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1.
J Antimicrob Chemother ; 76(Suppl 3): iii33-iii49, 2021 09 23.
Article in English | MEDLINE | ID: covidwho-1664107

ABSTRACT

OBJECTIVES: It is unclear whether real-time (rt)-PCR cycle threshold (Ct) values can be utilized to guide clinical and infection-control decisions. This systematic review assesses the association between respiratory pathogen rt-PCR Ct values and clinical presentation or outcomes. METHODS: We searched MEDLINE, EMBASE and Cochrane library databases on 14-17 January 2020 for studies reporting the presence or absence of an association between Ct values and clinical presentation or outcomes, excluding animal studies, reviews, meta-analyses, and non-English language studies. RESULTS: Among 33 studies identified (reporting on between 9 and 4918 participants by pathogen), influenza (n = 11 studies; 4918 participants), human rhinovirus (HRV, n = 11; 2012) and respiratory syncytial virus (RSV, n = 8; 3290) were the most-studied pathogens. Low influenza Ct values were associated with mortality in 1/3 studies, with increased disease severity/duration or ICU admission in 3/9, and with increased hospitalization or length of hospital stay (LOS) in 1/6. Low HRV Ct values were associated with increased disease severity/duration or ICU admission in 3/10 studies, and with increased hospitalization or LOS in 1/3. Low RSV Ct values were associated with increased disease severity/duration or ICU admission in 3/6 studies, and with increased hospitalization or LOS in 4/4. Contradictory associations were also identified for other respiratory pathogens. CONCLUSIONS: Respiratory infection Ct values may inform clinical and infection-control decisions. However, the study heterogeneity observed in this review highlights the need for standardized workflows to utilize Ct values as a proxy of genomic load and confirm their value for respiratory infection management.


Subject(s)
Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Hospitalization , Humans , Infant , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics
3.
Science ; 375(6577): 161-167, 2022 Jan 14.
Article in English | MEDLINE | ID: covidwho-1648160

ABSTRACT

The COVID-19 pandemic has underscored the critical need for broad-spectrum therapeutics against respiratory viruses. Respiratory syncytial virus (RSV) is a major threat to pediatric patients and older adults. We describe 4'-fluorouridine (4'-FlU, EIDD-2749), a ribonucleoside analog that inhibits RSV, related RNA viruses, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with high selectivity index in cells and human airway epithelia organoids. Polymerase inhibition within in vitro RNA-dependent RNA polymerase assays established for RSV and SARS-CoV-2 revealed transcriptional stalling after incorporation. Once-daily oral treatment was highly efficacious at 5 milligrams per kilogram (mg/kg) in RSV-infected mice or 20 mg/kg in ferrets infected with different SARS-CoV-2 variants of concern, initiated 24 or 12 hours after infection, respectively. These properties define 4'-FlU as a broad-spectrum candidate for the treatment of RSV, SARS-CoV-2, and related RNA virus infections.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/drug therapy , Respiratory Syncytial Virus Infections/drug therapy , Respiratory Syncytial Virus, Human/drug effects , SARS-CoV-2/drug effects , Uracil Nucleotides/pharmacology , Administration, Oral , Animals , Antiviral Agents/administration & dosage , Antiviral Agents/metabolism , COVID-19/virology , Cell Line , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Disease Models, Animal , Female , Ferrets , Humans , Mice , Mice, Inbred BALB C , Microbial Sensitivity Tests , Mononegavirales/drug effects , Mononegavirales/physiology , RNA-Dependent RNA Polymerase/metabolism , Respiratory Mucosa/virology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/physiology , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Transcription, Genetic , Uracil Nucleotides/administration & dosage , Uracil Nucleotides/metabolism , Virus Replication/drug effects
4.
Influenza Other Respir Viruses ; 16(3): 511-520, 2022 May.
Article in English | MEDLINE | ID: covidwho-1574843

ABSTRACT

BACKGROUND: Human respiratory syncytial virus (RSV) is a leading pathogen of acute respiratory tract disease among infants and young children. Compared with previous seasons, RSV outbreaks in Taiwan during the 2020-2021 season were delayed because of COVID-19 mitigation measures. We conducted this study to determine the association of viral factors with clinical characteristics of preschool children with RSV infection. METHODS: We performed a molecular epidemiology analysis of RSV among inpatient preschool children in Taiwan. In 80 nasopharyngeal samples positive for RSV, we sequenced and analyzed viral genotypes according to patient data. Patients' clinical data were obtained from medical files, and their clinical profiles were compared with those of RSV cases recorded during the 2014-2017 seasons. RESULTS: Phylogenetic analysis revealed that among the RSV-positive samples, all RSV strains identified during the 2020-2021 season belonged to the ON1 genotype. Most of the Taiwan ON1 strains were categorized into two well-supported clusters with distinct G protein amino acid substitution patterns that had never been demonstrated previously. Furthermore, the proportion of cases among children aged >24 months increased (P < 0.001). Compared with patients infected during the 2014-2017 seasons, patients infected during the 2020-2021 season were hospitalized for shorter days from hospital admission to dereference (P = 0.004) and had a greater need for oxygen supplements (P = 0.021) and systemic steroid therapy (P = 0.026). CONCLUSION: The delayed 2020-2021 RSV outbreak in Taiwan was caused by two novel RSV ON1.1 variants. How the change in RSV epidemiology affects future RSV outbreaks warrants exploration.


Subject(s)
COVID-19 , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Child, Preschool , Disease Outbreaks , Genotype , Humans , Infant , Phylogeny , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , Taiwan/epidemiology
5.
J Korean Med Sci ; 36(48): e328, 2021 Dec 13.
Article in English | MEDLINE | ID: covidwho-1572278

ABSTRACT

BACKGROUND: In the coronavirus disease 2019 (COVID-19) pandemic era, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus (Flu), and respiratory syncytial virus (RSV) is important in the rapid differential diagnosis in patients with respiratory symptoms. Three multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been recently developed commercially in Korea: PowerChek™ SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit (PowerChek; KogeneBiotech); STANDARD™ M Flu/SARS-CoV-2 Real-time Detection Kit (STANDARD M; SD BioSensor); and Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Allplex; Seegene). We evaluated the analytical and clinical performances of these kits. METHODS: A limit of detection tests were performed and cross-reactivity analysis was executed using clinical respiratory samples. Ninety-seven SARS-CoV-2-positive, 201 SARS-CoV-2-negative, 71 influenza A-positive, 50 influenza B-positive, 78 RSV-positive, and 207 other respiratory virus-positive nasopharyngeal swabs were tested using the three assays. The AdvanSure™ respiratory viruses rRT-PCR assay (AdvanSure; LG Life Sciences) was used as a comparator assay for RSV. RESULTS: Except in influenza B, in SARS-CoV-2 and influenza A, there were no significant differences in detecting specific genes of the viruses among the three assays. All three kits did not cross-react with common respiratory viruses. All three kits had greater than 92% positive percent agreement and negative percent agreement and ≥ 0.95 kappa value in the detection of SARS-CoV-2 and flu A/B. Allplex detected RSV more sensitively than AdvanSure. CONCLUSION: The overall performance of three multiplex rRT-PCR assays for the concurrent detection of SARS-CoV-2, influenza A/B, and RSV was comparable. These kits will promote prompt differential diagnosis of COVID-19, influenza, and RSV infection in the COVID-19 pandemic era.


Subject(s)
COVID-19/diagnosis , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction/methods , Nasopharynx/virology , RNA, Viral/analysis , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Cross Reactions , Humans , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/virology , Limit of Detection , Nucleocapsid Proteins/genetics , Polyproteins/genetics , RNA, Viral/metabolism , Reagent Kits, Diagnostic , Republic of Korea , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Matrix Proteins/genetics , Viral Proteins/genetics
6.
Diagn Microbiol Infect Dis ; 102(2): 115575, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1536508

ABSTRACT

COVID-19 symptomology may overlap with other circulating respiratory viruses that may also cause severe disease and for which there are specific and potentially life-saving treatments. The Abbott Alinity m Resp-4-Plex assay is a multiplex PCR assay that simultaneously detects and differentiates infection with SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus (RSV). We characterized its accuracy, precision, and analytical sensitivity. All were found to be robust for measures examined. In the context of sample-to-answer, near random access automation on the Alinity m platform, we believe that the Resp-4-Plex assay offers significant utility in addressing the current needs of the SARS-CoV-2 pandemic and future needs during anticipated endemic circulation of SARS-CoV-2 with other respiratory viruses.


Subject(s)
COVID-19/diagnosis , Influenza, Human/diagnosis , Molecular Diagnostic Techniques , Respiratory Syncytial Virus Infections/diagnosis , Female , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Limit of Detection , Male , Middle Aged , Multiplex Polymerase Chain Reaction , Nucleic Acid Amplification Techniques , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
7.
Virus Res ; 305: 198564, 2021 11.
Article in English | MEDLINE | ID: covidwho-1461877

ABSTRACT

The RSV-associated disease accounts for a significant health burden particularly in infants and young children who need to be hospitalized. Since continuous surveillance of circulating RSV genotypes is crucial worldwide, this study aimed to investigate the genetic diversity of RSV circulating strains causing upper or lower acute respiratory infection. Our attention was geared towards studying the cases hospitalized or outpatient in children younger than 2 years of age in Iran during 2018/2019. In this study, nasopharyngeal swabs collected from 206 children who presented with respiratory infection symptoms, were admitted to the referral pediatric ward of Bahrami children's hospital in Tehran, Iran. RSV-positive samples were detected via Nested RT-PCR. The glycoprotein gene was sequenced, and virus genotypes were confirmed through phylogenetic analysis by the MEGA X program. A total of 74 (35.92%) samples tested positive for RSV. Among them, sequencing was done in 10 specimens from 2018 (RSV-A: RSV-B=4:6) and 19 specimens from 2019 (RSV-A: RSV-B=16:3). According to phylogenetic analysis, all RSV-A strains were assigned as ON1 genotype and RSV-B strains were assigned as BA9 genotype. A new N-glycosylation site in Iranian BA9 and positive selection in ON1 genotype was observed. Phylogenetic characterization of strains in the current study revealed co-circulation of ON1 and BA9 as the only prevalent genotypes of both RSV-A and -B groups.


Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Child , Child, Preschool , Genotype , Humans , Infant , Iran/epidemiology , Phylogeny , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , Respiratory Tract Infections/epidemiology
8.
Med Microbiol Immunol ; 210(5-6): 277-282, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1449965

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has forced the implementation of unprecedented public health measures strategies which might also have a significant impact on the spreading of other viral pathogens such as influenza and Respiratory Syncytial Virus (RSV) . The present study compares the incidences of the most relevant respiratory viruses before and during the SARS-CoV-2 pandemic in emergency room patients. We analyzed the results of in total 14,946 polymerase chain reaction point-of-care tests (POCT-PCR) for Influenza A, Influenza B, RSV and SARS-CoV-2 in an adult and a pediatric emergency room between December 1, 2018 and March 31, 2021. Despite a fivefold increase in the number of tests performed, the positivity rate for Influenza A dropped from 19.32% (165 positives of 854 tests in 2018/19), 14.57% (149 positives of 1023 in 2019-20) to 0% (0 positives of 4915 tests) in 2020/21. In analogy, the positivity rate for Influenza B and RSV dropped from 0.35 to 1.47%, respectively, 10.65-21.08% to 0% for both in 2020/21. The positivity rate for SARS-CoV2 reached 9.74% (110 of 1129 tests performed) during the so-called second wave in December 2020. Compared to the two previous years, seasonal influenza and RSV incidence was eliminated during the COVID-19 pandemic. Corona-related measures and human behavior patterns could lead to a significant decline or even complete suppression of other respiratory viruses such as influenza and RSV.


Subject(s)
COVID-19/epidemiology , Influenza, Human/diagnosis , Point-of-Care Testing/statistics & numerical data , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Hospitals/statistics & numerical data , Humans , Incidence , Influenza, Human/epidemiology , Influenza, Human/virology , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Orthomyxoviridae/physiology , Pandemics , Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Syncytial Virus, Human/physiology , Retrospective Studies
9.
J Virol Methods ; 298: 114304, 2021 12.
Article in English | MEDLINE | ID: covidwho-1440233

ABSTRACT

The potential co-circulation of SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) could pose an unprecedented challenge to healthcare systems worldwide. Here, we compared the performance of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek) for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus with that of BioFire Respiratory Panel 2.1 (RP2.1) using 175 nasopharyngeal swab (NPS) specimens. Positive percent agreement and negative percent agreement of the PowerChek assay compared to RP2.1 were as follows: 100 % (40/40) and 100 % (135/135) for SARS-CoV-2; 100 % (39/39) and 100 % (136/136) for influenza A; 100 % (35/35) and 100 % (140/140) for influenza B; and 93.1 % (27/29) and 100 % (146/146) for RSV, respectively. The limit of detection (LOD) was accessed using RNA standards for each virus, and the LOD values of the PowerChek assay for SARS-CoV-2, influenza A and B, and RSV were 0.36, 1.24, 0.09, and 0.63 copies/µL, respectively. Our results demonstrate that the PowerChek assay is sensitive and accurate for detection of SARS-CoV-2, influenza A and B, and RSV, suggesting that this assay can be a valuable diagnostic tool when SARS-CoV-2, influenza, and RSV are co-circulating.


Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Humans , Influenza B virus/genetics , Influenza, Human/diagnosis , Nasopharynx , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2 , Sensitivity and Specificity
10.
Emerg Infect Dis ; 27(6): 1-9, 2021 06.
Article in English | MEDLINE | ID: covidwho-1304577

ABSTRACT

Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus.


Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Child , Genetic Variation , Genotype , Humans , Molecular Epidemiology , Phylogeny , Respiratory Syncytial Virus, Human/genetics
11.
Virol J ; 18(1): 104, 2021 05 29.
Article in English | MEDLINE | ID: covidwho-1257951

ABSTRACT

BACKGROUND: Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are leading causes of viral severe acute respiratory illnesses in childhood. Both the two viruses belong to the Pneumoviridae family and show overlapping clinical, epidemiological and transmission features. However, it is unknown whether these two viruses have similar geographic spread patterns which may inform designing and evaluating their epidemic control measures. METHODS: We conducted comparative phylogenetic and phylogeographic analyses to explore the spatial-temporal patterns of HMPV and RSV across Africa using 232 HMPV and 842 RSV attachment (G) glycoprotein gene sequences obtained from 5 countries (The Gambia, Zambia, Mali, South Africa, and Kenya) between August 2011 and January 2014. RESULTS: Phylogeographic analyses found frequently similar patterns of spread of RSV and HMPV. Viral sequences commonly clustered by region, i.e., West Africa (Mali, Gambia), East Africa (Kenya) and Southern Africa (Zambia, South Africa), and similar genotype dominance patterns were observed between neighbouring countries. Both HMPV and RSV country epidemics were characterized by co-circulation of multiple genotypes. Sequences from different African sub-regions (East, West and Southern Africa) fell into separate clusters interspersed with sequences from other countries globally. CONCLUSION: The spatial clustering patterns of viral sequences and genotype dominance patterns observed in our analysis suggests strong regional links and predominant local transmission. The geographical clustering further suggests independent introduction of HMPV and RSV variants in Africa from the global pool, and local regional diversification.


Subject(s)
Metapneumovirus , Paramyxoviridae Infections , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Africa/epidemiology , Humans , Metapneumovirus/genetics , Paramyxoviridae Infections/epidemiology , Phylogeny , Phylogeography , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Spatio-Temporal Analysis
12.
J Infect Dis ; 221(4): 534-543, 2020 02 03.
Article in English | MEDLINE | ID: covidwho-1207300

ABSTRACT

BACKGROUND: The safety and immunogenicity of live respiratory syncytial virus (RSV) candidate vaccine, LID/ΔM2-2/1030s, with deletion of RSV ribonucleic acid synthesis regulatory protein M2-2 and genetically stabilized temperature-sensitivity mutation 1030s in the RSV polymerase protein was evaluated in RSV-seronegative children. METHODS: Respiratory syncytial virus-seronegative children ages 6-24 months received 1 intranasal dose of 105 plaque-forming units (PFU) of LID/ΔM2-2/1030s (n = 21) or placebo (n = 11). The RSV serum antibodies, vaccine shedding, and reactogenicity were assessed. During the following RSV season, medically attended acute respiratory illness (MAARI) and pre- and postsurveillance serum antibody titers were monitored. RESULTS: Eighty-five percent of vaccinees shed LID/ΔM2-2/1030s vaccine (median peak nasal wash titers: 3.1 log10 PFU/mL by immunoplaque assay; 5.1 log10 copies/mL by reverse-transcription quantitative polymerase chain reaction) and had ≥4-fold rise in serum-neutralizing antibodies. Respiratory symptoms and fever were common (60% vaccinees and 27% placebo recipients). One vaccinee had grade 2 wheezing with rhinovirus but without concurrent LID/ΔM2-2/1030s shedding. Five of 19 vaccinees had ≥4-fold increases in antibody titers postsurveillance without RSV-MAARI, indicating anamnestic responses without significant illness after infection with community-acquired RSV. CONCLUSIONS: LID/ΔM2-2/1030s had excellent infectivity without evidence of genetic instability, induced durable immunity, and primed for anamnestic antibody responses, making it an attractive candidate for further evaluation.


Subject(s)
Gene Deletion , RNA-Dependent RNA Polymerase/genetics , Respiratory Syncytial Virus Infections/prevention & control , Respiratory Syncytial Virus Vaccines/immunology , Respiratory Syncytial Virus, Human/immunology , Vaccination , Viral Proteins/genetics , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Body Temperature , Double-Blind Method , Female , Humans , Immunogenicity, Vaccine , Infant , Male , Point Mutation , Respiratory Syncytial Virus Infections/immunology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus Vaccines/adverse effects , Respiratory Syncytial Virus, Human/genetics , Vaccines, Attenuated , Virus Replication/genetics
13.
Vaccine ; 39(21): 2811-2820, 2021 05 18.
Article in English | MEDLINE | ID: covidwho-1199115

ABSTRACT

Respiratory syncytial virus (RSV) is the most common cause of serious lower respiratory tract illness in infants and children and causes significant disease in the elderly and immunocompromised. Recently there has been an acceleration in the development of candidate RSV vaccines, monoclonal antibodies and therapeutics. However, the effects of RSV genomic variability on the implementation of vaccines and therapeutics remain poorly understood. To address this knowledge gap, the National Institute of Allergy and Infectious Diseases and the Fogarty International Center held a workshop to summarize what is known about the global burden and transmission of RSV disease, the phylogeographic dynamics and genomics of the virus, and the networks that exist to improve the understanding of RSV disease. Discussion at the workshop focused on the implications of viral evolution and genomic variability for vaccine and therapeutics development in the context of various immunization strategies. This paper summarizes the meeting, highlights research gaps and future priorities, and outlines what has been achieved since the meeting took place. It concludes with an examination of what the RSV community can learn from our understanding of SARS-CoV-2 genomics and what insights over sixty years of RSV research can offer the rapidly evolving field of COVID-19 vaccines.


Subject(s)
COVID-19 , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus Vaccines , Respiratory Syncytial Virus, Human , Aged , COVID-19 Vaccines , Child , Genomics , Humans , Infant , Respiratory Syncytial Virus Infections/prevention & control , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2
14.
Jpn J Infect Dis ; 73(6): 465-468, 2020 Nov 24.
Article in English | MEDLINE | ID: covidwho-976563

ABSTRACT

Human orthopneumovirus, also known as the respiratory syncytial virus (RSV), is a leading cause of respiratory tract infections in children worldwide. The World Health Organization has taken steps toward establishing a global surveillance system for RSV, based on the global influenza surveillance and response system initiated in 2015. The US Centers for Disease Control and Prevention (CDC) has developed a genetic detection method based on real-time reverse transcription polymerase chain reaction (RT-PCR), which is used in global RSV surveillance. In Japan, immunoassay-based rapid antigen detection kits are widely used for the detection of RSV. In this study, an ultra-rapid real-time RT-PCR method for the rapid detection of RSV was developed using the PCR1100 device based on the US CDC assay in order to detect RSV in comparable time to rapid test kits. The ultra-rapid real-time RT-PCR could detect RSV viral RNA in less than 20 min while maintaining sensitivity and specificity comparable to conventional real-time RT-PCR using large installed instruments. Furthermore, combining ultra-rapid real-time RT-PCR with the M1 Sample Prep kit reduced the total working time for the detection of RSV from clinical specimen to less than 25 min, suggesting this method could be used for point-of-care RSV testing.


Subject(s)
RNA, Viral/isolation & purification , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , Child , Humans , Japan , Nasopharynx/virology , Point-of-Care Testing , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Sensitivity and Specificity
15.
Diagn Microbiol Infect Dis ; 99(1): 115209, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-764481

ABSTRACT

Nasopharyngeal flocked swabs placed in viral transport media (VTM) are the preferred collection methodology for respiratory virus testing. Due to the rapid depletion of available reagents and swabs, we have validated an alternative swab placed in phosphate-buffered saline (PBS) for use in respiratory virus testing in a SARS-CoV-2 real-time polymerase chain reaction assay and a multiplexed respiratory virus panel. We collected nasopharyngeal (NP) swabs and oropharyngeal (OP) swabs from 10 healthy volunteers. Flocked swabs were placed in VTM and alternative swabs in PBS. In this feasibility study, we show that NP collection is better for detection of human material than OP collection, as measured by significantly lower RNase P gene cycle threshold values, and that a Dacron polyester swab in PBS shows equivalent detection of SARS-CoV-2 and RSV to a flocked swab in VTM in contrived specimens. Diluted SARS-CoV-2-positive patient specimens are detectable for up to 72 h at 4 °C.


Subject(s)
COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Specimen Handling/methods , COVID-19 Nucleic Acid Testing , Culture Media , Feasibility Studies , Humans , Nasopharynx/virology , Oropharynx/virology , Polyethylene Terephthalates , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , SARS-CoV-2/genetics
16.
Int J Legal Med ; 134(4): 1271-1274, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-378237

ABSTRACT

In the setting of the coronavirus disease 2019 (COVID-19) pandemic, only few data regarding lung pathology induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is available, especially without medical intervention interfering with the natural evolution of the disease. We present here the first case of forensic autopsy of a COVID-19 fatality occurring in a young woman, in the community. Diagnosis was made at necropsy and lung histology showed diffuse alveolar damage, edema, and interstitial pneumonia with a geographically heterogeneous pattern, mostly affecting the central part of the lungs. This death related to COVID-19 pathology highlights the heterogeneity and severity of central lung lesions after natural evolution of the disease.


Subject(s)
Betacoronavirus , Coronavirus Infections/pathology , Lung/pathology , Pneumonia, Viral/pathology , Adenoviridae/genetics , Adenoviridae/isolation & purification , Adult , Autopsy , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Bocavirus/genetics , Bocavirus/isolation & purification , C-Reactive Protein/analysis , COVID-19 , Coronavirus/genetics , Coronavirus/isolation & purification , Female , Humans , Influenzavirus A/genetics , Influenzavirus A/isolation & purification , Influenzavirus B/genetics , Influenzavirus B/isolation & purification , Macrophages/pathology , Megakaryocytes/pathology , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Neutrophils/pathology , Obesity, Morbid , Pandemics , Procalcitonin/blood , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2 , Switzerland , T-Lymphocytes/pathology
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