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1.
Emerg Microbes Infect ; 9(1): 246-255, 2020.
Article in English | MEDLINE | ID: covidwho-774889

ABSTRACT

Human coronavirus NL63 (HCoV-NL63) is primarily associated with common cold in children, elderly and immunocompromised individuals. Outbreaks caused by HCoV-NL63 are rare. Here we report a cluster of HCoV-NL63 cases with severe lower respiratory tract infection that arose in Guangzhou, China, in 2018. Twenty-three hospitalized children were confirmed to be HCoV-NL63 positive, and most of whom were hospitalized with severe pneumonia or acute bronchitis. Whole genomes of HCoV-NL63 were obtained using next-generation sequencing. Phylogenetic and single amino acid polymorphism analyses showed that this outbreak was associated with two subgenotypes (C3 and B) of HCoV-NL63. Half of patients were identified to be related to a new subgenotype C3. One unique amino acid mutation at I507 L in spike protein receptor binding domain (RBD) was detected, which segregated this subgenotype C3 from other known subgenotypes. Pseudotyped virus bearing the I507 L mutation in RBD showed enhanced entry into host cells as compared to the prototype virus. This study proved that HCoV-NL63 was undergoing continuous mutation and has the potential to cause severe lower respiratory disease in humans.


Subject(s)
Coronavirus Infections , Coronavirus NL63, Human/genetics , Respiratory Tract Infections/virology , Child, Preschool , China , Coronavirus NL63, Human/isolation & purification , Genotype , Humans , Infant , Phylogeny
2.
J Virol ; 94(18)2020 08 31.
Article in English | MEDLINE | ID: covidwho-640272

ABSTRACT

In recent years, nidoviruses have emerged as important respiratory pathogens of reptiles, affecting captive python populations. In pythons, nidovirus (recently reclassified as serpentovirus) infection induces an inflammation of the upper respiratory and alimentary tract which can develop into a severe, often fatal proliferative pneumonia. We observed pyogranulomatous and fibrinonecrotic lesions in organ systems other than the respiratory tract during full postmortem examinations on 30 serpentovirus reverse transcription-PCR (RT-PCR)-positive pythons of varying species originating from Switzerland and Spain. The observations prompted us to study whether this not yet reported wider distribution of lesions is associated with previously unknown serpentoviruses or changes in the serpentovirus genome. RT-PCR and inoculation of Morelia viridis cell cultures served to recruit the cases and obtain virus isolates. Immunohistochemistry and immunofluorescence staining against serpentovirus nucleoprotein demonstrated that the virus infects not only a broad spectrum of epithelia (respiratory and alimentary epithelium, hepatocytes, renal tubules, pancreatic ducts, etc.), but also intravascular monocytes, intralesional macrophages, and endothelial cells. With next-generation sequencing we obtained a full-length genome for a novel serpentovirus species circulating in Switzerland. Analysis of viral genomes recovered from pythons showing serpentovirus infection-associated respiratory or systemic disease did not reveal sequence association to phenotypes; however, functional studies with different strains are needed to confirm this observation. The results indicate that serpentoviruses have a broad cell and tissue tropism, further suggesting that the course of infection could vary and involve lesions in a broad spectrum of tissues and organ systems as a consequence of monocyte-mediated viral systemic spread.IMPORTANCE During the last years, python nidoviruses (now reclassified as serpentoviruses) have become a primary cause of fatal disease in pythons. Serpentoviruses represent a threat to captive snake collections, as they spread rapidly and can be associated with high morbidity and mortality. Our study indicates that, different from previous evidence, the viruses do not only affect the respiratory tract, but can spread in the entire body with blood monocytes, have a broad spectrum of target cells, and can induce a variety of lesions. Nidovirales is an order of animal and human viruses that comprises important zoonotic pathogens such as Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2. Serpentoviruses belong to the same order as the above-mentioned human viruses and show similar characteristics (rapid spread, respiratory and gastrointestinal tropism, etc.). The present study confirms the relevance of natural animal diseases to better understand the complexity of viruses of the order Nidovirales.


Subject(s)
Nidovirales Infections/virology , Nidovirales/physiology , Respiratory Tract Infections/virology , Animal Diseases/diagnosis , Animal Diseases/virology , Animals , Biopsy , Boidae/virology , Disease Susceptibility , Humans , Immunohistochemistry , Nidovirales/isolation & purification , Nidovirales Infections/diagnosis , Organ Specificity , Phenotype , Phylogeny , Recombination, Genetic , Respiratory Tract Infections/diagnosis , Viral Tropism , Virus Shedding
3.
Zhonghua Er Ke Za Zhi ; 58(8): 635-639, 2020 Aug 02.
Article in Chinese | MEDLINE | ID: covidwho-749115

ABSTRACT

Objective: To investigate the spectrum of pathogenic agents in pediatric patients with acute respiratory infections (ARI) during the outbreak of coronavirus infectious diseases 2019 (COVID-19). Methods: Three groups of children were enrolled into the prospective study during January 20 to February 20, 2020 from Capital Institute of Pediatrics, including children in the exposed group with ARI and epidemiological history associated with COVID-19 from whom both pharyngeal and nasopharyngeal swabs were collected, children in the ARI group without COVID-19 associated epidemiological history and children in the screening group for hospital admission, with neither COVID-19 associated epidemiological history nor ARI. Only nasopharyngeal swabs were collected in the ARI group and screening group. Each group is expected to include at least 30 cases. All specimens were tested for 2019-nCoV nucleic acid by two diagnostic kits from different manufacturers. All nasopharyngeal swabs were tested for multiple respiratory pathogens, whilst the results from the ARI group were compared with that in the correspondence periods of 2019 and 2018 used by t or χ(2) test. Results: A total of 244 children were enrolled into three groups, including 139 males and 105 females, the age was (5±4) years. The test of 2019-nCoV nucleic acid were negative in all children, and high positive rates of pathogens were detected in exposed (69.4%, 25/36) and ARI (55.3%, 73/132) groups, with the highest positive rate for mycoplasma pneumoniae (MP) (19.4%, 7/36 and 17.4%, 23/132, respectively), followed by human metapneumovirus (hMPV) (16.7%, 6/36 and 9.8%, 13/132, respectively). The positive rate (11.8%, 9/76) of pathogens in the screening group was low. In the same period of 2019, the positive rate of pathogens was 83.7% (77/92), with the highest rates for respiratory syncytial virus (RSV) A (29.3%, 27/92), followed by influenza virus (Flu) A (H1N1) (19.6%, 18/92) and adenovirus (ADV) (14.1%, 13/92), which showed significant difference with the positive rates of the three viruses in 2020 (RSV A: χ(2)=27.346, P<0.01; FluA (H1N1): χ(2)=28.083, P<0.01; ADV: χ(2)=7.848, P=0.005) . In 2018, the positive rate of pathogens was 61.0% (50/82), with the highest rate for human bocavirus (HBoV) (13.4%, 11/82) and followed by ADV (11.0%, 9/82), and significant difference was shown in the positive rate of HBoV with that in 2020 (χ(2)=6.776, P=0.009). Conclusions: The infection rate of 2019-nCoV is low among children in Beijing with no family clustering or no close contact, even with epidemiological history. The spectrum of pathogens of ARI in children during the research period is quite different from that in the previous years when the viral infections were dominant. MP is the highest positively detected one among the main pathogens during the outbreak of COVID-19 in Beijing where there is no main outbreak area.


Subject(s)
Disease Outbreaks , Metapneumovirus/isolation & purification , Mycoplasma pneumoniae/isolation & purification , Paramyxoviridae Infections/diagnosis , Respiratory Tract Infections/diagnosis , Beijing/epidemiology , Betacoronavirus , Child , Child, Preschool , Coronavirus , Coronavirus Infections , Female , Humans , Infant , Influenza A Virus, H1N1 Subtype , Male , Metapneumovirus/pathogenicity , Mycoplasma pneumoniae/pathogenicity , Pandemics , Paramyxoviridae Infections/epidemiology , Pediatrics , Pneumonia, Mycoplasma/diagnosis , Pneumonia, Mycoplasma/epidemiology , Pneumonia, Viral , Prospective Studies , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology
4.
Cien Saude Colet ; 25(9): 3365-3376, 2020 Sep.
Article in English, Portuguese | MEDLINE | ID: covidwho-740421

ABSTRACT

OBJECTIVES: to evaluate the effectiveness of non-woven face masks for the prevention of respiratory infections (MERS CoV, SARS-CoV, and SARS-CoV-2) in the population. METHODS: search in Medline, Embase, Cinahl, The Cochrane Library, Trip databases. Google Scholar, Rayyan and medRxiv were also consulted for complementary results. No filters related to date, language or publication status were applied. Titles and abstracts were screened, and later, full texts were evaluated. RESULTS: three studies were included: a randomized cluster clinical trial and two systematic reviews. The clinical trial indicates a potential benefit of medical masks to control the source of clinical respiratory disease infection. In one of the systematic reviews, it was not possible to establish a conclusive relationship between the use of the mask and protection against respiratory infection. Finally, another systematic review indicated that masks are effective in preventing the spread of respiratory viruses. CONCLUSION: Evidence points to the potential benefit of standard non-woven face masks. For the current pandemic scenario of COVID-19, education on the appropriate use of masks associated with individual protection measures is recommended.


Subject(s)
Coronavirus Infections/prevention & control , Masks , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Betacoronavirus/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Humans , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Pneumonia, Viral/epidemiology , Randomized Controlled Trials as Topic , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , Respiratory Tract Infections/virology , SARS Virus/isolation & purification , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/prevention & control , Severe Acute Respiratory Syndrome/virology
5.
Viruses ; 12(9)2020 08 29.
Article in English | MEDLINE | ID: covidwho-736748

ABSTRACT

The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.


Subject(s)
Respiratory Tract Infections/virology , Virus Diseases/virology , Zoonoses/virology , Animals , Coronavirus/genetics , Coronavirus/isolation & purification , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , High-Throughput Nucleotide Sequencing/methods , Humans , Metagenome , Metagenomics/methods , Pandemics , Phylogeny , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Respiratory Tract Infections/diagnosis , Virus Diseases/diagnosis , Zoonoses/diagnosis
6.
Infection ; 48(4): 489-495, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-725942

ABSTRACT

PURPOSE: To describe the burden, and characteristics, of influenza-like illness (ILI) associated with non-influenza respiratory viruses (NIRV). METHODS: We performed a prospective, multicenter, observational study of adults admitted with ILI during three influenza seasons (2012-2015). Patients were screened for picornavirus, respiratory syncytial virus (RSV), coronavirus, human metapneumovirus, adenovirus, bocavirus, parainfluenza virus, and influenza, by PCR on nasopharyngeal samples. We excluded patients coinfected with NIRV and influenza. RESULTS: Among 1421 patients enrolled, influenza virus was detected in 535 (38%), and NIRV in 215 (15%), mostly picornavirus (n = 61), RSV (n = 53), coronavirus 229E (n = 48), and human metapneumovirus (n = 40). In-hospital mortality was 5% (NIRV), 4% (influenza), and 5% (no respiratory virus). As compared to influenza, NIRV were associated with age (median, 73 years vs. 68, P = 0.026), chronic respiratory diseases (53% vs. 45%, P = 0.034), cancer (14% vs. 9%, P = 0.029), and immunosuppressive drugs (21% vs. 14%, P = 0.028), and inversely associated with diabetes (18% vs. 25%, P = 0.038). On multivariable analysis, only chronic respiratory diseases (OR 1.5 [1.1-2.0], P = 0.008), and diabetes (OR 0.5 [0.4-0.8], P = 0.01) were associated with NIRV detection. CONCLUSIONS: NIRV are common in adults admitted with ILI during influenza seasons. Outcomes are similar in patients with NIRV, influenza, or no respiratory virus.


Subject(s)
Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Viruses/isolation & purification , Aged , Aged, 80 and over , Coinfection/virology , Humans , Middle Aged , Prospective Studies , Viruses/classification
7.
Emerg Microbes Infect ; 9(1): 1958-1964, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-725886

ABSTRACT

Objectives Severe or critical COVID-19 is associated with intensive care unit admission, increased secondary infection rate, and would lead to significant worsened prognosis. Risks and characteristics relating to secondary infections in severe COVID-19 have not been described. Methods Severe and critical COVID-19 patients from Shanghai were included. We collected lower respiratory, urine, catheters, and blood samples according to clinical necessity and culture and mNGS were performed. Clinical and laboratory data were archived. Results We found 57.89% (22/38) patients developed secondary infections. The patient receiving invasive mechanical ventilation or in critical state has a higher chance of secondary infections (P<0.0001). The most common infections were respiratory, blood-stream and urinary infections, and in respiratory infections, the most detected pathogens were gram-negative bacteria (26, 50.00%), following by gram-positive bacteria (14, 26.92%), virus (6, 11.54%), fungi (4, 7.69%), and others (2, 3.85%). Respiratory Infection rate post high flow, tracheal intubation, and tracheotomy were 12.90% (4/31), 30.43% (7/23), and 92.31% (12/13) respectively. Secondary infections would lead to lower discharge rate and higher mortality rate. Conclusion Our study originally illustrated secondary infection proportion in severe and critical COVID-19 patients. Culture accompanied with metagenomics sequencing increased pathogen diagnostic rate. Secondary infections risks increased after receiving invasive respiratory ventilations and intravascular devices, and would lead to a lower discharge rate and a higher mortality rate.


Subject(s)
Bacteremia/pathology , Bacterial Infections/pathology , Coronavirus Infections/pathology , Fungemia/pathology , Mycoses/pathology , Opportunistic Infections/pathology , Pneumonia, Viral/pathology , Respiratory Tract Infections/pathology , Urinary Tract Infections/pathology , Aged , Bacteremia/microbiology , Bacteremia/mortality , Bacteremia/virology , Bacterial Infections/microbiology , Bacterial Infections/mortality , Bacterial Infections/virology , Betacoronavirus/pathogenicity , Coronavirus Infections/microbiology , Coronavirus Infections/mortality , Coronavirus Infections/virology , Critical Illness , Female , Fungemia/microbiology , Fungemia/mortality , Fungemia/virology , Fungi/pathogenicity , Gram-Negative Bacteria/pathogenicity , Gram-Positive Bacteria/pathogenicity , Humans , Intensive Care Units , Lung/microbiology , Lung/pathology , Lung/virology , Male , Middle Aged , Mycoses/microbiology , Mycoses/mortality , Mycoses/virology , Opportunistic Infections/microbiology , Opportunistic Infections/mortality , Opportunistic Infections/virology , Pandemics , Pneumonia, Viral/microbiology , Pneumonia, Viral/mortality , Pneumonia, Viral/virology , Respiration, Artificial/adverse effects , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/mortality , Respiratory Tract Infections/virology , Retrospective Studies , Risk , Severity of Illness Index , Survival Analysis , Urinary Tract Infections/microbiology , Urinary Tract Infections/mortality , Urinary Tract Infections/virology
8.
Emerg Microbes Infect ; 9(1): 1900-1911, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-695197

ABSTRACT

The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Genome, Viral/genetics , Pneumonia, Viral/virology , Quasispecies/genetics , Respiratory Tract Infections/virology , Spike Glycoprotein, Coronavirus/genetics , Adult , Aged , Computational Biology , Female , Gene Deletion , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Pandemics , RNA Cleavage , Sequence Analysis, RNA
9.
Medicine (Baltimore) ; 99(30): e21320, 2020 Jul 24.
Article in English | MEDLINE | ID: covidwho-682685

ABSTRACT

BACKGROUND: Assessing the effectiveness and safety of traditional Chinese medicine (TCM) for symptoms of upper respiratory tract of coronavirus disease 2019 is the main purpose of this systematic review protocol. METHODS: The following electronic databases will be searched from inception to Sep 2020: the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, EMBASE, Web of Science, TCM, China National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Scientific Journal Database (VIP database), and Wan-Fang Database. Search dates: from inception dates to June 2020. Language: English. Publication period: from inception dates to June 2020. The primary outcome is the time and rate of appearance of main symptoms (including coughing, pharyngalgia, and nasal obstruction). The secondary outcome is the length of hospital stay. Two independent reviewers will conduct the study selection, data extraction and assessment. RevMan V.5.3 will be used for the assessment of risk of bias and data synthesis. RESULTS: The results will provide a high-quality synthesis of current evidence for researchers in this subject area. CONCLUSION: The conclusion of our study will provide an evidence to judge whether TCM is effective and safe for the patients with symptoms of upper respiratory tract of coronavirus disease 2019. ETHICS AND DISSEMINATION: This protocol will not evaluate individual patient information or affect patient rights and therefore does not require ethical approval. Results from this review will be disseminated through peer-reviewed journals and conference reports. PROSPERO REGISTRATION NUMBER: CRD42020187422.


Subject(s)
Betacoronavirus , Coronavirus Infections/therapy , Medicine, Chinese Traditional/methods , Pneumonia, Viral/therapy , Respiratory Tract Infections/therapy , Coronavirus Infections/pathology , Coronavirus Infections/virology , Humans , Meta-Analysis as Topic , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Randomized Controlled Trials as Topic , Research Design , Respiratory System/virology , Respiratory Tract Infections/pathology , Respiratory Tract Infections/virology , Systematic Reviews as Topic , Treatment Outcome
10.
Influenza Other Respir Viruses ; 14(4): 365-373, 2020 07.
Article in English | MEDLINE | ID: covidwho-637288

ABSTRACT

BACKGROUND: Respiratory protective devices are critical in protecting against infection in healthcare workers at high risk of novel 2019 coronavirus disease (COVID-19); however, recommendations are conflicting and epidemiological data on their relative effectiveness against COVID-19 are limited. PURPOSE: To compare medical masks to N95 respirators in preventing laboratory-confirmed viral infection and respiratory illness including coronavirus specifically in healthcare workers. DATA SOURCES: MEDLINE, Embase, and CENTRAL from January 1, 2014, to March 9, 2020. Update of published search conducted from January 1, 1990, to December 9, 2014. STUDY SELECTION: Randomized controlled trials (RCTs) comparing the protective effect of medical masks to N95 respirators in healthcare workers. DATA EXTRACTION: Reviewer pair independently screened, extracted data, and assessed risk of bias and the certainty of the evidence. DATA SYNTHESIS: Four RCTs were meta-analyzed adjusting for clustering. Compared with N95 respirators; the use of medical masks did not increase laboratory-confirmed viral (including coronaviruses) respiratory infection (OR 1.06; 95% CI 0.90-1.25; I2  = 0%; low certainty in the evidence) or clinical respiratory illness (OR 1.49; 95% CI: 0.98-2.28; I2  = 78%; very low certainty in the evidence). Only one trial evaluated coronaviruses separately and found no difference between the two groups (P = .49). LIMITATIONS: Indirectness and imprecision of available evidence. CONCLUSIONS: Low certainty evidence suggests that medical masks and N95 respirators offer similar protection against viral respiratory infection including coronavirus in healthcare workers during non-aerosol-generating care. Preservation of N95 respirators for high-risk, aerosol-generating procedures in this pandemic should be considered when in short supply.


Subject(s)
Coronavirus Infections/prevention & control , Masks/standards , Occupational Exposure/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Respiratory Tract Infections/prevention & control , Ventilators, Mechanical/standards , Health Personnel , Humans , Infection Control/methods , Randomized Controlled Trials as Topic , Respiratory Protective Devices/standards , Respiratory Protective Devices/supply & distribution , Respiratory Tract Infections/virology
11.
Forensic Sci Med Pathol ; 16(3): 457-462, 2020 09.
Article in English | MEDLINE | ID: covidwho-615460

ABSTRACT

Death due to respiratory infection is commonly encountered at autopsy. With only one opportunity to obtain samples for identification of a causative agent, it is important to ensure that sampling regimes are optimized to provide the greatest detection, without the expense and redundancy that can arise from over-sampling. This study was performed retrospectively using data from Coronial autopsies over the period 2012-2019 from which swabs from the nasopharyngeal region, trachea and lung parenchyma, in addition to samples of lung tissue, had been submitted for multiplex PCR detection of respiratory pathogens. From 97 cases with all four samples, there were 24 with at least one positive result for viral infection. Some cases had multiple positive results and a total of 27 respiratory tract viruses were identified, of which rhinovirus, influenza A virus and respiratory syncytial virus were the most common. Seventeen of the 27 viral infections (63%) were identified in all four samples. However, in nearly all cases (96%) the nasopharyngeal swab detected the infective agent when the multiplex PCR panel had detected infection in any of the four sample types. A nasopharyngeal swab is considered to be an optimal sample for detection of respiratory tract viral infection. As the samples analyzed were acquired before the appearance of the COVID-19 virus, the applicability of this finding for COVID-19 screening is not established.


Subject(s)
DNA, Viral/isolation & purification , Lung/virology , Multiplex Polymerase Chain Reaction , Nasopharynx/virology , Respiratory Tract Infections/diagnosis , Specimen Handling , Virology , Virus Diseases/diagnosis , Viruses/isolation & purification , Adult , Aged , Aged, 80 and over , Autopsy , Cause of Death , DNA, Viral/classification , DNA, Viral/genetics , Female , Humans , Infant , Male , Middle Aged , Predictive Value of Tests , Reproducibility of Results , Respiratory Tract Infections/virology , Retrospective Studies , Virus Diseases/virology , Viruses/classification , Viruses/genetics
12.
Small ; 16(32): e2002169, 2020 08.
Article in English | MEDLINE | ID: covidwho-612774

ABSTRACT

The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. COVID-19 diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates and are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis and impeding epidemic containment. Combining the advantages of targeted amplification and long-read, real-time nanopore sequencing, herein, nanopore targeted sequencing (NTS) is developed to detect SARS-CoV-2 and other respiratory viruses simultaneously within 6-10 h, with a limit of detection of ten standard plasmid copies per reaction. Compared with its specificity for five common respiratory viruses, the specificity of NTS for SARS-CoV-2 reaches 100%. Parallel testing with approved real-time reverse transcription-polymerase chain reaction kits for SARS-CoV-2 and NTS using 61 nucleic acid samples from suspected COVID-19 cases show that NTS identifies more infected patients (22/61) as positive, while also effectively monitoring for mutated nucleic acid sequences, categorizing types of SARS-CoV-2, and detecting other respiratory viruses in the test sample. NTS is thus suitable for COVID-19 diagnosis; moreover, this platform can be further extended for diagnosing other viruses and pathogens.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Nanopores , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Betacoronavirus/classification , Coronavirus Infections/epidemiology , DNA, Viral/genetics , DNA, Viral/isolation & purification , Genes, Viral , Humans , Limit of Detection , Mutation , Nanotechnology , Nucleic Acid Amplification Techniques/statistics & numerical data , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/genetics , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
13.
Infection ; 48(4): 627-629, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-611636

ABSTRACT

The COVID-19 pandemic has affected most countries of the world. As corona viruses are highly prevalent in the cold season, the question remains whether or not the pandemic will improve with increasing temperatures in the Northern hemisphere. We use data from a primary care registry of almost 15,000 patients over 20 years to retrieve information on viral respiratory infection outbreaks. Our analysis suggests that the severity of the pandemic will be softened by the seasonal change to summer.


Subject(s)
Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Respiratory Tract Infections/epidemiology , Seasons , Temperature , Betacoronavirus , Coronavirus Infections/transmission , Global Health , Humans , Pandemics , Pneumonia, Viral/transmission , Registries , Respiratory Tract Infections/transmission , Respiratory Tract Infections/virology
14.
Viruses ; 12(6)2020 06 10.
Article in English | MEDLINE | ID: covidwho-592266

ABSTRACT

There is currently debate about human coronavirus (HCoV) seasonality and pathogenicity, as epidemiological data are scarce. Here, we provide epidemiological and clinical features of HCoV patients with acute respiratory infection (ARI) examined in primary care general practice. We also describe HCoV seasonality over six influenza surveillance seasons (week 40 to 15 of each season) from the period 2014/2015 to 2019/2020 in Corsica (France). A sample of patients of all ages presenting for consultation for influenza-like illness (ILI) or ARI was included by physicians of the French Sentinelles Network during this period. Nasopharyngeal samples were tested for the presence of 21 respiratory pathogens by real-time RT-PCR. Among the 1389 ILI/ARI patients, 105 were positive for at least one HCoV (7.5%). On an annual basis, HCoVs circulated from week 48 (November) to weeks 14-15 (May) and peaked in week 6 (February). Overall, among the HCoV-positive patients detected in this study, HCoV-OC43 was the most commonly detected virus, followed by HCoV-NL63, HCoV-HKU1, and HCoV-229E. The HCoV detection rates varied significantly with age (p = 0.00005), with the age group 0-14 years accounting for 28.6% (n = 30) of HCoV-positive patients. Fever and malaise were less frequent in HCoV patients than in influenza patients, while sore throat, dyspnoea, rhinorrhoea, and conjunctivitis were more associated with HCoV positivity. In conclusion, this study demonstrates that HCoV subtypes appear in ARI/ILI patients seen in general practice, with characteristic outbreak patterns primarily in winter. This study also identified symptoms associated with HCoVs in patients with ARI/ILI. Further studies with representative samples should be conducted to provide additional insights into the epidemiology and clinical features of HCoVs.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Respiratory Tract Infections/epidemiology , Adolescent , Adult , Aged , Child , Child, Preschool , Coronavirus Infections/diagnosis , Disease Outbreaks , Female , Humans , Infant , Infant, Newborn , Influenza, Human/epidemiology , Male , Middle Aged , Nasopharynx/virology , Primary Health Care , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Seasons , Young Adult
15.
J Immunol ; 205(2): 313-320, 2020 07 15.
Article in English | MEDLINE | ID: covidwho-530300

ABSTRACT

Aging impairs immunity to promote diseases, especially respiratory viral infections. The current COVID-19 pandemic, resulting from SARS-CoV-2, induces acute pneumonia, a phenotype that is alarmingly increased with aging. In this article, we review findings of how aging alters immunity to respiratory viral infections to identify age-impacted pathways common to several viral pathogens, permitting us to speculate about potential mechanisms of age-enhanced mortality to COVID-19. Aging generally leads to exaggerated innate immunity, particularly in the form of elevated neutrophil accumulation across murine and large animal studies of influenza infection. COVID-19 patients who succumb exhibit a 2-fold increase in neutrophilia, suggesting that exaggerated innate immunity contributes to age-enhanced mortality to SARS-CoV-2 infection. Further investigation in relevant experimental models will elucidate the mechanisms by which aging impacts respiratory viral infections, including SARS-CoV-2. Such investigation could identify therapies to reduce the suffering of the population at large, but especially among older people, infected with respiratory viruses.


Subject(s)
Aging/pathology , Betacoronavirus/physiology , Coronavirus Infections/immunology , Coronavirus Infections/pathology , Pneumonia, Viral/immunology , Pneumonia, Viral/pathology , Respiratory Tract Infections/virology , Cardiovascular Diseases/pathology , Cardiovascular Diseases/virology , Cytokines/immunology , Humans , Influenza, Human/immunology , Influenza, Human/pathology , Pandemics , Respiratory Tract Infections/pathology , SARS Virus/physiology
16.
Emerg Infect Dis ; 26(6): 1345-1348, 2020 06.
Article in English | MEDLINE | ID: covidwho-526236

ABSTRACT

We describe 2 cases of coronavirus disease in patients with mild upper respiratory symptoms. Both patients worked on a cruise ship quarantined off the coast of Japan. One patient had persistent, low-grade upper respiratory tract symptoms without fever. The other patient had rapid symptom cessation but persistent viral RNA detection.


Subject(s)
Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Ships , Adult , Betacoronavirus , Female , Humans , Japan , Male , Pandemics , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology
17.
J Clin Virol ; 129: 104470, 2020 08.
Article in English | MEDLINE | ID: covidwho-478301

ABSTRACT

In Italy, the first SARS-CoV-2 infections were diagnosed in Rome, Lazio region, at the end of January 2020, but sustained transmission occurred later, since the end of February. From 1 February to 12 April 2020, 17,164 nasopharyngeal swabs were tested by real time PCR for the presence of SARS-CoV-2 at the Laboratory of Virology of National Institute for Infectious Diseases "Lazzaro Spallanzani" (INMI) in Rome. In the same period, coincident with the winter peak of influenza and other respiratory illnesses, 847 samples were analyzed by multiplex PCR assay for the presence of common respiratory pathogens. In our study the time trend of SARS-CoV-2 and that of other respiratory pathogens in the same observation period were analysed. Overall, results obtained suggest that the spread of the pandemic SARS-CoV-2 virus did not substantially affect the time trend of other respiratory infections in our region, highlighting no significant difference in rates of SARS-CoV-2 infection in patients with or without other respiratory pathogens. Therefore, in the present scenario of COVID-19 pandemic, differential diagnosis resulting positive for common respiratory pathogen(s) should not exclude testing of SARS-CoV-2.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus/isolation & purification , Influenza, Human/epidemiology , Nasopharynx/virology , Orthomyxoviridae/isolation & purification , Respiratory Tract Infections/epidemiology , Coronavirus/classification , Coronavirus Infections/virology , Humans , Influenza, Human/virology , Multiplex Polymerase Chain Reaction , Orthomyxoviridae/classification , Respiratory Tract Infections/virology , Rome/epidemiology
18.
Pediatr Infect Dis J ; 39(8): 653-657, 2020 08.
Article in English | MEDLINE | ID: covidwho-388714

ABSTRACT

BACKGROUND: Human coronaviruses (HCoVs) have been recognized as causative agents of respiratory tract infections.Our aim was to describe HCoV infections in hospitalized children in a prospective surveillance study for 14 years and compare them with other respiratory viruses. METHODS: As a part of an ongoing prospective study to identify the etiology of viral respiratory infections in Spain, we performed the analysis of HCoV infections in children hospitalized in a secondary hospital in Madrid, between October 2005 and June 2018. Clinical data of HCoV patients were compared with those infected by rhinovirus, respiratory syncytial virus and influenza. RESULTS: The study population consisted of 5131 hospitalizations for respiratory causes in children. A total of 3901 cases (75.9%) had a positive viral identification and 205 cases (4.1%) were positive for HCoV. Only 41 cases (20%) of HCoV infection were detected as single infections. Episodes of recurrent wheezing were the most common diagnosis, and 112 children (54%) had hypoxia. Clinical data in HCoV cases were similar to those associated with rhinovirus; however, patients with HCoV were younger. Other viruses were associated with hypoxia more frequently than cases with HCoV; high fever was more common in influenza infections and bronchiolitis in respiratory syncytial virus group. Although a slight peak of circulation appears mostly in winter, HCoV has been detected throughout the year as well. CONCLUSIONS: HCoV infections represent a small fraction of respiratory infections that require hospitalization in children and their characteristics do not differ greatly from other respiratory viral infections.


Subject(s)
Bronchiolitis, Viral/epidemiology , Coronavirus Infections/epidemiology , Hospitalization , Pneumonia, Viral/epidemiology , Adolescent , Age Distribution , Betacoronavirus , Bronchiolitis, Viral/physiopathology , Bronchiolitis, Viral/virology , Child , Child, Preschool , Coronavirus Infections/physiopathology , Coronavirus Infections/virology , Coronavirus NL63, Human , Coronavirus OC43, Human , Female , Fever/physiopathology , Humans , Hypoxia/physiopathology , Infant , Infant, Newborn , Influenza, Human/epidemiology , Influenza, Human/physiopathology , Influenza, Human/virology , Male , Middle East Respiratory Syndrome Coronavirus , Pandemics , Picornaviridae Infections/epidemiology , Picornaviridae Infections/physiopathology , Picornaviridae Infections/virology , Pneumonia, Viral/physiopathology , Pneumonia, Viral/virology , Prospective Studies , Respiratory Sounds/physiopathology , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/physiopathology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/physiopathology , Respiratory Tract Infections/virology , Rhinovirus , SARS Virus , Seasons , Severe Acute Respiratory Syndrome , Severity of Illness Index , Spain/epidemiology
19.
CMAJ ; 192(27): E745-E755, 2020 07 06.
Article in English | MEDLINE | ID: covidwho-343300

ABSTRACT

BACKGROUND: The safety and efficacy of convalescent plasma in severe coronavirus disease 2019 (COVID-19) remain uncertain. To support a guideline on COVID-19 management, we conducted a systematic review and meta-analysis of convalescent plasma in COVID-19 and other severe respiratory viral infections. METHODS: In March 2020, we searched international and Chinese biomedical literature databases, clinical trial registries and prepublication sources for randomized controlled trials (RCTs) and nonrandomized studies comparing patients receiving and not receiving convalescent plasma. We included patients with acute coronavirus, influenza and Ebola virus infections. We conducted a meta-analysis using random-effects models and assessed the quality of evidence using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. RESULTS: Of 1099 unique records, 6 studies were eligible, and none of these included patients with COVID-19. One nonrandomized study (n = 40) on convalescent plasma in severe acute respiratory syndrome coronavirus (SARS-CoV) provided uninformative results regarding mortality (relative risk [RR] 0.10, 95% confidence interval [CI] CI 0.01 to 1.70). Pooled estimates from 4 RCTs on influenza (n = 572) showed no convincing effects on deaths (4 RCTs, RR 0.94, 95% CI 0.49 to 1.81), complete recovery (2 RCTs, odds ratio 1.04, 95% CI 0.69 to 1.64) or length of stay (3 RCTs, mean difference -1.62, 95% CI -3.82 to 0.58, d). The quality of evidence was very low for all efficacy outcomes. Convalescent plasma caused few or no serious adverse events in influenza RCTs (RR 0.85, 95% CI 0.56 to 1.29, low-quality evidence). INTERPRETATION: Studies of non-COVID-19 severe respiratory viral infections provide indirect, very low-quality evidence that raises the possibility that convalescent plasma has minimal or no benefit in the treatment of COVID-19 and low-quality evidence that it does not cause serious adverse events.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/therapy , Pneumonia, Viral/therapy , Respiratory Tract Infections/therapy , Clinical Trials as Topic , Coronavirus Infections/physiopathology , Evidence-Based Medicine , Humans , Immunization, Passive , Influenza, Human/physiopathology , Influenza, Human/therapy , Pandemics , Pneumonia, Viral/physiopathology , Respiratory Tract Infections/physiopathology , Respiratory Tract Infections/virology , Risk Assessment , Treatment Outcome
20.
Anal Chem ; 92(14): 9699-9705, 2020 07 21.
Article in English | MEDLINE | ID: covidwho-342681

ABSTRACT

A novel coronavirus (SARS-CoV-2) was recently identified in patients with acute respiratory disease and spread quickly worldwide. A specific and rapid diagnostic method is important for early identification. The reverse-transcription recombinase-aided amplification (RT-RAA) assay is a rapid detection method for several pathogens. Assays were performed within 5-15 min as a one-step single tube reaction at 39 °C. In this study, we established two RT-RAA assays for the S and orf1ab gene of SARS-CoV-2 using clinical specimens for validation. The analytical sensitivity of the RT-RAA assay was 10 copies for the S and one copy for the orf1ab gene per reaction. Cross-reactions were not observed with any of the other respiratory pathogens. A 100% agreement between the RT-RAA and real-time PCR assays was accomplished after testing 120 respiratory specimens. These results demonstrate that the proposed RT-RAA assay will be beneficial as it is a faster, more sensitive, and more specific tool for the detection of SARS-CoV-2.


Subject(s)
Betacoronavirus/chemistry , Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Nucleic Acid Amplification Techniques/methods , Pneumonia, Viral/diagnosis , Polymerase Chain Reaction/methods , Bacteria/chemistry , Bacteria/genetics , Cross Reactions , DNA Probes , Genes, Viral , Humans , Pandemics , Plasmids , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , Sensitivity and Specificity , Viral Proteins/genetics , Viruses/chemistry , Viruses/genetics
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