital admissions and in-hospital mortality associated with all-cause and virus-specific acute lower respiratory infections in children and adolescents aged 5–19 years between 1995 and 2019: a systematic review and modelling study

2021 ◽  
Vol 6 (7) ◽  
pp. e006014
Author(s):  
Xin Wang ◽  
You Li ◽  
Xin Mei ◽  
Erin Bushe ◽  
Harry Campbell ◽  
...  
Keyword(s):  
Systematic Review ◽  
Respiratory Syncytial Virus ◽  
Hospital Admissions ◽  
Respiratory Infections ◽  
Human Metapneumovirus ◽  
Parainfluenza Virus ◽  
Acute Lower Respiratory Infections ◽  
Hospital Deaths ◽  
Syncytial Virus ◽  
Human Parainfluenza Virus

IntroductionThe burden of acute lower respiratory infections (ALRI), and common viral ALRI aetiologies among 5–19 years are less well understood. We conducted a systematic review to estimate global burden of all-cause and virus-specific ALRI in 5–19 years.MethodsWe searched eight databases and Google for studies published between 1995 and 2019 and reporting data on burden of all-cause ALRI or ALRI associated with influenza virus, respiratory syncytial virus, human metapneumovirus and human parainfluenza virus. We assessed risk of bias using a modified Newcastle-Ottawa Scale. We developed an analytical framework to report burden by age, country and region when there were sufficient data (all-cause and influenza-associated ALRI hospital admissions). We estimated all-cause ALRI in-hospital deaths and hospital admissions for ALRI associated with respiratory syncytial virus, human metapneumovirus and human parainfluenza virus by region.ResultsGlobally, an estimated 5.5 million (UR 4.0–7.8) all-cause ALRI hospital admissions occurred annually between 1995 and 2019 in 5–19 year olds, causing 87 900 (UR 40 300–180 600) in-hospital deaths annually. Influenza virus and respiratory syncytial virus were associated with 1 078 600 (UR 4 56 500–2 650 200) and 231 800 (UR 142 700–3 73 200) ALRI hospital admissions in 5–19 years. Human metapneumovirus and human parainfluenza virus were associated with 105 500 (UR 57 200–181 700) and 124 800 (UR 67 300–228 500) ALRI hospital admissions in 5–14 years. About 55% of all-cause ALRI hospital admissions and 63% of influenza-associated ALRI hospital admissions occurred in those 5–9 years globally. All-cause and influenza-associated ALRI hospital admission rates were highest in upper-middle income countries, Asia-Pacific region and the Latin America and Caribbean region.ConclusionIncidence and mortality data for all-cause and virus-specific ALRI in 5–19 year olds are scarce. The lack of data in low-income countries and Eastern Europe and Central Asia, South Asia, and West and Central Africa warrants efforts to improve the development and access to healthcare services, diagnostic capacity, and data reporting.

scholarly journals The interferon regulatory factor IRF5 is differentially expressed in the blood of patients with viral co-infections.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Influenza A ◽  
Macrophage Polarization ◽  
Cell Lineage ◽  
Interferon Regulatory Factor ◽  
Human Rhinovirus ◽  
Differentially Expressed ◽  
Influenza B ◽  
Regulatory Factor ◽  
Transcriptional Responses ◽  
Human Coronavirus

Co-infection is a process by which the same host can be infected with two pathogens. By mining published microarray data (1), we found that the gene encoding the interferon regulatory factor 5 (IRF5) was among the genes most differentially expressed in the blood of seven patients with viral co-infections: in one patient with human coronavirus OC43 and Influenza A co-infection, in one patient with human coronavirus NL63 and Human Rhinovirus co-infection, and in five patients with Influenza B and Human Rhinovirus co-infection. IRF5 has described functions in macrophage polarization, T-cell lineage specification (2), B-cell development (3), innate immune signal transduction (4) and in transcriptional responses to viral infection (5), and could potentially be relevant to processes underlying viral co-infection.

scholarly journals Genetic Analysis of Human Parainfluenza Virus Type 4-Associated with Severe Acute Respiratory Infection Among Children in Luohe City, Henan Province, China, During 2017-2018

2021 ◽  
Author(s):  
Shanshan Zhou ◽  
Naiying Mao ◽  
Yan Zhang ◽  
Aili Cui ◽  
Zhen Zhu ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Acute Respiratory Infection ◽  
Clinical Characteristics ◽  
Henan Province ◽  
Parainfluenza Virus ◽  
Rt Pcr ◽  
Severe Acute Respiratory Infection ◽  
Center Hospital ◽  
Hn Gene ◽  
Human Parainfluenza Virus

Abstract During 2017–2018, Nasopharyngeal aspirates (NPAs) from 627 hospitalized patients with SARI at Luohe Center Hospital were tested by RT-PCR for human parainfluenza virus 4(HPIV-4). 14 (2.2%) of 627 samples were positive for HPIV-4. The complete nucleotide sequence of the HN gene from 9 positive samples was amplified and sequenced successfully. Genetic analysis showed that the HPIV-4 strains circulating in Luohe city are more closely related to HPIV-4A. Our study indicated that there were multiple lineages of HPIV-4 circulating in Henan Province in China during the study period, which will improve our understanding of the epidemiological and clinical characteristics of HPIV-4.

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