Detection of respiratory viruses by real-time polymerase chain reaction in outpatients with acute respiratory infection
subject: Respiratory Infections, real-time PCR, Multiplex, Viruses
description: Viruses are the major contributors to the morbidity and mortality of upper and lower acute respiratory infections (ARIs) for all age groups. The aim of this study was to determine the frequencies for a large range of respiratory viruses using a sensitive molecular detection technique in specimens from outpatients of all ages with ARIs. Nasopharyngeal aspirates were obtained from 162 individuals between August 2007-August 2009. Twenty-three pathogenic respiratory agents, 18 respiratory viruses and five bacteria were investigated using multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) and indirect immunofluorescence assay (IIF). Through IIF, 33 (20.4%) specimens with respiratory virus were recognised, with influenza virus representing over half of the positive samples. Through a multiplex real-time RT-PCR assay, 88 (54.3%) positive samples were detected; the most prevalent respiratory viral pathogens were influenza, human rhinovirus and respiratory syncytial virus (RSV). Six cases of viral co-detection were observed, mainly involving RSV. The use of multiplex real-time RT-PCR increased the viral detection by 33.9% and revealed a larger number of respiratory viruses implicated in ARI cases, including the most recently described respiratory viruses [human bocavirus, human metapneumovirus, influenza A (H1N1) pdm09 virus, human coronavirus (HCoV) NL63 and HCoV HKU1].
creator: Ronaldo Bragança Martins Júnior, Sharon Carney, Daniel Goldemberg, Lucas Bonine, Liliana Cruz Spano, Marilda Siqueira, Rita Elizabeth Checon
source: Memórias do Instituto Oswaldo Cruz.
publisher: Instituto Oswaldo Cruz, Ministério da Saúde
date: 2014
language: EN
identifier: DOI: 10.1590/0074-0276140046
coverage: Arctic medicine. Tropical medicine, Microbiology

Detection of Respiratory Viruses in Deceased Persons, Spain, 2017
subject: influenza, respiratory virus, Respiratory Syncytial Virus, coronavirus, Mortality, cause of death
description: During the 2016–17 influenza season in Spain, we tested specimens from 57 elderly deceased persons for respiratory viruses. Influenza viruses were detected in 18% of the specimens and any respiratory virus in 47%. Only 7% of participants had received a diagnosis of infection with the detected virus before death.
creator: Ana Navascués, Itziar Casado, Alejandra Pérez-García, Aitziber Aguinaga, Iván Martínez-Baz, Yugo Floristán, Carmen Ezpeleta, Jesús Castilla
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2018
language: EN
identifier: DOI: 10.3201/eid2407.180162
coverage: Infectious and parasitic diseases, Medicine

Detection of SARS Coronavirus in Patients with Suspected SARS
subject: SARS, severe acute respiratory syndrome, SARS-coronavirus, virus, Epidemiology, Transmission
description: Cases of severe acute respiratory syndrome (SARS) were investigated for SARS coronavirus (SARS-CoV) through RNA tests, serologic response, and viral culture. Of 537 specimens from patients in whom SARS was clinically diagnosed, 332 (60%) had SARS-CoV RNA in one or more clinical specimens, compared with 1 (0.3%) of 332 samples from controls. Of 417 patients with clinical SARS from whom paired serum samples were available, 92% had an antibody response. Rates of viral RNA positivity increased progressively and peaked at day 11 after onset of illness. Although viral RNA remained detectable in respiratory secretions and stool and urine specimens for >30 days in some patients, virus could not be cultured after week 3 of illness. Nasopharyngeal aspirates, throat swabs, or sputum samples were the most useful clinical specimens in the first 5 days of illness, but later in the illness viral RNA could be detected more readily in stool specimens.
creator: Kwok H. Chan, Leo L.L.M. Poon, V.C.C. Cheng, Yi Guan, I. F. N. Hung, Joseph S.M. Peiris, Loretta Y.C. Yam, Wing H. Seto, Kwok Y. Yuen, Joseph S. Malik Peiris
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2004
language: EN
identifier: DOI: 10.3201/eid1002.030610
coverage: Infectious and parasitic diseases, Medicine

Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis
subject: severe acute respiratory syndrome, SARS, coronavirus, COV, Taiwan, perspective
description: The severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to be transmitted primarily through dispersal of droplets, but little is known about the load of SARS-CoV in oral droplets. We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 102 to 5.93 x 106 copies/mL) and saliva (7.08 x 103 to 6.38 x 108 copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. Immunofluorescence study showed replication of SARS-CoV in the cells derived from throat wash, demonstrating the possibility of developing a convenient antigen detection assay. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four cases, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis.
creator: Wei-Kung Wang, Shey-Ying Chen, I-Jung Liu, Yee-Chun Chen, Huiling Chen, Chao-Fu Yang, Pei-Jer Chen, Shiou-Hwei Yeh, Chuan-Liang Kao, Li-Min Huang, Po-Ren Hsueh, Jann-Tay Wang, Wang-Hwei Sheng, Chi-Tai Fang, Chien-Ching Hung, Szu-Min Hsieh, Chan-Ping Su, Wen-Chu Chiang, Jyh-Yuan Yang, Jih-Hui Lin, Szu-Chia Hsieh, Hsien-Ping Hu, Yu-Ping Chiang, Jin-Town Wang, Pan-Chyr Yang, Shan-Chwen Chang
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2004
language: EN
identifier: DOI: 10.3201/eid1007.031113
coverage: Infectious and parasitic diseases, Medicine

Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan
subject: SARS, Respiratory Infections, covid-19, SARS-CoV-2, severe acute respiratory syndrome coronavirus 2, Hemodialysis
description: We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Healthcare workers should observe strict standard and contact precautions and use appropriate personal protective equipment when handling hemodialysis circuitry from patients with diagnosed coronavirus disease.
creator: Ayako Okuhama, Masahiro Ishikane, Daisuke Katagiri, Kohei Kanda, Takato Nakamoto, Noriko Kinoshita, Naoto Nunose, Takashi Fukaya, Isao Kondo, Harutaka Katano, Tadaki Suzuki, Norio Ohmagari, Fumihiko Hinoshita
source: Emerging Infectious Diseases
publisher: Centers for Disease Control and Prevention
date: 2020
coverage: Medicine, Infectious and parasitic diseases

Detection of SARS-CoV-2 in placental but not fetal tissues in the second trimester.
creator: Jacob E Valk, Alexander M Chong, Anne-Catrin Uhlemann, Larisa Debelenko
source: Journal of perinatology : official journal of the California Perinatal Association
date: 2021

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 RNA in Blood Donations
creator: Noor e Saba, Akhlaaq Wazeer, Zahida Qasim, Usman Waheed
source: Journal of Laboratory Physicians
publisher: Thieme Medical and Scientific Publishers Pvt. Ltd.
date: 2020
coverage: Medicine

Detection of swine transmissible gastroenteritis coronavirus using loop-mediated isothermal amplification
description: Abstract A conserved nucleic acid fragment of the nucleocapsid gene of Swine Transmissible Gastroenteritis Coronavirus (TGEV) was chosen as the target, six special primers were designed successfully. Loop-mediated isothermal amplification (LAMP) was developed to detect the TGEV by incubation at 60°C for 1 h and the product specificity was confirmed by HphI digestion. Standard curves with high accuracy for TGEV quantization was constructed by adding 1 × SYBR greenI in the LAMP reaction. The assay established in this study was found to detect only the TGEV and no cross-reaction with other viruses, demonstrating its high specificity. By using serial sample dilutions as templates, the detection limit of LAMP was about 10 pg RNA, 10 times more sensitive than that of PCR and could be comparable to the nest-PCR.
creator: Chen Qin, Li Jian, Fang Xue-En, Xiong Wei
source: Virology Journal
publisher: BMC
date: 2010
language: EN
identifier: DOI: 10.1186/1743-422X-7-206
coverage: Infectious and parasitic diseases

Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva.
description: In recent years, there have been increasing numbers of infectious disease outbreaks that spread rapidly to population centers resulting from global travel, population vulnerabilities, environmental factors, and ecological disasters such as floods and earthquakes. Some examples of the recent outbreaks are the Ebola epidemic in West Africa, Middle East respiratory syndrome coronavirus (MERS-Co) in the Middle East, and the Zika outbreak through the Americas. We have created a generic protocol for detection of pathogen RNA and/or DNA using loop-mediated isothermal amplification (LAMP) and reverse dot-blot for detection (RDB) and processed automatically in a microfluidic device. In particular, we describe how a microfluidic assay to detect HIV viral RNA was converted to detect Zika virus (ZIKV) RNA. We first optimized the RT-LAMP assay to detect ZIKV RNA using a benchtop isothermal amplification device. Then we implemented the assay in a microfluidic device that will allow analyzing 24 samples simultaneously and automatically from sample introduction to detection by RDB technique. Preliminary data using saliva samples spiked with ZIKV showed that our diagnostic system detects ZIKV RNA in saliva. These results will be validated in further experiments with well-characterized ZIKV human specimens of saliva. The described strategy and methodology to convert the HIV diagnostic assay and platform to a ZIKV RNA detection assay provides a model that can be readily utilized for detection of the next emerging or re-emerging infectious disease.
creator: Maite Sabalza, Rubina Yasmin, Cheryl A Barber, Talita Castro, Daniel Malamud, Beum Jun Kim, Hui Zhu, Richard A Montagna, William R. Abrams
source: PLoS ONE
publisher: Public Library of Science (PLoS)
date: 2018
language: EN
identifier: DOI: 10.1371/journal.pone.0192398
coverage: Science, Medicine

Detection rate and clinical impact of respiratory viruses in children with Kawasaki disease
subject: Coronary aneurysm, Mucocutaneous lymph node syndrome, Respiratory tract infections, Viruses, Reverse Transcriptase Polymerase Chain Reaction
description: PurposeThe purpose of this prospective case-control study was to survey the detection rate of respiratory viruses in children with Kawasaki disease (KD) by using multiplex reverse transcriptase-polymerase chain reaction (RT-PCR), and to investigate the clinical implications of the prevalence of respiratory viruses during the acute phase of KD.MethodsRT-PCR assays were carried out to screen for the presence of respiratory syncytial virus A and B, adenovirus, rhinovirus, parainfluenza viruses 1 to 4, influenza virus A and B, metapneumovirus, bocavirus, coronavirus OC43/229E and NL63, and enterovirus in nasopharyngeal secretions of 55 KD patients and 78 control subjects.ResultsVirus detection rates in KD patients and control subjects were 32.7% and 30.8%, respectively (P=0.811). However, there was no significant association between the presence of any of the 15 viruses and the incidence of KD. Comparisons between the 18 patients with positive RT-PCR results and the other 37 KD patients revealed no significant differences in terms of clinical findings (including the prevalence of incomplete presentation of the disease) and coronary artery diameter.ConclusionA positive RT-PCR for currently epidemic respiratory viruses should not be used as an evidence against the diagnosis of KD. These viruses were not associated with the incomplete presentation of KD and coronary artery dilatation.
creator: Ja Hye Kim, Jeong Jin Yu, Jina Lee, Mina Kim, Hong Ki Ko, Hyung-Soon Choi, Young-Hwue Kim, Jae-Kon Ko
source: Korean Journal of Pediatrics
publisher: Korean Pediatric Society
date: 2012
language: EN
identifier: DOI: 10.3345/kjp.2012.55.12.470
coverage: Pediatrics