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1.
Signal Transduct Target Ther ; 8(1): 149, 2023 04 07.
Article in English | MEDLINE | ID: covidwho-2305506

ABSTRACT

Human diseases, particularly infectious diseases and cancers, pose unprecedented challenges to public health security and the global economy. The development and distribution of novel prophylactic and therapeutic vaccines are the prioritized countermeasures of human disease. Among all vaccine platforms, viral vector vaccines offer distinguished advantages and represent prominent choices for pathogens that have hampered control efforts based on conventional vaccine approaches. Currently, viral vector vaccines remain one of the best strategies for induction of robust humoral and cellular immunity against human diseases. Numerous viruses of different families and origins, including vesicular stomatitis virus, rabies virus, parainfluenza virus, measles virus, Newcastle disease virus, influenza virus, adenovirus and poxvirus, are deemed to be prominent viral vectors that differ in structural characteristics, design strategy, antigen presentation capability, immunogenicity and protective efficacy. This review summarized the overall profile of the design strategies, progress in advance and steps taken to address barriers to the deployment of these viral vector vaccines, simultaneously highlighting their potential for mucosal delivery, therapeutic application in cancer as well as other key aspects concerning the rational application of these viral vector vaccines. Appropriate and accurate technological advances in viral vector vaccines would consolidate their position as a leading approach to accelerate breakthroughs in novel vaccines and facilitate a rapid response to public health emergencies.


Subject(s)
Communicable Diseases , Orthomyxoviridae , Viral Vaccines , Animals , Humans , Viral Vaccines/genetics , Viral Vaccines/therapeutic use , Genetic Vectors , Orthomyxoviridae/genetics , Adenoviridae/genetics
3.
Viruses ; 15(2)2023 02 08.
Article in English | MEDLINE | ID: covidwho-2233643

ABSTRACT

Reverse transcription polymerase chain reaction (RT-PCR) on respiratory tract swabs has become the gold standard for sensitive and specific detection of influenza virus, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this retrospective analysis, we report on the successive implementation and routine use of multiplex RT-PCR testing for patients admitted to the Internal Medicine Emergency Department (ED) at a tertiary care center in Western Austria, one of the hotspots in the early coronavirus disease 2019 (COVID-19) pandemic in Europe. Our description focuses on the use of the Cepheid® Xpert® Xpress closed RT-PCR system in point-of-care testing (POCT). Our indications for RT-PCR testing changed during the observation period: From the cold season 2016/2017 until the cold season 2019/2020, we used RT-PCR to diagnose influenza or RSV infection in patients with fever and/or respiratory symptoms. Starting in March 2020, we used the RT-PCR for SARS-CoV-2 and a multiplex version for the combined detection of all these three respiratory viruses to also screen subjects who did not present with symptoms of infection but needed in-hospital medical treatment for other reasons. Expectedly, the switch to a more liberal RT-PCR test strategy resulted in a substantial increase in the number of tests. Nevertheless, we observed an immediate decline in influenza virus and RSV detections in early 2020 that coincided with public SARS-CoV-2 containment measures. In contrast, the extensive use of the combined RT-PCR test enabled us to monitor the re-emergence of influenza and RSV detections, including asymptomatic cases, at the end of 2022 when COVID-19 containment measures were no longer in place. Our analysis of PCR results for respiratory viruses from a real-life setting at an ED provides valuable information on the epidemiology of those infections over several years, their contribution to morbidity and need for hospital admission, the risk for nosocomial introduction of such infection into hospitals from asymptomatic carriers, and guidance as to how general precautions and prophylactic strategies affect the dynamics of those infections.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Respiratory Syncytial Virus, Human , Humans , SARS-CoV-2/genetics , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Retrospective Studies , COVID-19/diagnosis , COVID-19/epidemiology , Respiratory Syncytial Virus, Human/genetics , Emergency Service, Hospital , Orthomyxoviridae/genetics
4.
Arch Virol ; 168(2): 53, 2023 Jan 07.
Article in English | MEDLINE | ID: covidwho-2174214

ABSTRACT

The prevalence of coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus among referred patients in Hamadan province, Iran, from November 2, 2021, to January 30, 2022, was evaluated. Samples were obtained from 14,116 individuals with COVID-19 symptoms and screened for SARS-CoV-2 and influenza viruses using a multiplex real-time PCR panel assay. Of these patients, 14.19%, 17.11%, and 1.35% were infected with influenza virus, SARS-CoV-2, and both viruses, respectively. The majority of the coinfected patients were female outpatients aged 19-60 years.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , Orthomyxoviridae , Humans , Female , Male , COVID-19/epidemiology , SARS-CoV-2 , Coinfection/epidemiology , Pandemics , Orthomyxoviridae/genetics
5.
Viruses ; 14(12)2022 12 12.
Article in English | MEDLINE | ID: covidwho-2163618

ABSTRACT

Defective interfering particles (DIPs) are particles containing defective viral genomes (DVGs) generated during viral replication. DIPs have been found in various RNA viruses, especially in influenza viruses. Evidence indicates that DIPs interfere with the replication and encapsulation of wild-type viruses, namely standard viruses (STVs) that contain full-length viral genomes. DIPs may also activate the innate immune response by stimulating interferon synthesis. In this review, the underlying generation mechanisms and characteristics of influenza virus DIPs are summarized. We also discuss the potential impact of DIPs on the immunogenicity of live attenuated influenza vaccines (LAIVs) and development of influenza vaccines based on NS1 gene-defective DIPs. Finally, we review the antiviral strategies based on influenza virus DIPs that have been used against both influenza virus and SARS-CoV-2. This review provides systematic insights into the theory and application of influenza virus DIPs.


Subject(s)
COVID-19 , Influenza Vaccines , Orthomyxoviridae , Humans , Antiviral Agents , Defective Interfering Viruses , Defective Viruses/physiology , SARS-CoV-2 , Orthomyxoviridae/genetics , Virus Replication/genetics
6.
Int J Environ Res Public Health ; 19(20)2022 Oct 17.
Article in English | MEDLINE | ID: covidwho-2071470

ABSTRACT

Dependent on the excretion pattern, wastewater monitoring of viruses can be a valuable approach to characterizing their circulation in the human population. Using polyethylene glycol precipitation and reverse transcription-quantitative PCR, the occurrence of RNA of SARS-CoV-2 and influenza viruses A/B in the raw wastewater of two treatment plants in Germany between January and May 2022 was investigated. Due to the relatively high incidence in both exposal areas (plant 1 and plant 2), SARS-CoV-2-specific RNA was determined in all 273 composite samples analyzed (concentration of E gene: 1.3 × 104 to 3.2 × 106 gc/L). Despite a nation-wide low number of confirmed infections, influenza virus A was demonstrated in 5.2% (concentration: 9.8 × 102 to 8.4 × 104 gc/L; plant 1) and in 41.6% (3.6 × 103 to 3.0 × 105 gc/L; plant 2) of samples. Influenza virus B was detected in 36.0% (7.2 × 102 to 8.5 × 106 gc/L; plant 1) and 57.7% (9.6 × 103 to 2.1 × 107 gc/L; plant 2) of wastewater samples. The results of the study demonstrate the frequent detection of two primary respiratory viruses in wastewater and offer the possibility to track the epidemiology of influenza by wastewater-based monitoring.


Subject(s)
COVID-19 , Orthomyxoviridae , Viruses , Humans , SARS-CoV-2/genetics , Wastewater , Cities , COVID-19/epidemiology , RNA , Orthomyxoviridae/genetics , Polyethylene Glycols , RNA, Viral/genetics
7.
J Med Virol ; 94(12): 5802-5807, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1990495

ABSTRACT

The global outbreak of coronavirus disease 2019 (COVID-19), an emerging disease caused by severe acute respiratory syndrome virus-2 (SARS-CoV-2), and strict restrictions implemented to control the infection have impacted the circulation and transmission of common seasonal viruses worldwide and subsequently the rate of hospitalizations in children at young ages. Respiratory syncytial virus (RSV) surprisingly disappeared in 2020-2021 in many countries due to lockdown and precautions were taken because of the COVID-19 pandemic. Herein, we showed a notable change in the rate of hospitalization and reported an unpredictable outbreak of RSV in a small proportion of children admitted to a children's hospital in Dezful (a city in Southwest Iran) in the early spring of 2022. We performed a descriptive study of hospitalized young children (aged ≤ 5 years) with acute respiratory infections. Together with clinical information, 30 nasopharyngeal swabs were prospectively collected and 3 important respiratory viruses (RSV, influenza viruses, and SARS-CoV-2) were tested through the real-time polymerase chain reaction (real-time PCR) method. The age distribution of 30 hospital-admitted children was 1 month to 5 years old and males were the most included subjects 18/30 (60%) in this study. Although the viral genome of SARS-CoV-2 and influenza viruses was not detected, the presence of RSV was confirmed in 16/30 (53.33%) patients. Results showed that the majority of RSV-infected cases were males 10/16 (62.5%), within 12 months of life, and had changes in parameters of the complete blood count. Almost all patients with RSV infection had a cough as the most common clinical manifestation and had no history of past medical conditions as a risk factor. The presented study is the first investigation that documented an outbreak of RSV infection in young children reported since the onset of the COVID-19 outbreak in Iran. Our cases highlight the potential threats of important but neglected pathogens during the ongoing pandemic as described here for RSV, which would be challenging by easing the preimposed restrictions.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Respiratory Tract Infections , Viruses , COVID-19/epidemiology , Child , Child, Preschool , Communicable Disease Control , Disease Outbreaks , Female , Humans , Influenza, Human/epidemiology , Iran/epidemiology , Male , Orthomyxoviridae/genetics , Pandemics , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2 , Viruses/genetics
8.
Infect Dis Poverty ; 11(1): 74, 2022 Jun 29.
Article in English | MEDLINE | ID: covidwho-1910355

ABSTRACT

BACKGROUND: During the coronavirus disease 2019 (COVID-19) pandemic, seasonal influenza activity declined globally and remained below previous seasonal levels, but intensified in China since 2021. Preventive measures to COVID-19 accompanied by different epidemic characteristics of influenza in different regions of the world. To better respond to influenza outbreaks under the COVID-19 pandemic, we analyzed the epidemiology, antigenic and genetic characteristics, and antiviral susceptibility of influenza viruses in the mainland of China during 2020-2021. METHODS: Respiratory specimens from influenza like illness cases were collected by sentinel hospitals and sent to network laboratories in Chinese National Influenza Surveillance Network. Antigenic mutation analysis of influenza virus isolates was performed by hemagglutination inhibition assay. Next-generation sequencing was used for genetic analyses. We also conducted molecular characterization and phylogenetic analysis of circulating influenza viruses. Viruses were tested for resistance to antiviral medications using phenotypic and/or sequence-based methods. RESULTS: In the mainland of China, influenza activity recovered in 2021 compared with that in 2020 and intensified during the traditional influenza winter season, but it did not exceed the peak in previous years. Almost all viruses isolated during the study period were of the B/Victoria lineage and were characterized by genetic diversity, with the subgroup 1A.3a.2 viruses currently predominated. 37.8% viruses tested were antigenically similar to reference viruses representing the components of the vaccine for the 2020-2021 and 2021-2022 Northern Hemisphere influenza seasons. In addition, China has a unique subgroup of 1A.3a.1 viruses. All viruses tested were sensitive to neuraminidase inhibitors and endonuclease inhibitors, except two B/Victoria lineage viruses identified to have reduced sensitivity to neuraminidase inhibitors. CONCLUSIONS: Influenza activity increased in the mainland of China in 2021, and caused flu season in the winter of 2021-2022. Although the diversity of influenza (sub)type decreases, B/Victoria lineage viruses show increased genetic and antigenic diversity. The world needs to be fully prepared for the co-epidemic of influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus globally.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/epidemiology , China/epidemiology , Humans , Influenza, Human/epidemiology , Neuraminidase/genetics , Orthomyxoviridae/genetics , Pandemics , Phylogeny , SARS-CoV-2 , Seasons
9.
PLoS One ; 17(3): e0264855, 2022.
Article in English | MEDLINE | ID: covidwho-1896450

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
10.
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
11.
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
12.
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
13.
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
14.
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
15.
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
17.
Epidemiol Infect ; 149: e226, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1537267

ABSTRACT

The corona virus disease-2019 (COVID-19) pandemic began in Wuhan, China, and quickly spread around the world. The pandemic overlapped with two consecutive influenza seasons (2019/2020 and 2020/2021). This provided the opportunity to study community circulation of influenza viruses and severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) in outpatients with acute respiratory infections during these two seasons within the Bavarian Influenza Sentinel (BIS) in Bavaria, Germany. From September to March, oropharyngeal swabs collected at BIS were analysed for influenza viruses and SARS-CoV-2 by real-time polymerase chain reaction. In BIS 2019/2020, 1376 swabs were tested for influenza viruses. The average positive rate was 37.6%, with a maximum of over 60% (in January). The predominant influenza viruses were Influenza A(H1N1)pdm09 (n = 202), Influenza A(H3N2) (n = 144) and Influenza B Victoria lineage (n = 129). In all, 610 of these BIS swabs contained sufficient material to retrospectively test for SARS-CoV-2. SARS-CoV-2 RNA was not detectable in any of these swabs. In BIS 2020/2021, 470 swabs were tested for influenza viruses and 457 for SARS-CoV-2. Only three swabs (0.6%) were positive for Influenza, while SARS-CoV-2 was found in 30 swabs (6.6%). We showed that no circulation of SARS-CoV-2 was detectable in BIS during the 2019/2020 influenza season, while virtually no influenza viruses were found in BIS 2020/2021 during the COVID-19 pandemic.


Subject(s)
COVID-19/epidemiology , Influenza, Human/epidemiology , Sentinel Surveillance , COVID-19/diagnosis , Germany/epidemiology , Humans , Incidence , Influenza, Human/diagnosis , Oropharynx/virology , Orthomyxoviridae/classification , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , RNA, Viral/genetics , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Seasons
18.
Med Microbiol Immunol ; 210(5-6): 277-282, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1449965

ABSTRACT

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


Subject(s)
COVID-19/epidemiology , Influenza, Human/diagnosis , Point-of-Care Testing/statistics & numerical data , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Hospitals/statistics & numerical data , Humans , Incidence , Influenza, Human/epidemiology , Influenza, Human/virology , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Orthomyxoviridae/physiology , Pandemics , Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Syncytial Virus, Human/physiology , Retrospective Studies
19.
Chem Pharm Bull (Tokyo) ; 69(10): 984-988, 2021.
Article in English | MEDLINE | ID: covidwho-1445702

ABSTRACT

Membrane-based rapid test reagents including immunochromatography are widely used in clinical practice. Recently, high-sensitive reagents based on the immunochromatography method, such as silver amplification method and time resolved fluorescence method for influenza testing, has been developed and early confirmation of infection can be achieved. Furthermore, genetic testing, automated all the steps from extraction till detection, is getting popular. Genetic testing of mycoplasma by Smart Gene Myco system and Coronavirus disease 2019 (COVID-19) test is a good example of membrane-based rapid test reagents. This system uses silica particle-containing membrane filter and enable to shorten the assay time by automates pre-treatment process for removing contamination substances in the sample which affect polymerase-chain-reaction amplification. We hope utilized genetic testing application will help quick confirmation of COVID-19 positive patient and prevent the collapse of medical system under COVID-19 development.


Subject(s)
Chromatography, Affinity/methods , Point-of-Care Systems , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing , Genetic Testing , Humans , Influenza, Human/diagnosis , Influenza, Human/virology , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
20.
Cell Mol Life Sci ; 78(21-22): 6735-6744, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1377320

ABSTRACT

Kallikrein-related peptidases (KLKs) or kallikreins have been linked to diverse (patho) physiological processes, such as the epidermal desquamation and inflammation, seminal clot liquefaction, neurodegeneration, and cancer. Recent mounting evidence suggests that KLKs also represent important regulators of viral infections. It is well-established that certain enveloped viruses, including influenza and coronaviruses, require proteolytic processing of their hemagglutinin or spike proteins, respectively, to infect host cells. Similarly, the capsid protein of the non-enveloped papillomavirus L1 should be proteolytically cleaved for viral uncoating. Consequently, extracellular or membrane-bound proteases of the host cells are instrumental for viral infections and represent potential targets for drug development. Here, we summarize how extracellular proteolysis mediated by the kallikreins is implicated in the process of influenza (and potentially coronavirus and papillomavirus) entry into host cells. Besides direct proteolytic activation of viruses, KLK5 and 12 promote viral entry indirectly through proteolytic cascade events, like the activation of thrombolytic enzymes that also can process hemagglutinin, while additional functions of KLKs in infection cannot be excluded. In the light of recent evidence, KLKs represent potential host targets for the development of new antivirals. Humanized animal models to validate their key functions in viral infections will be valuable.


Subject(s)
COVID-19/enzymology , COVID-19/virology , Host Microbial Interactions/physiology , Kallikreins/metabolism , SARS-CoV-2 , Virus Diseases/enzymology , Animals , Asthma/etiology , Coronavirus/genetics , Coronavirus/pathogenicity , Coronavirus/physiology , Host Microbial Interactions/genetics , Humans , Orthomyxoviridae/genetics , Orthomyxoviridae/pathogenicity , Orthomyxoviridae/physiology , Papillomavirus Infections/enzymology , Papillomavirus Infections/virology , Picornaviridae Infections/complications , Picornaviridae Infections/enzymology , Picornaviridae Infections/virology , Protein Processing, Post-Translational , Proteolysis , Rhinovirus/pathogenicity , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , SARS-CoV-2/physiology , Varicella Zoster Virus Infection/enzymology , Varicella Zoster Virus Infection/virology , Viral Proteins/genetics , Viral Proteins/metabolism , Virus Diseases/virology , Virus Internalization
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