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1.
PLoS One ; 17(9): e0273697, 2022.
Article in English | MEDLINE | ID: covidwho-2065114

ABSTRACT

BACKGROUND: Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia. METHODS: The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples. RESULTS: Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease. CONCLUSIONS: Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.


Subject(s)
COVID-19 , Enterovirus , Respiratory Tract Infections , Viruses , Adult , COVID-19/epidemiology , Enterovirus/genetics , Female , Humans , Malaysia/epidemiology , Male , Pandemics , Real-Time Polymerase Chain Reaction , Rhinovirus/genetics , Viruses/genetics
2.
Viruses ; 14(5)2022 04 28.
Article in English | MEDLINE | ID: covidwho-1884366

ABSTRACT

Genetic recombination in RNA viruses is an important evolutionary mechanism. It contributes to population diversity, host/tissue adaptation, and compromises vaccine efficacy. Both the molecular mechanism and initial products of recombination are relatively poorly understood. We used an established poliovirus-based in vitro recombination assay to investigate the roles of sequence identity and RNA structure, implicated or inferred from an analysis of circulating recombinant viruses, in the process. In addition, we used next-generation sequencing to investigate the early products of recombination after cellular coinfection with different poliovirus serotypes. In independent studies, we find no evidence for a role for RNA identity or structure in determining recombination junctions location. Instead, genome function and fitness are of greater importance in determining the identity of recombinant progeny. These studies provide further insights into this important evolutionary mechanism and emphasize the critical nature of the selection process on a mixed virus population.


Subject(s)
Enterovirus Infections , Enterovirus , Poliovirus , Antigens, Viral , Enterovirus/genetics , Genome, Viral , Humans , Poliovirus/genetics , RNA , Recombination, Genetic
3.
J Med Virol ; 94(9): 4502-4507, 2022 09.
Article in English | MEDLINE | ID: covidwho-1872243

ABSTRACT

The outbreak of COVID-19 epidemic has enabled the establishment and application of various rapid detection methods. It is particularly important to establish a fast and accurate detection method for enterovirus, which will be beneficial for clinical diagnosis, epidemic prevention and control, and timely traceability. Through establishing an ultra-fast reverse transcription-polymerase chain reaction (RT-PCR) equipment, this study aimed to evaluate the sensitivity and specificity of the testing method of enterovirus nucleic acids based on ultra-fast real-time fluorescence RT-PCR technology. A total of 61 cases were sampled, which were then transported and preserved. After the nucleic acid extraction, the nucleic acids of the same sample were tested with the enterovirus nucleic acid detection kit produced by Guangzhou Da An Gene Company and the ultra-fast RT-PCR equipment system established in this study. ABI7500Fast and Ahram biosystems S1 fast equipment were used for amplification detection. If the sample had an S-shaped amplification curve in the FAM channel and the Ct value ≤40.00, the result was positive. The sensitivity, precision, and accuracy of the detection method were then verified. This study established a novel testing method to achieve enterovirus nucleic acid detection within 24 min. The sensitivity detection limit of the method was 1.0 × 102 copies/ml. The coefficients of variation for repeated detection of the high, medium, and low concentration samples were 2.644%, 1.674%, and 4.281%, respectively, with good detection repeatability. In addition, a total of 29 cases were positive by the ultra-fast RT-PCR detection method in 61 suspected samples, which was consistent with the conventional fluorescent RT-PCR method. The established rapid detection method can greatly shorten the time for providing a detection report, which may greatly improve the efficiency of diagnosis and treatment.


Subject(s)
COVID-19 , Enterovirus Infections , Enterovirus , Nucleic Acids , COVID-19/diagnosis , Enterovirus/genetics , Enterovirus Infections/diagnosis , Humans , Pilot Projects , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Technology
4.
Virol J ; 19(1): 70, 2022 04 20.
Article in English | MEDLINE | ID: covidwho-1862136

ABSTRACT

BACKGROUND: Enterovirus (EV), parechovirus (HPeV), herpes simplex virus 1 and 2 (HSV1/2) are common viruses leading to viral central nervous system (CNS) infections which are increasingly predominant but exhibit deficiency in definite pathogen diagnosis with gold-standard quantitative PCR method. Previous studies have shown that droplet digital PCR (ddPCR) has great potential in pathogen detection and quantification, especially in low concentration samples. METHODS: Targeting four common viruses of EV, HPeV, HSV1, and HSV2 in cerebrospinal fluid (CSF), we developed a multiplex ddPCR assay using probe ratio-based multiplexing strategy, analyzed the performance, and evaluated it in 97 CSF samples collected from patients with suspected viral CNS infections on a two-channel ddPCR detection system. RESULTS: The four viruses were clearly distinguished by their corresponding fluorescence amplitude. The limits of detection for EV, HPeV, HSV1, and HSV2 were 5, 10, 5, and 10 copies per reaction, respectively. The dynamic range was at least four orders of magnitude spanning from 2000 to 2 copies per reaction. The results of 97 tested clinical CSF specimens were identical to those deduced from qPCR/qRT-PCR assays using commercial kits. CONCLUSION: The multiplex ddPCR assay was demonstrated to be an accurate and robust method which could detect EV, HPeV, HSV1, and HSV2 simultaneously. It provides a useful tool for clinical diagnosis and disease monitoring of viral CNS infections.


Subject(s)
Central Nervous System Viral Diseases , Enterovirus Infections , Enterovirus , Herpesvirus 1, Human , Parechovirus , Picornaviridae Infections , Enterovirus/genetics , Enterovirus Infections/diagnosis , Herpesvirus 1, Human/genetics , Herpesvirus 2, Human/genetics , Humans , Parechovirus/genetics , Real-Time Polymerase Chain Reaction/methods
5.
PLoS One ; 17(1): e0262874, 2022.
Article in English | MEDLINE | ID: covidwho-1643288

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.


Subject(s)
Adenoviruses, Human/genetics , COVID-19/epidemiology , Enterovirus/genetics , Respiratory Tract Infections/epidemiology , Rhinovirus/genetics , SARS-CoV-2/genetics , Adenoviruses, Human/classification , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19/virology , Child , Child, Preschool , Enterovirus/classification , Female , Hand Disinfection/methods , Humans , Infant , Infant, Newborn , Japan/epidemiology , Male , Masks/supply & distribution , Middle Aged , Multiplex Polymerase Chain Reaction , Nasopharynx/virology , Prevalence , Quarantine/organization & administration , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/prevention & control , Respiratory Tract Infections/virology , Rhinovirus/classification , SARS-CoV-2/pathogenicity
6.
Sci Total Environ ; 799: 149386, 2021 Dec 10.
Article in English | MEDLINE | ID: covidwho-1545398

ABSTRACT

To support public-health-related disease surveillance and monitoring, it is crucial to concentrate both enveloped and non-enveloped viruses from domestic wastewater. To date, most concentration methods were developed for non-enveloped viruses, and limited studies have directly compared the recovery efficiency of both types of viruses. In this study, the effectiveness of two different concentration methods (Concentrating pipette (CP) method and an adsorption-extraction (AE) method amended with MgCl2) were evaluated for untreated wastewater matrices using three different viruses (SARS-CoV-2 (seeded), human adenovirus 40/41 (HAdV 40/41), and enterovirus (EV)) and a wastewater-associated bacterial marker gene targeting Lachnospiraceae (Lachno3). For SARS-CoV-2, the estimated mean recovery efficiencies were significantly greater by as much as 5.46 times, using the CP method than the AE method amended with MgCl2. SARS-CoV-2 RNA recovery was greater for samples with higher titer seeds regardless of the method, and the estimated mean recovery efficiencies using the CP method were 25.1 ± 11% across ten WWTPs when wastewater samples were seeded with 5 × 104 gene copies (GC) of SARS-CoV-2. Meanwhile, the AE method yielded significantly greater concentrations of indigenous HAdV 40/41 and Lachno3 from wastewater compared to the CP method. Finally, no significant differences in indigenous EV concentrations were identified in comparing the AE and CP methods. These data indicate that the most effective concentration method varies by microbial analyte and that the priorities of the surveillance or monitoring program should be considered when choosing the concentration method.


Subject(s)
COVID-19 , Enterovirus , Viruses , Enterovirus/genetics , Humans , RNA, Viral , SARS-CoV-2 , Sewage , Waste Water
7.
Microbiol Spectr ; 9(2): e0083121, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1476399

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.


Subject(s)
COVID-19/complications , Coinfection/virology , Respiratory Tract Infections/complications , Respiratory Tract Infections/virology , Adenoviridae/genetics , Adenoviridae/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Child , Enterovirus/genetics , Enterovirus/isolation & purification , Female , Humans , Male , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Middle Aged , Retrospective Studies , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , Wisconsin , Young Adult
8.
Virol J ; 18(1): 202, 2021 10 09.
Article in English | MEDLINE | ID: covidwho-1463255

ABSTRACT

BACKGROUND: The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. METHODS: This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children's Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. RESULTS: A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001). CONCLUSIONS: Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.


Subject(s)
Antibiosis , COVID-19/epidemiology , Respiratory Tract Diseases/epidemiology , SARS-CoV-2/isolation & purification , Adenoviruses, Human/genetics , Adenoviruses, Human/isolation & purification , Adolescent , COVID-19/virology , Child , Child, Hospitalized , Child, Preschool , China , Enterovirus/genetics , Enterovirus/isolation & purification , Female , Humans , Infant , Influenza A virus/genetics , Influenza A virus/isolation & purification , Male , Metapneumovirus/genetics , Metapneumovirus/isolation & purification , Mycoplasma pneumoniae/genetics , Mycoplasma pneumoniae/isolation & purification , Nasopharynx/microbiology , Nasopharynx/virology , Prevalence , Respiratory Syncytial Viruses/genetics , Respiratory Syncytial Viruses/isolation & purification , Respiratory Tract Diseases/microbiology , Respiratory Tract Diseases/virology , Respirovirus/genetics , Respirovirus/isolation & purification , SARS-CoV-2/genetics
9.
Viruses ; 13(9)2021 09 10.
Article in English | MEDLINE | ID: covidwho-1411079

ABSTRACT

We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900-2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.


Subject(s)
Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Enterovirus/genetics , Waste Water/microbiology , Water Microbiology , Arizona/epidemiology , Enterovirus/isolation & purification , Enterovirus Infections/history , High-Throughput Nucleotide Sequencing , History, 21st Century , Humans , Phylogeny , RNA, Viral , Seasons , Wastewater-Based Epidemiological Monitoring
10.
Viruses ; 13(8)2021 08 12.
Article in English | MEDLINE | ID: covidwho-1355050

ABSTRACT

We aimed to assess the duration of nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA persistence in adults self-confined at home after acute infection; and to identify the associations of SARS-CoV-2 persistence with respiratory virus co-detection and infection transmission. A cross-sectional intra-household study was conducted in metropolitan Barcelona (Spain) during the time period of April to June 2020. Every adult who was the first family member reported as SARS-CoV-2-positive by reverse transcription polymerase chain reaction (RT-PCR) as well as their household child contacts had nasopharyngeal swabs tested by a targeted SARS-CoV-2 RT-PCR and a multiplex viral respiratory panel after a 15 day minimum time lag. Four-hundred and four households (404 adults and 708 children) were enrolled. SARS-CoV-2 RNA was detected in 137 (33.9%) adults and 84 (11.9%) children. Rhinovirus/Enterovirus (RV/EV) was commonly found (83.3%) in co-infection with SARS-CoV-2 in adults. The mean duration of SARS-CoV-2 RNA presence in adults' nasopharynx was 52 days (range 26-83 days). The persistence of SARS-CoV-2 was significantly associated with RV/EV co-infection (adjusted odds ratio (aOR) 9.31; 95% CI 2.57-33.80) and SARS-CoV-2 detection in child contacts (aOR 2.08; 95% CI 1.24-3.51). Prolonged nasopharyngeal SARS-CoV-2 RNA persistence beyond the acute infection phase was frequent in adults quarantined at home during the first epidemic wave; which was associated with RV/EV co-infection and could enhance intra-household infection transmission.


Subject(s)
COVID-19/complications , COVID-19/virology , Coinfection , Enterovirus Infections/complications , Picornaviridae Infections/complications , SARS-CoV-2/isolation & purification , Adolescent , Adult , Antibodies, Viral/blood , COVID-19/epidemiology , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Cross-Sectional Studies , Enterovirus/genetics , Enterovirus/isolation & purification , Family Health , Female , Humans , Infant , Male , Middle Aged , Nasopharynx/virology , Quarantine , RNA, Viral/analysis , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Time Factors , Young Adult
11.
Viruses ; 13(5)2021 05 06.
Article in English | MEDLINE | ID: covidwho-1224252

ABSTRACT

Due to the outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), combined with the risk of polio importation from Ukraine, we evaluated the presence of SARS-CoV-2 and enteroviruses in 25 sewage water samples from Romania, concentrated using the WHO method between January 2020 and January 2021. Surveillance for enteroviruses and SARS-CoV-2 are relevant in the calculation of prevalence estimates as well as early detection of the introduction or disappearance of these viruses. For SARS-CoV-2 detection, we used two immunochromatographic nucleocapsid antigenic tests as well as real-time PCR assays, produced for respiratory samples. The isolation of cell culture lines, in accordance with the WHO recommendations, was carried out for enterovirus detection. Twenty-three of the samples investigated were positive in rapid tests for SARS-CoV-2, while the RNA of SARS-CoV-2, detected with Respiratory 2.1 plus a panel Biofire Film array, was present in eight samples. The Allplex 2019-nCoV assay was used for the validation of the tests. There were three genes detected in one sample, E, RdPR, and N, two genes, E and RdPR, in one sample, two genes, RdPR and N, in four samples, one gene, RdPR, in five samples and one gene, N, in one sample. Eight samples were positive for non-polio enteroviruses, and no poliovirus strains were isolated. This study suggests the presence of SARS-CoV-2 and enteroviruses in Romanian sewage water in 2020. As such, our results indicate that a rapid, more specific test should be developed especially for the detection of SARS-CoV-2 in sewage water.


Subject(s)
Environmental Monitoring/methods , SARS-CoV-2/isolation & purification , Sewage/virology , COVID-19/genetics , COVID-19/metabolism , Disease Outbreaks , Enterovirus/genetics , Enterovirus Infections/virology , Humans , Pilot Projects , Real-Time Polymerase Chain Reaction , Romania/epidemiology , SARS-CoV-2/pathogenicity , Water
12.
Clin Chem ; 66(7): 966-972, 2020 07 01.
Article in English | MEDLINE | ID: covidwho-197877

ABSTRACT

BACKGROUND: More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. METHODS: To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2. RESULTS: Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients' respiratory symptoms. CONCLUSION: Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Metagenomics , Pneumonia, Viral/diagnosis , Superinfection/diagnosis , Betacoronavirus/classification , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/genetics , Coronavirus Infections/virology , Enterovirus/classification , Enterovirus/genetics , Enterovirus/isolation & purification , Humans , Nasopharynx/virology , Pandemics , Phylogeny , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , RNA, Viral/chemistry , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Sequence Analysis, RNA , Superinfection/virology
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