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1.
Viruses ; 12(6)2020 06 10.
Article in English | MEDLINE | ID: covidwho-1726022

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 , SARS-CoV-2 , Seasons , Young Adult
2.
Sci Rep ; 11(1): 19930, 2021 10 07.
Article in English | MEDLINE | ID: covidwho-1462026

ABSTRACT

Transmission of SARS-CoV-2 by aerosols has played a significant role in the rapid spread of COVID-19 across the globe. Indoor environments with inadequate ventilation pose a serious infection risk. Whilst vaccines suppress transmission, they are not 100% effective and the risk from variants and new viruses always remains. Consequently, many efforts have focused on ways to disinfect air. One such method involves use of minimally hazardous 222 nm far-UVC light. Whilst a small number of controlled experimental studies have been conducted, determining the efficacy of this approach is difficult because chamber or room geometry, and the air flow within them, influences both far-UVC illumination and aerosol dwell times. Fortunately, computational multiphysics modelling allows the inadequacy of dose-averaged assessment of viral inactivation to be overcome in these complex situations. This article presents the first validation of the WYVERN radiation-CFD code for far-UVC air-disinfection against survival fraction measurements, and the first measurement-informed modelling approach to estimating far-UVC susceptibility of viruses in air. As well as demonstrating the reliability of the code, at circa 70% higher, our findings indicate that aerosolized human coronaviruses are significantly more susceptible to far-UVC than previously thought.


Subject(s)
Coronavirus 229E, Human/radiation effects , Coronavirus Infections/prevention & control , Coronavirus OC43, Human/radiation effects , Disinfection/methods , Ultraviolet Rays , Virus Inactivation/radiation effects , Aerosols/isolation & purification , Air Microbiology , COVID-19/prevention & control , Computer Simulation , Coronavirus 229E, Human/isolation & purification , Coronavirus 229E, Human/physiology , Coronavirus OC43, Human/isolation & purification , Coronavirus OC43, Human/physiology , Disinfection/instrumentation , Equipment Design , Humans , Models, Biological
3.
J Clin Virol ; 136: 104754, 2021 03.
Article in English | MEDLINE | ID: covidwho-1385860

ABSTRACT

OBJECTIVES: The four seasonal coronaviruses 229E, NL63, OC43, and HKU1 are frequent causes of respiratory infections and show annual and seasonal variation. Increased understanding about these patterns could be informative about the epidemiology of SARS-CoV-2. METHODS: Results from PCR diagnostics for the seasonal coronaviruses, and other respiratory viruses, were obtained for 55,190 clinical samples analyzed at the Karolinska University Hospital, Stockholm, Sweden, between 14 September 2009 and 2 April 2020. RESULTS: Seasonal coronaviruses were detected in 2130 samples (3.9 %) and constituted 8.1 % of all virus detections. OC43 was most commonly detected (28.4 % of detections), followed by NL63 (24.0 %), HKU1 (17.6 %), and 229E (15.3 %). The overall fraction of positive samples was similar between seasons, but at species level there were distinct biennial alternating peak seasons for the Alphacoronaviruses, 229E and NL63, and the Betacoronaviruses, OC43 and HKU1, respectively. The Betacoronaviruses peaked earlier in the winter season (Dec-Jan) than the Alphacoronaviruses (Feb-Mar). Coronaviruses were detected across all ages, but diagnostics were more frequently requested for paediatric patients than adults and the elderly. OC43 and 229E incidence was relatively constant across age strata, while that of NL63 and HKU1 decreased with age. CONCLUSIONS: Both the Alphacoronaviruses and Betacoronaviruses showed alternating biennial winter incidence peaks, which suggests some type of immune mediated interaction. Symptomatic reinfections in adults and the elderly appear relatively common. Both findings may be of relevance for the epidemiology of SARS-CoV-2.


Subject(s)
COVID-19/epidemiology , Common Cold/epidemiology , Coronavirus 229E, Human/isolation & purification , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Deltacoronavirus/isolation & purification , Female , Humans , Male , Retrospective Studies , SARS-CoV-2 , Seasons , Sweden
4.
FEMS Microbiol Lett ; 368(16)2021 09 01.
Article in English | MEDLINE | ID: covidwho-1377968

ABSTRACT

Limited research exists on the potential for leather to act as a fomite of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or endemic coronaviruses including human coronavirus (HCoV) OC43; this is important for settings such as the shoe manufacturing industry. Antiviral coating of leather hides could limit such risks. This study aimed to investigate the stability and transfer of HCoVOC43 on different leathers, as a surrogate for SARS-CoV-2, and assess the antiviral efficacy of a silver-based leather coating. The stability of HCoV-OC43 (6.6 log10) on patent, full-grain calf, corrected grain finished and nubuck leathers (silver additive-coated and uncoated) was measured by titration on BHK-21 cells. Transfer from leather to cardboard and stainless steel was determined. HCoV-OC43 was detectable for 6 h on patent, 24 h on finished leather and 48 h on calf leather; no infectious virus was recovered from nubuck. HCoV-OC43 transferred from patent, finished and calf leathers onto cardboard and stainless steel up to 2 h post-inoculation (≤3.1-5.5 log10), suggesting that leathers could act as fomites. Silver additive-coated calf and finished leathers were antiviral against HCoV-OC43, with no infectious virus recovered after 2 h and limited transfer to other surfaces. The silver additive could reduce potential indirect transmission of HCoV-OC43 from leather.


Subject(s)
Coronavirus Infections/transmission , Coronavirus OC43, Human/isolation & purification , Fomites/virology , Animals , Antiviral Agents/pharmacology , COVID-19/transmission , Cell Line , Coronavirus OC43, Human/drug effects , Cricetinae , Disease Transmission, Infectious/prevention & control , Fomites/classification , Humans , SARS-CoV-2/drug effects , SARS-CoV-2/isolation & purification , Silver/pharmacology
5.
Viruses ; 13(7)2021 07 13.
Article in English | MEDLINE | ID: covidwho-1314758

ABSTRACT

Human coronaviruses, including SARS-CoV-2, are known to spread mainly via close contact and respiratory droplets. However, other potential means of transmission may be present. Fomite-mediated transmission occurs when viruses are deposited onto a surface and then transfer to a subsequent individual. Surfaces can become contaminated directly from respiratory droplets or from a contaminated hand. Due to mask mandates in many countries around the world, the former is less likely. Hands can become contaminated if respiratory droplets are deposited on them (i.e., coughing or sneezing) or through contact with fecal material where human coronaviruses (HCoVs) can be shed. The focus of this paper is on whether human coronaviruses can transfer efficiently from contaminated hands to food or food contact surfaces. The surfaces chosen were: stainless steel, plastic, cucumber and apple. Transfer was first tested with cellular maintenance media and three viruses: two human coronaviruses, 229E and OC43, and murine norovirus-1, as a surrogate for human norovirus. There was no transfer for either of the human coronaviruses to any of the surfaces. Murine norovirus-1 did transfer to stainless steel, cucumber and apple, with transfer efficiencies of 9.19%, 5.95% and 0.329%, respectively. Human coronavirus OC43 transfer was then tested in the presence of fecal material, and transfer was observed for stainless steel (0.52%), cucumber (19.82%) and apple (15.51%) but not plastic. This study indicates that human coronaviruses do not transfer effectively from contaminated hands to contact surfaces without the presence of fecal material.


Subject(s)
COVID-19/transmission , Coronavirus Infections/transmission , Food Microbiology , SARS-CoV-2/physiology , COVID-19/virology , Cell Line , Common Cold/transmission , Coronavirus/isolation & purification , Coronavirus 229E, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Equipment Contamination , Feces/virology , Fomites , Foodborne Diseases/virology , Humans , Norovirus/isolation & purification , Stainless Steel
6.
J Occup Environ Hyg ; 18(9): 461-475, 2021 09.
Article in English | MEDLINE | ID: covidwho-1291249

ABSTRACT

Environmental air sampling of the SARS-CoV-2 virus in occupational and community settings is pertinent to reduce and monitor the spread of the COVID pandemic. However, there is a general lack of standardized procedures for airborne virus sampling and limited knowledge of how sampling and storage stress impact the recovery of captured airborne viruses. Since filtration is one of the commonly used methods to capture airborne viruses, this study analyzed the effect of sampling and storage stress on SARS-CoV-2 surrogate virus (human coronavirus OC43, or HCoV-OC43) captured by filters. HCoV-OC43, a simulant of the SARS-CoV-2, was aerosolized and captured by PTFE-laminated filters. The impact of sampling stress was evaluated by comparing the RNA yields recovered when sampled at 3 L/min and 10 L/min and for 10 min and 60 min; in one set of experiments, additional stress was added by passing clean air through filters with the virus for 1, 5, and 15 hr. The impact of storage stress was designed to examine RNA recovery from filters at room temperature (25 °C) and refrigerated conditions (4 °C) for up to 1 week of storage. To our knowledge, this is the first report on using HCoV-OC43 aerosol in air sampling experiments, and the mode diameter of the virus aerosolized from the growth medium was 40-60 nm as determined by SMPS + CPC system (TSI Inc.) and MiniWRAS (Grimm Inc.) measurements. No significant difference was found in virus recovery between the two sampling flow rates and different sampling times (p > 0.05). However, storage at room temperature (25 °C) yielded ∼2x less RNA than immediate processing and storage at refrigerated conditions (4 °C). Therefore, it is recommended to store filter samples with viruses at 4 °C up to 1 week if the immediate analysis is not feasible. Although the laminated PTFE filter used in this work purposefully does not include a non-PTFE backing, the general recommendations for handling and storing filter samples with viral particles are likely to apply to other filter types.


Subject(s)
Air Filters/virology , COVID-19/epidemiology , Coronavirus OC43, Human/isolation & purification , Specimen Handling/methods , Specimen Handling/standards , Environmental Monitoring , Humans , Pandemics , SARS-CoV-2 , Temperature , Time Factors
7.
Pan Afr Med J ; 38: 244, 2021.
Article in English | MEDLINE | ID: covidwho-1257121

ABSTRACT

INTRODUCTION: acute respiratory tract infections (ARIs) are responsible for significant proportions of illnesses and deaths annually. Most of ARIs are of viral etiology, with human coronaviruses (HCoVs) playing a key role. This study was conducted prior to the outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to provide evidence about the sero-epidemiology of HCoVs in rural areas of Ghana. METHODS: this was a cross-sectional study conducted as part of a large epidemiological study investigating the occurrence of respiratory viruses in 3 rural areas of Ghana; Buoyem, Kwamang and Forikrom. Serum samples were collected and tested for the presence of IgG-antibodies to three HCoVs; HCoV-229E, HCoV-OC43 and HCoV-NL63 using immunofluorescence assay. RESULTS: of 201 subjects enrolled into the study, 97 (48.3%) were positive for all three viruses. The most prevalent virus was HCoV-229E (23%; 95% CI: 17.2 - 29.3), followed by HCoV-OC43 (17%; 95% CI: 12.4 - 23.4), then HCoV-NL63 (8%, 95% CI: 4.6 - 12.6). Subjects in Kwamang had the highest sero-prevalence for HCoV-NL63 (68.8%). human coronaviruses-229E (41.3%) and HCoV-OC43 (45.7%) were much higher in Forikrom compared to the other study areas. There was however no statistical difference between place of origin and HCoVs positivity. Although blood group O+ and B+ were most common among the recruited subjects, there was no significant association (p = 0.163) between blood group and HCoV infection. CONCLUSION: this study reports a 48.3% sero-prevalence of HCoVs (OC43, NL63 and 229E) among rural communities in Ghana. The findings provide useful baseline data that could inform further sero-epidemiological studies on SARS-CoV-2 in Africa.


Subject(s)
Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Adult , Coronavirus Infections/virology , Cross-Sectional Studies , Female , Ghana/epidemiology , Humans , Immunoglobulin G/blood , Male , Middle Aged , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Rural Population/statistics & numerical data , Seroepidemiologic Studies , Young Adult
8.
mSphere ; 6(3)2021 05 12.
Article in English | MEDLINE | ID: covidwho-1230164

ABSTRACT

Human coronavirus (HCoV)-OC43 rarely shows a cytopathic effect (CPE) after infection of various cell lines, and the indirect immunoperoxidase assay (IPA), a relatively complex procedure, has long been used as an alternative assay. Because HCoV-OC43 uses cell-surface transmembrane protease serine 2 (TMPRSS2) for cell entry, VeroE6 cells expressing TMPRSS2 may show a clear CPE after HCoV-OC43 infection. The aim of this study was to construct a 50% tissue culture infectious dose (TCID50) assay for HCoV-OC43 based on CPE evaluation using VeroE6/TMPRSS2 cells. VeroE6/TMPRSS2 cells showed clear CPEs 3 to 4 days after low-titer HCoV-OC43 infection. Evaluation of viral kinetics indicated that the viral titer in the culture supernatant of VeroE6/TMPRSS2 cells in the early stages of infection was higher than that of other cells. In comparison, between the CPE-based and the IPA-based (i.e., the reference titer) methods, the titer measured with CPE evaluation 4 to 5 days after infection using VeroE6/TMPRSS2 cells showed a much smaller difference from the reference titer than that measured using other cells. Thus, the TCID50 assay using CPE evaluation with VeroE6/TMPRSS2 cells provides the correct titer value and will greatly contribute to future research on HCoV-OC43.IMPORTANCE HCoV-OC43 rarely shows a cytopathic effect (CPE) in infected cell lines, and thus the plaque and TCID50 assays by CPE observation are not applicable for titration; the indirect immunoperoxidase assay (IPA) is used instead. However, the IPA is relatively complex, time-consuming, costly, and not suitable for simultaneous titration of many samples. We developed a TCID50 assay using CPE evaluation with TMPRSS2-expressing VeroE6/TMPRSS2 cells that provides the same accuracy as the conventional IPA-based viral titration and does not require any staining procedures using antibodies or substrates. This titration method will greatly contribute to future research on HCoV-OC43 by allowing simple, low-cost, and accurate titration of this virus.


Subject(s)
Coronavirus OC43, Human/physiology , Cytopathogenic Effect, Viral , Receptors, Virus/metabolism , Serine Endopeptidases/metabolism , Viral Load/methods , Animals , Cell Line, Tumor , Chlorocebus aethiops , Coronavirus OC43, Human/isolation & purification , Humans , Immunoenzyme Techniques , Receptors, Virus/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Serine Endopeptidases/genetics , Vero Cells/virology , Virus Cultivation , Virus Internalization , Virus Replication
9.
Virol J ; 18(1): 89, 2021 04 30.
Article in English | MEDLINE | ID: covidwho-1209064

ABSTRACT

BACKGROUND: A novel coronavirus (SARS-CoV-2) emerging has put global public health institutes on high alert. Little is known about the epidemiology and clinical characteristics of human coronaviruses infections in relation to infections with other respiratory viruses. METHODS: From February 2017 to December 2019, 3660 respiratory samples submitted to Zhejiang Children Hospital with acute respiratory symptoms were tested for four human coronaviruses RNA by a novel two-tube multiplex reverse transcription polymerase chain reaction assays. Samples were also screened for the occurrence of SARS-CoV-2 by reverse transcription-PCR analysis. RESULTS: Coronavirus RNAs were detected in 144 (3.93%) specimens: HCoV-HKU1 in 38 specimens, HCoV-NL63 in 62 specimens, HCoV-OC43 in 38 specimens and HCoV-229E in 8 specimens. Genomes for SARS-CoV-2 were absent in all specimens by RT-PCR analysis during the study period. The majority of HCoV infections occurred during fall months. No significant differences in gender, sample type, year were seen across species. 37.5 to 52.6% of coronaviruses detected were in specimens testing positive for other respiratory viruses. Phylogenic analysis identified that Zhejiang coronaviruses belong to multiple lineages of the coronaviruses circulating in other countries and areas. CONCLUSION: Common HCoVs may have annual peaks of circulation in fall months in the Zhejiang province, China. Genetic relatedness to the coronaviruses in other regions suggests further surveillance on human coronaviruses in clinical samples are clearly needed to understand their patterns of activity and role in the emergence of novel coronaviruses.


Subject(s)
COVID-19/diagnosis , Multiplex Polymerase Chain Reaction/methods , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Adolescent , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19/complications , COVID-19/genetics , COVID-19/physiopathology , Child , Child, Preschool , China/epidemiology , Coronavirus/genetics , Coronavirus/isolation & purification , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/isolation & purification , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/isolation & purification , Female , Hospitalization , Humans , Infant , Infant, Newborn , Male , Phylogeny , Respiratory Tract Infections/complications , Respiratory Tract Infections/etiology , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics
10.
Virol J ; 18(1): 93, 2021 05 01.
Article in English | MEDLINE | ID: covidwho-1208555

ABSTRACT

BACKGROUND: SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms. METHODS: This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. RESULTS: SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. CONCLUSIONS: Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Coinfection/epidemiology , SARS-CoV-2/isolation & purification , Alberta/epidemiology , Canada/epidemiology , Coronavirus/isolation & purification , Coronavirus 229E, Human/isolation & purification , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/isolation & purification , Cross Reactions , Female , Humans , Male , Orthomyxoviridae/isolation & purification , Pandemics , Prevalence , Retrospective Studies
12.
Arch Virol ; 166(3): 929-933, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1046769

ABSTRACT

This is the first study of respiratory infections in Córdoba, Argentina, caused by endemic human coronavirus (HCoV)-OC43 and HCOV-229E, which circulated during 2011-2012 at a 3% rate, either as single or multiple infections. They were detected mainly in children, but HCoV-229E was also found in adults. HCoV-229E was detected in five out of 631 samples (0.8%), and HCoV-OC43 was found in 14 out of 631 (2.2%) samples. Clinical manifestations ranged from fever to respiratory distress, and a significant association of HCoV-229E with asthma was observed. Further studies and surveillance are needed to provide better clinical insights, early diagnosis, and medical care of patients, as well as to contribute to epidemiology modeling and prevention.


Subject(s)
Common Cold/epidemiology , Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/isolation & purification , Adolescent , Adult , Aged , Argentina , Child , Child, Preschool , Common Cold/virology , Coronavirus 229E, Human/genetics , Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Cross-Sectional Studies , Humans , Infant , Middle Aged , Retrospective Studies , Seasons , Young Adult
13.
J Clin Microbiol ; 59(1)2020 12 17.
Article in English | MEDLINE | ID: covidwho-991749

ABSTRACT

Broad 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 (R 2, 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.


Subject(s)
Betacoronavirus/isolation & purification , COVID-19/diagnosis , Coronavirus OC43, Human/isolation & purification , Influenza A virus/isolation & purification , Metapneumovirus/isolation & purification , SARS-CoV-2/isolation & purification , Betacoronavirus/genetics , COVID-19 Nucleic Acid Testing/methods , Coinfection/virology , Coronavirus OC43, Human/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Humans , Influenza A virus/genetics , Metagenome , Metagenomics , Metapneumovirus/genetics , SARS-CoV-2/genetics
14.
J Microbiol Biotechnol ; 30(10): 1495-1499, 2020 Oct 28.
Article in English | MEDLINE | ID: covidwho-914599

ABSTRACT

The study of climate and respiratory viral infections using big data may enable the recognition and interpretation of relationships between disease occurrence and climatic variables. In this study, realtime reverse transcription quantitative PCR (qPCR) methods were used to identify Human respiratory coronaviruses (HCoV). infections in patients below 10 years of age with respiratory infections who visited Dankook University Hospital in Cheonan, South Korea, from January 1, 2012, to December 31, 2018. Out of the 9010 patients who underwent respiratory virus real-time reverse transcription qPCR test, 364 tested positive for HCoV infections. Among these 364 patients, 72.8% (n = 265) were below 10 years of age. Data regarding the frequency of infections was used to uncover the seasonal pattern of the two viral strains, which was then compared with local meteorological data for the same time period. HCoV-229E and HCoV-OC43 showed high infection rates in patients below 10 years of age. There was a negative relationship between HCoV-229E and HCoV-OC43 infections with air temperature and wind-chill temperatures. Both HCoV-229E and HCoV-OC43 rates of infection were positively related to atmospheric pressure, while HCoV-229E was also positively associated with particulate matter concentrations. Our results suggest that climatic variables affect the rate in which children below 10 years of age are infected with HCoV. These findings may help to predict when prevention strategies may be most effective.


Subject(s)
Climate , Coronavirus Infections/epidemiology , Coronavirus OC43, Human , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Child , Child, Preschool , Coronavirus/genetics , Coronavirus 229E, Human/isolation & purification , Coronavirus 229E, Human/metabolism , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/isolation & purification , Coronavirus OC43, Human/metabolism , Female , Humans , Infant , Infant, Newborn , Male , Prevalence , Real-Time Polymerase Chain Reaction , Republic of Korea/epidemiology , Retrospective Studies
15.
Medicine (Baltimore) ; 99(33): e21520, 2020 Aug 14.
Article in English | MEDLINE | ID: covidwho-740194

ABSTRACT

RATIONALE: Information regarding the clinical features and outcomes of pneumonia due to an infection with human coronavirus (HCoV)-OC43 in children with cancer is rare. This report presents the clinical features in terms of chest CT scan images which may be used to identify cases of HCoV-OC43 infection induced pneumonia in immunocompromised children. PATIENT CONCERNS: We report here a girl with acute lymphoblastic leukemia who developed respiratory symptoms during febrile neutropenia. Rapid clinical progression and nodular lesions on her chest X-ray and computed tomography scans were suggestive of a pulmonary fungal infection. DIAGNOSIS: A series of tests eventually confirmed the exclusive presence of HCoV-OC43 by the FilmArray Respiratory Panel from a throat swab sample. INTERVENTIONS: After the diagnosis was confirmed, the antimicrobial agents initially administered were discontinued. OUTCOMES: Although the chest CT scan images looked severe, the clinical course of the infection induced pneumonia was benign. The respiratory status of the patient was completely resolved in 2 weeks. LESSONS: This report highlights the importance of early identification of respiratory viruses, via the realization of their clinical characteristics, which helps reduce the duration of administration of antimicrobial agents in this setting.


Subject(s)
Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications , Child , Coronavirus Infections/complications , Coronavirus OC43, Human/isolation & purification , Febrile Neutropenia/complications , Female , Humans , Immunocompromised Host , Pneumonia, Viral/complications , Polymerase Chain Reaction
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