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1.
Anal Bioanal Chem ; 414(16): 4685-4696, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1877814

ABSTRACT

Respiratory illness caused by influenza virus is a serious public health problem worldwide. As the symptoms of influenza virus infection are similar to those of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is essential to distinguish these two viruses. Therefore, to properly respond to a pathogen, a detection method that is capable of rapid and accurate diagnosis in a hospital or at home is required. To satisfy this need, we applied loop-mediated isothermal amplification (LAMP) and an isothermal nucleic acid amplification technique, along with a system to analyze the results without specialized equipment, a lateral flow assay (LFA). Using the platform developed in this study, all processes, from sample preparation to detection, can be performed without special equipment. Unlike existing PCR methods, the nucleic acid amplification can be performed in the field because hot packs do not require electricity. Thus, the designed platform can provide rapid results without the need to transport the samples to a laboratory or hospital. These advantages are not limited to operations in developing countries with poor access to medical systems. In conclusion, the developed technology is a promising tool for infectious disease management that allows for rapid identification of infectious diseases and appropriate treatment of patients.


Subject(s)
COVID-19 , Orthomyxoviridae , COVID-19/diagnosis , Humans , Nucleic Acid Amplification Techniques/methods , Orthomyxoviridae/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
2.
Viruses ; 14(5)2022 05 13.
Article in English | MEDLINE | ID: covidwho-1875806

ABSTRACT

The newest type of influenza virus, influenza D virus (IDV), was isolated in 2011. IDV circulates in several animal species worldwide, causing mild respiratory illness in its natural hosts. Importantly, IDV does not cause clinical disease in humans and does not spread easily from person to person. Here, we review what is known about the host-pathogen interactions that may limit IDV illness. We focus on early immune interactions between the virus and infected host cells in our summary of what is known about IDV pathogenesis. This work establishes a foundation for future research into IDV infection and immunity in mammalian hosts.


Subject(s)
Orthomyxoviridae Infections , Orthomyxoviridae , Thogotovirus , Animals , Biology , Humans , Mammals , Respiratory System
3.
Viruses ; 14(6)2022 May 27.
Article in English | MEDLINE | ID: covidwho-1869817

ABSTRACT

 Newly emerging and seasonal respiratory viruses have a great impact on public health[...].


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Paramyxoviridae Infections , Vaccines , COVID-19/prevention & control , Humans , Membrane Glycoproteins , Parainfluenza Virus 1, Human , SARS-CoV-2
4.
Phytother Res ; 36(5): 2109-2115, 2022 May.
Article in English | MEDLINE | ID: covidwho-1858908

ABSTRACT

Respiratory viruses pose a significant threat to global health. They initially infect the naso- and oropharyngeal regions, where they amplify, cause symptoms, and may also be transmitted to new hosts. Preventing initial infection or reducing viral loads upon infection might soothe symptoms, prevent dissemination into the lower airways, or transmission to the next individual. Several natural products have well-described direct antiviral activity or may ameliorate symptoms of respiratory infections. We thus analyzed the potential of plant-derived products to inactivate respiratory viral pathogens and determined the antiviral activity of black chokeberry (Aronia melanocarpae [Michx.] Elliott), elderberry (Sambucus nigra L.), and pomegranate (Punica granatum L.) juice, as well as green tea (Camellia sinensis [L.] Kuntze) on the infectivity of the surrogate-modified vaccinia virus Ankara, and the respiratory viruses severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (IAV), and adenovirus Type 5. Black chokeberry and pomegranate juice, and green tea reduced SARS-CoV-2 and IAV titers by ≥80% or ≥99%. This suggests that oral rinsing with these products may reduce viral loads in the oral cavity which might prevent viral transmission.


Subject(s)
COVID-19 , Orthomyxoviridae , Antiviral Agents/pharmacology , Humans , SARS-CoV-2 , Tea
5.
Int J Infect Dis ; 121: 184-189, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1851260

ABSTRACT

CURRENT SITUATION: The global influenza surveillance and response system (GISRS), coordinated by the World Health Organization (WHO), is a global framework for surveillance of influenza and other respiratory viruses, data collection, laboratory capacity building, genomic data submission and archival, standardization, and calibration of reagents and vaccine strains, production of seasonal influenza vaccines and creating a facilitatory regulatory environment for the same. GAPS: WHO-designated national influenza centers (NICs) are entrusted with establishing surveillance in their respective countries. National and subnational surveillance remains weak in most parts of the world because of varying capacities of the NICs, lack of funds, poor human and veterinary surveillance mechanisms, lack of intersectoral coordination, and varying commitments of the local government. WAY FORWARD: As influenza viruses have a wide variety of nonhuman hosts, it is critical to strengthen surveillance at local levels for timely detection of untypable or novel strains with potential to cause epidemics or pandemics. In this article, we have proposed possible strategies to strengthen and expand local capacities for respiratory virus surveillance through the designated NICs of the WHO.


Subject(s)
Influenza Vaccines , Influenza, Human , Orthomyxoviridae , Global Health , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Orthomyxoviridae/genetics , Pandemics/prevention & control , World Health Organization
6.
Cell Biol Int ; 46(7): 1009-1020, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1843866

ABSTRACT

Almost a century after the devastating pandemic of the Spanish flu, humankind is facing the relatively comparable global outbreak of COVID-19. COVID-19 is an infectious disease caused by SARS-CoV-2 with an unprecedented transmission pattern. In the face of the recent repercussions of COVID-19, many have argued that the clinical experience with influenza through the last century may have tremendous implications in the containment of this newly emerged viral disease. During the last 2 years, from the emergence of COVID-19, tremendous advances have been made in diagnosing and treating coinfections. Several approved vaccines are available now for the primary prevention of COVID-19 and specific treatments exist to alleviate symptoms. The present review article aims to discuss the pathophysiology, diagnosis, and treatment of SARS-CoV-2 and influenza A virus coinfection while delivering a bioinformatics-based insight into this subject matter.


Subject(s)
COVID-19 , Coinfection , Influenza Pandemic, 1918-1919 , Influenza, Human , Orthomyxoviridae , Coinfection/diagnosis , Coinfection/epidemiology , Computational Biology , History, 20th Century , Humans , Influenza, Human/epidemiology , Influenza, Human/prevention & control , SARS-CoV-2
7.
Elife ; 112022 May 09.
Article in English | MEDLINE | ID: covidwho-1835657

ABSTRACT

The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5-10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.


Subject(s)
COVID-19 , Orthomyxoviridae , COVID-19/diagnosis , Humans , Pandemics , RNA, Viral/analysis , SARS-CoV-2/genetics , Saliva , Sensitivity and Specificity
8.
Int J Environ Res Public Health ; 19(6)2022 03 08.
Article in English | MEDLINE | ID: covidwho-1818079

ABSTRACT

BACKGROUND: Healthcare workers (HCWs) are more exposed to influenza infection, and the influenza vaccination is recommended each year, to reduce the risk of influenza infection and prevent influenza transmission. This study is a cross-sectional study and the objectives were to determine the rate of influenza virus infection among HCWs in the 2019-2020 influenza season. METHODS: Between January and March 2020, a survey was carried out in 2 hospitals and 15 primary health-care settings (PHCS) in Wroclaw (Poland). The novel point-of-care testing Flu SensDx device was used, which detects the M1 protein of the influenza virus using electrochemical impedance spectroscopy from biological material (throat/nasal swabs). RESULTS: A total of 150 samples were collected. The majority of participating HCWs by profession were 83 physicians (55.3%) and half (51.3%) of the participating HCWs worked in PHCS. Influenza vaccination coverage was 61.3% in 2019-2020 and 46.0% in the 2018-2019 season for all participants. Of the participating HCWs, 44.0% were positive tested by the Flu SensDx device. There were no statistically significant differences among the positive tested HCWs, their influenza immunization history, and the presence of symptoms of influenza-like illness (p > 0.05). CONCLUSION: Although the results of the present study suggest that influenza vaccination does not reduce the frequency of influenza virus detection by Flu SensDx testing in the HCWs participants, larger studies are needed to estimate the incidence of influenza virus infection among HCWs to understand the underlying mechanism and fine-tune policies aimed at reducing nosocomial infections.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , COVID-19/epidemiology , Cross-Sectional Studies , Health Personnel , Humans , Incidence , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Seasons
9.
PLoS One ; 17(4): e0266474, 2022.
Article in English | MEDLINE | ID: covidwho-1817483

ABSTRACT

Respiratory infectious diseases pose a serious threat worldwide, and novel antiviral materials are highly demanded. Photocatalytic nanoparticles have been developed to inhibit indirect transmission of pathogens by acting as surface coating materials. During development of such antiviral materials, researchers use bacteriophages as model viruses due to their safety and experimental efficiency. Screening methods are used to identify potential antiviral materials, and better screening technologies will accelerate the discovery of antiviral treatments. In this study, we constructed a novel platform to evaluate antiviral activity of surface coating materials using the M13 bacteriophage and phagemid system derived from phage display technology. The evaluation results generated by this system for the two tested antiviral materials were comparable to those for the materials tested on the Qß bacteriophage and influenza virus using traditional screening methods. The experimental system developed in this study provides rapid and effective screening and can be applied to the development of novel antiviral materials.


Subject(s)
Antiviral Agents , Orthomyxoviridae , Antiviral Agents/pharmacology , Bacteriophage M13
10.
Viruses ; 14(4)2022 04 12.
Article in English | MEDLINE | ID: covidwho-1786082

ABSTRACT

Influenza-like illness (ILI) can be caused by a range of respiratory viruses. The present study investigates the contribution of influenza and other respiratory viruses, the occurrence of viral co-infections, and the persistence of the viruses after ILI onset in older adults. During the influenza season 2014-2015, 2366 generally healthy community-dwelling older adults (≥60 years) were enrolled in the study. Viruses were identified by multiplex ligation-dependent probe-amplification assay in naso- and oropharyngeal swabs taken during acute ILI phase, and 2 and 8 weeks later. The ILI incidence was 10.7%, which did not differ between vaccinated and unvaccinated older adults; influenza virus was the most frequently detected virus (39.4%). Other viruses with significant contribution were: rhinovirus (17.3%), seasonal coronavirus (9.8%), respiratory syncytial virus (6.7%), and human metapneumovirus (6.3%). Co-infections of influenza virus with other viruses were rare. The frequency of ILI cases in older adults in this 2014-2015 season with low vaccine effectiveness was comparable to that of the 2012-2013 season with moderate vaccine efficacy. The low rate of viral co-infections observed, especially for influenza virus, suggests that influenza virus infection reduces the risk of simultaneous infection with other viruses. Viral persistence or viral co-infections did not affect the clinical outcome of ILI.


Subject(s)
Coinfection , Coronavirus , Influenza, Human , Orthomyxoviridae , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Virus Diseases , Aged , Coinfection/epidemiology , Humans , Infant , Virus Diseases/epidemiology
11.
Virol J ; 18(1): 177, 2021 08 28.
Article in English | MEDLINE | ID: covidwho-1767103

ABSTRACT

BACKGROUND: The development of an influenza RNA-dependent RNA polymerase (RdRp) inhibitor is required; therefore, a method for evaluating the activity of influenza RdRp needs to be developed. The current method uses an ultracentrifuge to separate viral particles and quantifies RdRp activity with radioisotope-labeled nucleosides, such as 32P-GTP. This method requires special equipment and radioisotope management, so it cannot be implemented in all institutions. We have developed a method to evaluate the mRNA transcription activity of RdRp without using ultracentrifugation and radioisotopes. RESULTS: RdRp was extracted from viral particles that were purified from the culture supernatant using anionic polymer-coated magnetic beads that can concentrate influenza virus particles from the culture supernatant in approximately 30 min. A strand-specific real-time reverse transcription polymerase chain reaction (RT-PCR) method was developed based on reverse transcription using tagged primers. RT primers were designed to bind to a sequence near the 3' end of mRNA containing a poly A tail for specific recognition of the mRNA, with an 18-nucleotide tag attached to the 5' end of the sequence. The RT reaction was performed with this tagged RT primer, and the amount of mRNA was analyzed using real-time qPCR. Real-time qPCR using the tag sequence as the forward primer and a segment-specific reverse primer ensured the specificity for quantifying the mRNA of segments 1, 4, and 5. The temperature, reaction time, and Mg2+ concentration were determined to select the optimum conditions for in vitro RNA synthesis by RdRp, and the amount of synthesized mRNAs of segments 1, 4, and 5 was determined with a detection sensitivity of 10 copies/reaction. In addition, mRNA synthesis was inhibited by ribavirin triphosphate, an RdRp inhibitor, thus indicating the usefulness of this evaluation method for screening RdRp inhibitors. CONCLUSION: This method makes it possible to analyze the RdRp activity even in a laboratory where ultracentrifugation and radioisotopes cannot be used. This novel method for measuring influenza virus polymerase activity will further promote research to identify compounds that inhibit viral mRNA transcription activity of RdRp.


Subject(s)
Influenza, Human , Orthomyxoviridae , RNA-Dependent RNA Polymerase , Reverse Transcription , Humans , Orthomyxoviridae/genetics , RNA, Messenger/genetics , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction
12.
Viruses ; 14(3)2022 03 03.
Article in English | MEDLINE | ID: covidwho-1767152

ABSTRACT

Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3'-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and influenza A FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and was found to occur with the homologous domains of influenza B and C FluPols. The N-half domain of RPB4 was found to be critical in this interaction. Punctual mutants generated at conserved positions between influenza A, B, and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defects. These results suggest that FluPol interacts with several domains of Pol II (the CTD to bind Pol II), initiating host transcription and a second transcription on RPB4 to locate FluPol at the proximity of the 5'-end of nascent host mRNA.


Subject(s)
Influenza, Human , Orthomyxoviridae , Humans , Orthomyxoviridae/genetics , RNA Polymerase II/metabolism , RNA, Messenger/genetics , RNA, Viral/genetics , RNA, Viral/metabolism , RNA-Dependent RNA Polymerase/genetics , Viral Transcription , Virus Replication
13.
Immun Inflamm Dis ; 10(4): e609, 2022 04.
Article in English | MEDLINE | ID: covidwho-1763241

ABSTRACT

INTRODUCTION: Myxovirus resistance protein 1 (MxA) is a biomarker that is elevated in patients with viral infections. The goal of this study was to evaluate the diagnostic value of MxA in diagnosing COVID-19 infections in the emergency department (ED) patients. METHODS: This was a single-center prospective observational cohort study including patients with a suspected COVID-19 infection. The primary outcome of this study was a confirmed COVID-19 infection by RT-PCR test. MxA was assessed using an enzyme immunoassay on whole blood and receiver operating chart and area under the curve (AUC) analysis was conducted. Sensitivity, specificity, negative predictive value, and positive predictive value of MxA on diagnosing COVID-19 at the optimal cut-off of MxA was determined. RESULTS: In 2021, 100 patients were included. Of these patients, 77 patients had COVID-19 infection and 23 were non-COVID-19. Median MxA level was significantly higher (p < .001) in COVID-19 patients compared to non-COVID-19 patients, respectively 1933 and 0.1 ng/ml. The AUC of MxA on a confirmed COVID-19 infection was 0.941 (95% CI: 0.867-1.000). The optimal cut-off point of MxA was 252 ng/ml. At this cut-off point, the sensitivity of MxA on a confirmed COVID-19 infection was 94% (95% CI: 85%-98%) and the specificity was 91% (95% CI: 72%-99%). CONCLUSION: MxA accurately distinguishes COVID-19 infections from bacterial infections and noninfectious diagnoses in the ED in patients with a suspected COVID-19 infection. If the results can be validated, MxA could improve the diagnostic workup and patient flow in the ED.


Subject(s)
COVID-19 , Orthomyxoviridae , COVID-19/diagnosis , Emergency Service, Hospital , Humans , Myxovirus Resistance Proteins , Prospective Studies
14.
Sci Rep ; 12(1): 4947, 2022 03 23.
Article in English | MEDLINE | ID: covidwho-1758377

ABSTRACT

The COVID-19 pandemic required increased testing capacity, enabling rapid case identification and effective contract tracing to reduce transmission of disease. The BioFire FilmArray is a fully automated nucleic acid amplification test system providing specificity and sensitivity associated with gold standard molecular methods. The FilmArray Respiratory Panel 2.1 targets 22 viral and bacterial pathogens, including SARS-CoV-2 and influenza virus. While each panel provides a robust output of information regarding pathogen detection, the specimen throughput is low. This study evaluates the FilmArray Respiratory Panel 2.1 using 33 pools of contrived nasal samples and 22 pools of clinical nasopharyngeal specimens to determine the feasibility of increasing testing capacity, while maintaining detection of both SARS-CoV-2 and influenza virus. We observed 100% detection and 90% positive agreement for SARS-CoV-2 and 98% detection and 95% positive agreement for influenza viruses with pools of contrived or clinical specimens, respectively. While discordant results were mainly attributed to loss in sensitivity, the sensitivity of the pooling assay was well within accepted limits of detection for a nucleic acid amplification test. Overall, this study provides evidence supporting the use of pooling patient specimens, one in four with the FilmArray Respiratory Panel 2.1 for the detection of SARS-CoV-2 and influenza virus.


Subject(s)
COVID-19 , Orthomyxoviridae , Respiratory Tract Infections , COVID-19/diagnosis , Humans , Molecular Diagnostic Techniques/methods , Orthomyxoviridae/genetics , Pandemics , SARS-CoV-2/genetics
15.
Viruses ; 14(3)2022 03 17.
Article in English | MEDLINE | ID: covidwho-1753690

ABSTRACT

SARS-CoV-2/influenza virus co-infection studies have focused on hospitalized patients who usually had grave sequelae. Here, we report SARS-CoV-2/influenza virus co-infection cases from both community and hospital settings reported through integrated ILI/SARI (Influenza Like Illness/Severe Acute Respiratory Infection) sentinel surveillance established by the Indian Council of Medical Research. We describe the disease progression and outcomes in these cases. Out of 13,467 samples tested from 4 July 2021-31 January 2022, only 5 (0.04%) were of SARS-CoV-2/influenza virus co-infection from 3 different sites in distinct geographic regions. Of these, three patients with extremes of age required hospital admission, but none required ICU admission or mechanical ventilation. No mortality was reported. The other two co-infection cases from community settings were managed at home. This is the first report on SARS-CoV-2/Influenza virus co-infection from community as well as hospital settings in India and shows that influenza viruses are circulating in the community even during COVID-19. The results emphasize the need for continuous surveillance for multiple respiratory pathogens for effective public health management of ILI/SARI cases in line with the WHO (World Health Organization) recommendations.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , Orthomyxoviridae , COVID-19/epidemiology , Coinfection/epidemiology , Humans , Influenza, Human/complications , Influenza, Human/epidemiology , SARS-CoV-2 , Seasons , Sentinel Surveillance
16.
Biosens Bioelectron ; 207: 114169, 2022 Jul 01.
Article in English | MEDLINE | ID: covidwho-1748198

ABSTRACT

Isothermal amplification methods are a promising trend in virus detection because of their superiority in rapidity and sensitivity. However, the generation of false positives and limited multiplexity are major bottlenecks that must be addressed. In this study, we developed a multiplex Argonaute (Ago)-based nucleic acid detection system (MULAN) that integrates rapid isothermal amplification with the multiplex inclusiveness of a single Ago for simultaneous detection of multiple targets such as SARS-CoV-2 and influenza viruses. Owing to its high specificity, MULAN can distinguish targets at a single-base resolution for mutant genotyping. Moreover, MULAN also supports portable and visible devices with a limit of detection of five copies per reaction. Validated by SARS-CoV-2 pseudoviruses and clinical samples of influenza viruses, MULAN showed 100% agreement with quantitative reverse-transcription PCR. These results demonstrated that MULAN has great potential to facilitate reliable, easy, and quick point-of-care diagnosis for promoting the control of infectious diseases.


Subject(s)
Biosensing Techniques , COVID-19 , Orthomyxoviridae , COVID-19/diagnosis , Humans , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Orthomyxoviridae/genetics , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
17.
Viruses ; 14(3)2022 03 15.
Article in English | MEDLINE | ID: covidwho-1742733

ABSTRACT

Viral replication and transmissibility are the principal causes of endemic and pandemic disease threats. There remains a need for broad-spectrum antiviral agents. The most common respiratory viruses are endemic agents such as coronaviruses, respiratory syncytial viruses, and influenza viruses. Although vaccines are available for SARS-CoV-2 and some influenza viruses, there is a paucity of effective antiviral drugs, while for RSV there is no vaccine available, and therapeutic treatments are very limited. We have previously shown that probenecid is safe and effective in limiting influenza A virus replication and SARS-CoV-2 replication, along with strong evidence showing inhibition of RSV replication in vitro and in vivo. This review article will describe the antiviral activity profile of probenecid against these three viruses.


Subject(s)
COVID-19 , Orthomyxoviridae , Respiratory Syncytial Virus, Human , COVID-19/drug therapy , Drug Repositioning , Humans , Probenecid/pharmacology , SARS-CoV-2
18.
PLoS One ; 17(3): e0264949, 2022.
Article in English | MEDLINE | ID: covidwho-1742012

ABSTRACT

BACKGROUND: In the context of COVID-19 pandemic in Catalonia (Spain), the present study analyses respiratory samples collected by the primary care network using Acute Respiratory Infections Sentinel Surveillance System (PIDIRAC) during the 2019-2020 season to complement the pandemic surveillance system in place to detect SARS-CoV-2. The aim of the study is to describe whether SARS-CoV-2 was circulating before the first confirmed case was detected in Catalonia, on February 25th, 2020. METHODS: The study sample was made up of all samples collected by the PIDIRAC primary care network as part of the Influenza and Acute Respiratory Infections (ARI) surveillance system activities. The study on respiratory virus included coronavirus using multiple RT-PCR assays. All positive samples for human coronavirus were subsequently typed for HKU1, OC43, NL63, 229E. Every respiratory sample was frozen at-80°C and retrospectively studied for SARS-CoV-2 detection. A descriptive study was performed, analysing significant differences among variables related to SARS-CoV- 2 cases comparing with rest of coronaviruses cases through a bivariate study with Chi-squared test and statistical significance at 95%. RESULTS: Between October 2019 and April 2020, 878 respiratory samples from patients with acute respiratory infection or influenza syndrome obtained by PIDIRAC were analysed. 51.9% tested positive for influenza virus, 48.1% for other respiratory viruses. SARS-CoV-2 was present in 6 samples. The first positive SARS-CoV-2 case had symptom onset on 2 March 2020. These 6 cases were 3 men and 3 women, aged between 25 and 50 years old. 67% had risk factors, none had previous travel history nor presented viral coinfection. All of them recovered favourably. CONCLUSION: Sentinel Surveillance PIDIRAC enhances global epidemiological surveillance by allowing confirmation of viral circulation and describes the epidemiology of generalized community respiratory viruses' transmission in Catalonia. The system can provide an alert signal when identification of a virus is not achieved in order to take adequate preparedness measures.


Subject(s)
COVID-19/diagnosis , Coronavirus/classification , Orthomyxoviridae/classification , RNA, Viral/genetics , Respiratory Tract Infections/virology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , Child , Child, Preschool , Coronavirus/genetics , Coronavirus/isolation & purification , Female , Humans , Infant , Male , Middle Aged , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Primary Health Care , Retrospective Studies , Sentinel Surveillance , Spain/epidemiology , Young Adult
19.
PLoS One ; 17(3): e0264855, 2022.
Article in English | MEDLINE | ID: covidwho-1736511

ABSTRACT

Since December 2019 the world has been facing the outbreak of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Identification of infected patients and discrimination from other respiratory infections have so far been accomplished by using highly specific real-time PCRs. Here we present a rapid multiplex approach (RespiCoV), combining highly multiplexed PCRs and MinION sequencing suitable for the simultaneous screening for 41 viral and five bacterial agents related to respiratory tract infections, including the human coronaviruses NL63, HKU1, OC43, 229E, Middle East respiratory syndrome coronavirus, SARS-CoV, and SARS-CoV-2. RespiCoV was applied to 150 patient samples with suspected SARS-CoV-2 infection and compared with specific real-time PCR. Additionally, several respiratory tract pathogens were identified in samples tested positive or negative for SARS-CoV-2. Finally, RespiCoV was experimentally compared to the commercial RespiFinder 2SMART multiplex screening assay (PathoFinder, The Netherlands).


Subject(s)
Bacteria/genetics , COVID-19/diagnosis , High-Throughput Nucleotide Sequencing/methods , RNA Viruses/genetics , Respiratory Tract Infections/diagnosis , SARS-CoV-2/genetics , Bacteria/isolation & purification , COVID-19/virology , Coronavirus/genetics , Coronavirus/isolation & purification , DNA, Bacterial/chemistry , DNA, Bacterial/metabolism , Herpesvirus 1, Human/genetics , Herpesvirus 1, Human/isolation & purification , Humans , Multiplex Polymerase Chain Reaction , Nanopores , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , RNA Viruses/isolation & purification , RNA, Viral/chemistry , RNA, Viral/metabolism , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , SARS-CoV-2/isolation & purification
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