Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 67
Filter
1.
Viruses ; 14(11)2022 Oct 31.
Article in English | MEDLINE | ID: covidwho-2113143

ABSTRACT

This study aimed to analyze the genetic and evolutionary characteristics of the influenza A/H3N2 viruses circulating in Myanmar from 2015 to 2019. Whole genomes from 79 virus isolates were amplified using real-time polymerase chain reaction and successfully sequenced using the Illumina iSeq100 platforms. Eight individual phylogenetic trees were retrieved for each segment along with those of the World Health Organization (WHO)-recommended Southern Hemisphere vaccine strains for the respective years. Based on the WHO clades classification, the A/H3N2 strains in Myanmar from 2015 to 2019 collectively belonged to clade 3c.2. These strains were further defined based on hemagglutinin substitutions as follows: clade 3C.2a (n = 39), 3C.2a1 (n = 2), and 3C.2a1b (n = 38). Genetic analysis revealed that the Myanmar strains differed from the Southern Hemisphere vaccine strains each year, indicating that the vaccine strains did not match the circulating strains. The highest rates of nucleotide substitution were estimated for hemagglutinin (3.37 × 10-3 substitutions/site/year) and neuraminidase (2.89 × 10-3 substitutions/site/year). The lowest rate was for non-structural protein segments (4.19 × 10-5 substitutions/site/year). The substantial genetic diversity that was revealed improved phylogenetic classification. This information will be particularly relevant for improving vaccine strain selection.


Subject(s)
Influenza A virus , Influenza Vaccines , Influenza, Human , Humans , Influenza, Human/prevention & control , Influenza A Virus, H3N2 Subtype/genetics , Influenza A virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinins , Phylogeny , Myanmar/epidemiology , Sequence Analysis, DNA , Seasons
2.
Virology ; 576: 105-110, 2022 11.
Article in English | MEDLINE | ID: covidwho-2061964

ABSTRACT

As SARS-CoV-2 and influenza viruses co-circulate, co-infections with these viruses generate an increasing concern to public health. To evaluate the prevalence and clinical impacts of SARS-CoV-2 and influenza A virus co-infections during the 2021-2022 influenza season, SARS-CoV-2-positive samples from 462 individuals were collected from October 2021 to January 2022. Of these individuals, 152 tested positive for influenza, and the monthly co-infection rate ranged from 7.1% to 48%. Compared to the Delta variant, individuals infected with Omicron were less likely to be co-infected and hospitalized, and individuals who received influenza vaccines were less likely to become co-infected. Three individuals had two samples collected on different dates, and all three developed a co-infection after their initial SARS-CoV-2 infection. This study demonstrates high prevalence of co-infections in central Missouri during the 2021-2022 influenza season, differences in co-infection prevalence between the Delta and the Omicron waves, and the importance of influenza vaccinations against co-infections.


Subject(s)
COVID-19 , Coinfection , Influenza A virus , Influenza Vaccines , Influenza, Human , Humans , Influenza, Human/epidemiology , SARS-CoV-2 , Coinfection/epidemiology , Cross-Sectional Studies , Seasons , Missouri/epidemiology , COVID-19/epidemiology , Influenza A virus/genetics
3.
Transbound Emerg Dis ; 69(5): e1445-e1459, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2052989

ABSTRACT

The Mexican lineage H5N2 low pathogenic avian influenza viruses (LPAIVs) were first detected in 1994 and mutated to highly pathogenic avian influenza viruses (HPAIVs) in 1994-1995 causing widespread outbreaks in poultry. By using vaccination and other control measures, the HPAIVs were eradicated but the LPAIVs continued circulating in Mexico and spread to several other countries. To get better resolution of the phylogenetics of this virus, the full genome sequences of 44 H5N2 LPAIVs isolated from 1994 to 2011, and 6 detected in 2017 and 2019, were analysed. Phylogenetic incongruence demonstrated genetic reassortment between two separate groups of the Mexican lineage H5N2 viruses between 2005 and 2010. Moreover, the recent H5N2 viruses reassorted with previously unidentified avian influenza viruses. Bayesian phylogeographic results suggested that mechanical transmission involving human activity is the most probable cause of the virus spillover to Central American, Caribbean, and East Asian countries. Increased infectivity and transmission of a 2011 H5N2 LPAIV in chickens compared to a 1994 virus demonstrates improved adaptation to chickens, while low virus shedding, and limited contact transmission was observed in mallards with the same 2011 virus. The sporadic increase in basic amino acids in the HA cleavage site, changes in potential N-glycosylation sites in the HA, and truncations of PB1-F2 should be further examined in relation to the increased infectivity and transmission in poultry. The genetic changes that occur as this lineage of H5N2 LPAIVs continues circulating in poultry is concerning not only because of the effect of these changes on vaccination efficacy, but also because of the potential of the viruses to mutate to the highly pathogenic form. Continued vigilance and surveillance efforts, and the pathogenic and genetic characterization of circulating viruses, are required for the effective control of this virus.


Subject(s)
Influenza A Virus, H5N2 Subtype , Influenza A virus , Influenza in Birds , Amino Acids, Basic/genetics , Animals , Bayes Theorem , Chickens , Humans , Influenza A Virus, H5N2 Subtype/genetics , Influenza A virus/genetics , Mexico/epidemiology , Phylogeny , Poultry
4.
Infect Genet Evol ; 104: 105356, 2022 10.
Article in English | MEDLINE | ID: covidwho-2036365

ABSTRACT

An H3N1 avian influenza virus was detected in a laying hens farm in May 2019 which had experienced 25% mortality in Northern France. The complete sequencing of this virus showed that all segment sequences belonged to the Eurasian lineage and were phylogenetically very close to many of the Belgian H3N1 viruses detected in 2019. The French virus presented two genetic particularities with NA and NS deletions that could be related to virus adaptation from wild to domestic birds and could increase virulence, respectively. Molecular data of H3N1 viruses suggest that these two deletions occurred at two different times.


Subject(s)
Influenza A virus , Influenza in Birds , Animals , Chickens , Female , Influenza A virus/genetics , Phylogeny
5.
PLoS One ; 17(9): e0274222, 2022.
Article in English | MEDLINE | ID: covidwho-2021957

ABSTRACT

INTRODUCTION: Using respiratory virus rapid diagnostic tests in the emergency department could allow better and faster clinical management. Point-of-care PCR instruments now provide results in less than 30 minutes. The objective of this study was to assess the impact of the use of a rapid molecular diagnostic test, the cobas® Influenza A/B & RSV Assay, during the clinical management of emergency department patients. METHODS: Patients (adults and children) requiring admission or suffering from an underlying condition at risk of respiratory complications were prospectively recruited in the emergency department of four hospitals in the Brussels region. Physicians' intentions regarding admission, isolation, antibiotic, and antiviral use were collected before and after performing the rapid molecular test. Additionally, a comparison of the analytical performance of this test against antigen rapid tests and viral culture was performed as well as a time-to-result evaluation. RESULTS: Among the 293 patients recruited, 90 had a positive PCR, whereas 44 had a positive antigen test. PCR yielded a sensitivity of 100% for all targets. Antigen tests yielded sensitivities ranging from 66.7% for influenza B to 83.3% for respiratory syncytial virus (RSV). The use of PCR allowed a decrease in the overall need for isolation and treatment by limiting the isolation of negative patients and antibiotic use for positive patients. Meanwhile, antiviral treatments better targeted patients with a positive influenza PCR. CONCLUSION: The use of a rapid influenza and RSV molecular test improves the clinical management of patients admitted to the emergency department by providing a fast and reliable result. Their additional cost compared to antigen tests should be balanced with the benefit of their analytical performance, leading to efficient reductions in the need for isolation and antibiotic use.


Subject(s)
Herpesvirus 1, Cercopithecine , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Adult , Anti-Bacterial Agents/therapeutic use , Antiviral Agents , Child , Emergency Service, Hospital , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , Sensitivity and Specificity
6.
J Appl Microbiol ; 133(6): 3534-3545, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2001658

ABSTRACT

INTRODUCTION: Quantitative reverse transcription PCR (RT-qPCR) is the leading tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given that it will almost certainly continue to coexist with other respiratory viruses in the coming years, our study aimed to design a multiplex PCR system not affected by supplier outages and with reduced cost compared to the existing commercially available kits. METHODS AND RESULTS: In this study, combinations of four primers/probe sets were used to construct a flexible RT-qPCR assay which is capable of discriminating between SARS-CoV-2 and the seasonal human coronavirus HCoV-OC43, or even influenza A virus. Additionally, the human RPP30 gene was used as an internal control. To demonstrate the robustness of the assay, it was applied to a collection of 150 clinical samples. The results showed 100% sensitivity and specificity compared to the automatized system used at the hospital and were better when indeterminate samples were analysed. CONCLUSIONS: This study provides an efficient method for the simultaneous detection of SARS-CoV-2, HCoV-OC43 and influenza A virus, and its efficacy has been tested on clinical samples showing outstanding results. SIGNIFICANCE AND IMPACT OF THE STUDY: The multiplex RT-qPCR design offers an accessible and economical alternative to commercial detection kits for hospitals and laboratories with limited economic resources or facing situations of supply shortage.


Subject(s)
COVID-19 , Influenza A virus , Humans , SARS-CoV-2/genetics , Multiplex Polymerase Chain Reaction/methods , Influenza A virus/genetics , COVID-19/diagnosis , Sensitivity and Specificity , Nasopharynx
7.
Infect Genet Evol ; 104: 105355, 2022 10.
Article in English | MEDLINE | ID: covidwho-1996425

ABSTRACT

The rampant spread of highly pathogenic avian influenza A (H5N6) virus has drawn additional concerns along with ongoing Covid-19 pandemic. Due to its migration-related diffusion, the situation is deteriorating. Without an existing effective therapy and vaccines, it will be baffling to take control measures. In this regard, we propose a revers vaccinology approach for prediction and design of a multi-epitope peptide based vaccine. The induction of humoral and cell-mediated immunity seems to be the paramount concern for a peptide vaccine candidate; thus, antigenic B and T cell epitopes were screened from the surface, membrane and envelope proteins of the avian influenza A (H5N6) virus, and passed through several immunological filters to determine the best possible one. Following that, the selected antigenic with immunogenic epitopes and adjuvant were linked to finalize the multi-epitope-based peptide vaccine by appropriate linkers. For the prediction of an effective binding, molecular docking was carried out between the vaccine and immunological receptors (TLR8). Strong binding affinity and good docking scores clarified the stringency of the vaccines. Furthermore, molecular dynamics simulation was performed within the highest binding affinity complex to observe the stability, and minimize the designed vaccine's high mobility region to order to increase its stability. Then, Codon optimization and other physicochemical properties were performed to reveal that the vaccine would be suitable for a higher expression at cloning level and satisfactory thermostability condition. In conclusion, predicting the overall in silico assessment, we anticipated that our designed vaccine would be a plausible prevention against avian influenza A (H5N6) virus.


Subject(s)
COVID-19 , Influenza A virus , Influenza in Birds , Influenza, Human , Animals , Computational Biology , Epitopes, B-Lymphocyte , Epitopes, T-Lymphocyte , Humans , Influenza A virus/genetics , Influenza in Birds/prevention & control , Influenza, Human/prevention & control , Molecular Docking Simulation , Pandemics , Peptides , Toll-Like Receptor 8 , Vaccines, Subunit
8.
Nat Med ; 28(9): 1944-1955, 2022 09.
Article in English | MEDLINE | ID: covidwho-1991643

ABSTRACT

Influenza A virus's (IAV's) frequent genetic changes challenge vaccine strategies and engender resistance to current drugs. We sought to identify conserved and essential RNA secondary structures within IAV's genome that are predicted to have greater constraints on mutation in response to therapeutic targeting. We identified and genetically validated an RNA structure (packaging stem-loop 2 (PSL2)) that mediates in vitro packaging and in vivo disease and is conserved across all known IAV isolates. A PSL2-targeting locked nucleic acid (LNA), administered 3 d after, or 14 d before, a lethal IAV inoculum provided 100% survival in mice, led to the development of strong immunity to rechallenge with a tenfold lethal inoculum, evaded attempts to select for resistance and retained full potency against neuraminidase inhibitor-resistant virus. Use of an analogous approach to target SARS-CoV-2, prophylactic administration of LNAs specific for highly conserved RNA structures in the viral genome, protected hamsters from efficient transmission of the SARS-CoV-2 USA_WA1/2020 variant. These findings highlight the potential applicability of this approach to any virus of interest via a process we term 'programmable antivirals', with implications for antiviral prophylaxis and post-exposure therapy.


Subject(s)
COVID-19 , Influenza A virus , Animals , Antiviral Agents/pharmacology , COVID-19/drug therapy , Influenza A virus/genetics , Mice , Neuraminidase , RNA, Viral/genetics , SARS-CoV-2
9.
Diagn Microbiol Infect Dis ; 104(2): 115764, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1982919

ABSTRACT

The COVID-19 pandemic highlighted the significance of readily available and easily performed viral testing for surveillance during future infectious pandemics. The objectives of this study were: to assess the performance of the Xpert Xpress Flu and/or RSV test, a multiplex PCR assay for detecting influenza A and B virus and respiratory syncytial virus nucleic acids in respiratory tract specimens, relative to the Quidel Lyra Influenza A+B assay and the Prodesse ProFlu+ assay, and the system's ease of use by minimally trained operators. Overall, the Xpert Xpress Flu/RSV test demonstrated a high positive and negative percent agreement with the comparator assays, and was easy to use and interpret results, based on the operators' feedback. We concluded that the Xpert Xpress Flu/RSV test is sensitive, specific, and easy to use for the diagnosis of influenza and RSV by minimally trained operators and can be a valuable tool in future infectious clusters or pandemics.


Subject(s)
COVID-19 , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , COVID-19/diagnosis , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Molecular Diagnostic Techniques/methods , Nasopharynx , Pandemics , Real-Time Polymerase Chain Reaction/methods , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , Sensitivity and Specificity
10.
Methods Mol Biol ; 2511: 79-88, 2022.
Article in English | MEDLINE | ID: covidwho-1941368

ABSTRACT

Detection and mutation surveillance of SARS-CoV-2 are crucial for combating the COVID-19 pandemic. Here we describe a lab-based method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus and monitor mutations for up to 96 samples in real time. The method proved to be rapid and sensitive (limit of detection: 29 viral RNA copies/µL of extracted nucleic acid) in detecting SARS-CoV-2 in clinical samples. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses.


Subject(s)
COVID-19 , Coinfection , Nucleic Acid Amplification Techniques , SARS-CoV-2 , Adenoviruses, Human/genetics , COVID-19/diagnosis , Coinfection/diagnosis , Humans , Influenza A virus/genetics , Limit of Detection , Mutation , Nucleic Acid Amplification Techniques/methods , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
11.
Methods Mol Biol ; 2511: 53-65, 2022.
Article in English | MEDLINE | ID: covidwho-1941366

ABSTRACT

COVID-19 disease caused by the novel SARS-CoV-2 virus represents a new challenge for healthcare systems. The molecular confirmation of infection is crucial to guide public health decision-making. This task could be made more difficult during the next influenza season. Thus, a rapid and user-friendly diagnostic test to discriminate SARS-CoV-2 from influenza viruses is urgently needed. Here, we present a multiplex quantitative polymerase chain reaction (qPCR) assay capable of distinguishing SARS-CoV-2 from influenza A and B cases. This assay benefits from the use of an inhibitor tolerant PCR mix which obviates the need for the rate-limiting extraction step, allowing for a more rapid and accurate analysis.


Subject(s)
COVID-19 , Herpesvirus 1, Cercopithecine , Influenza A virus , Influenza, Human , COVID-19/diagnosis , Diagnostic Tests, Routine , Humans , Influenza A virus/genetics , Influenza B virus , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
12.
Immunogenetics ; 74(1): 149-165, 2022 02.
Article in English | MEDLINE | ID: covidwho-1906024

ABSTRACT

Birds are important hosts for many RNA viruses, including influenza A virus, Newcastle disease virus, West Nile virus and coronaviruses. Innate defense against RNA viruses in birds involves detection of viral RNA by pattern recognition receptors. Several receptors of different classes are involved, such as endosomal toll-like receptors and cytoplasmic retinoic acid-inducible gene I-like receptors, and their downstream adaptor proteins. The function of these receptors and their antagonism by viruses is well established in mammals; however, this has received less attention in birds. These receptors have been characterized in a few bird species, and the completion of avian genomes will permit study of their evolution. For each receptor, functional work has established ligand specificity and activation by viral infection. Engagement of adaptors, regulation by modulators and the supramolecular organization of proteins required for activation are incompletely understood in both mammals and birds. These receptors bind conserved nucleic acid agonists such as single- or double-stranded RNA and generally show purifying selection, particularly the ligand binding regions. However, in birds, these receptors and adaptors differ between species, and between individuals, suggesting that they are under selection for diversification over time. Avian receptors and signalling pathways, like their mammalian counterparts, are targets for antagonism by a variety of viruses, intent on escape from innate immune responses.


Subject(s)
Influenza A virus , RNA , Animals , Birds/genetics , Humans , Immunity, Innate/genetics , Influenza A virus/genetics , Ligands , Mammals/genetics
13.
Diagn Microbiol Infect Dis ; 104(1): 115743, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1894958

ABSTRACT

We report the first Italian case of SARS-CoV-2 and influenza A virus super-infection. Laboratory diagnosis revealed the presence of both agents' RNA specific sequences by molecular methods and infectious influenza A virus by cell culture methods.


Subject(s)
COVID-19 , Influenza A virus , Influenza, Human , COVID-19/diagnosis , Clinical Laboratory Techniques , Humans , Influenza A virus/genetics , Influenza, Human/diagnosis , SARS-CoV-2
14.
PLoS Pathog ; 18(5): e1010328, 2022 05.
Article in English | MEDLINE | ID: covidwho-1885352

ABSTRACT

During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results suggest that the CTD-binding modes of IAV and IBV may represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery.


Subject(s)
Influenza A virus , Influenza, Human , Humans , Influenza A virus/genetics , Influenza B virus/metabolism , Phylogeny , RNA Polymerase II/genetics , RNA Polymerase II/metabolism , RNA-Dependent RNA Polymerase/genetics , Virus Replication/genetics
15.
Microbiol Spectr ; 10(3): e0039922, 2022 06 29.
Article in English | MEDLINE | ID: covidwho-1854248

ABSTRACT

Xpert Xpress SARS-CoV-2/Flu/RSV is a rapid diagnostic test currently approved for the detection of SARS-CoV-2 using upper respiratory tract specimens. This study attempts to assess the performance of this assay using upper and lower respiratory tract specimens by comparing its results to the lab-developed PCR test. We assessed the performance of GeneXpert for the detection of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus for upper respiratory tract specimens. In addition, the SARS-CoV-2 detection was evaluated for lower respiratory tract specimens (bronchoalveolar lavage and tracheal aspirate). Precision and reproducibility of the test were also assessed using samples with varying cycle threshold values. Xpert Xpress SARS-CoV-2/Flu/RSV shows 100% positive and negative agreements for all four targets when tested using upper respiratory tract specimens. For lower respiratory tract specimens, tracheal aspirate and bronchoalveolar lavage samples respectively show 96% and 100% positive percent agreement for SARS-Cov-2 target only. No positive flu/RSV samples were included for lower respiratory tract specimens. Both samples show 100% negative percent agreement. The precision and reproducibility assay also showed 100% correspondence. Xpert Xpress SARS-CoV-2/Flu/RSV can be potentially used for SARS-Cov-2 detection in lower respiratory tract specimens. Performance passed our study acceptance criteria and shows promising implications as a point of care detection assay. IMPORTANCE Cepheid's Xpert Xpress SARS-CoV-2/Flu/RSV provides a means of rapid diagnosis that can help in hospital bed management and patient flow. It is also important for each microbiology lab to increase its capacity and most importantly have a different platform to overcome the anticipated reagent shortage at times of peak community transmission. There is limited evidence on using it for lower respiratory tract specimens. Here we present our validation for upper respiratory tract specimens as well as a potential use for lower respiratory specimens (BAL and TA), and we discuss some of the applications we have been using in our organization.


Subject(s)
COVID-19 , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus, Human , Bronchoalveolar Lavage , COVID-19/diagnosis , COVID-19 Testing , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Molecular Diagnostic Techniques/methods , Nasopharynx , Reproducibility of Results , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2 , Sensitivity and Specificity
16.
Pathology ; 54(4): 466-471, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1799763

ABSTRACT

During the COVID-19 pandemic, sample pooling has proven an effective strategy to overcome the limitations of reagent shortages and expand laboratory testing capacity. The inclusion of influenza and respiratory syncytial virus (RSV) in a multiplex tandem PCR platform with SARS-CoV-2 provides useful diagnostic and infection control information. This study aimed to evaluate the performance of the influenza and RSV targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay, including the effect of pooling samples on target detection. RSV target detection in clinical samples was compared to the Cepheid Xpert Xpress Flu/RSV assay as a reference standard. Samples were then tested in pools of four and detection rates were compared. Owing to the unavailability of clinical samples for influenza, only the effect of sample pooling on simulated samples was evaluated for these targets. RSV was detected in neat clinical samples with a positive percent agreement (PPA) of 100% and negative percent agreement (NPA) of 99.5% compared to the reference standard, demonstrating 99.7% agreement. This study demonstrates that sample pooling by four increases the average Ct value by 2.24, 2.29, 2.20 and 1.91 cycles for the target's influenza A, influenza A typing, influenza B and RSV, respectively. The commercial AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay was able to detect influenza and RSV at an intermediate concentration within the limit of detection of the assay. Further studies to explore the applicability of sample pooling at the lower limit of detection of the assay is needed. Nevertheless, sample pooling has shown to be a viable strategy to increase testing throughput and reduce reagent usage. In addition, the multiplexed platform targeting various respiratory viruses assists with public health and infection control responses, clinical care, and patient management.


Subject(s)
COVID-19 , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , COVID-19/diagnosis , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Molecular Diagnostic Techniques , Nasopharynx , Pandemics , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2 , Sensitivity and Specificity
17.
Microb Biotechnol ; 15(5): 1301-1317, 2022 05.
Article in English | MEDLINE | ID: covidwho-1752469

ABSTRACT

The COVID-19 pandemic goes into its third year and the world population is longing for an end to the pandemic. Computer simulations of the future development of the pandemic have wide error margins and predictions on the evolution of new viral variants of SARS-CoV-2 are uncertain. It is thus tempting to look into the development of historical viral respiratory pandemics for insight into the dynamic of pandemics. The Spanish flu pandemic of 1918 caused by the influenza virus H1N1 can here serve as a potential model case. Epidemiological observations on the shift of influenza mortality from very young and old subjects to high mortality in young adults delimitate the pandemic phase of the Spanish flu from 1918 to 1920. The identification and sequencing of the Spanish flu agent allowed following the H1N1 influenza virus after the acute pandemic phase. During the 1920s H1N1 influenza virus epidemics with substantial mortality were still observed. As late as 1951, H1N1 strains of high virulence evolved but remained geographically limited. Until 1957, the H1N1 virus evolved by accumulation of mutations ('antigenic drift') and some intratypic reassortment. H1N1 viruses were then replaced by the pandemic H2N2 influenza virus from 1957, which was in 1968 replaced by the pandemic H3N2 influenza virus; both viruses were descendants from the Spanish flu agent but showed the exchange of entire gene segments ('antigenic shift'). In 1977, H1N1 reappeared from an unknown source but caused only mild disease. However, H1N1 achieved again circulation in the human population and is now together with the H3N2 influenza virus an agent of seasonal influenza winter epidemics.


Subject(s)
COVID-19 , Influenza A Virus, H1N1 Subtype , Influenza A virus , Influenza Pandemic, 1918-1919 , Influenza, Human , History, 20th Century , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Influenza A virus/genetics , Pandemics , SARS-CoV-2 , Young Adult
18.
Brief Bioinform ; 23(3)2022 05 13.
Article in English | MEDLINE | ID: covidwho-1740806

ABSTRACT

Inhibition of host protein functions using established drugs produces a promising antiviral effect with excellent safety profiles, decreased incidence of resistant variants and favorable balance of costs and risks. Genomic methods have produced a large number of robust host factors, providing candidates for identification of antiviral drug targets. However, there is a lack of global perspectives and systematic prioritization of known virus-targeted host proteins (VTHPs) and drug targets. There is also a need for host-directed repositioned antivirals. Here, we integrated 6140 VTHPs and grouped viral infection modes from a new perspective of enriched pathways of VTHPs. Clarifying the superiority of nonessential membrane and hub VTHPs as potential ideal targets for repositioned antivirals, we proposed 543 candidate VTHPs. We then presented a large-scale drug-virus network (DVN) based on matching these VTHPs and drug targets. We predicted possible indications for 703 approved drugs against 35 viruses and explored their potential as broad-spectrum antivirals. In vitro and in vivo tests validated the efficacy of bosutinib, maraviroc and dextromethorphan against human herpesvirus 1 (HHV-1), hepatitis B virus (HBV) and influenza A virus (IAV). Their drug synergy with clinically used antivirals was evaluated and confirmed. The results proved that low-dose dextromethorphan is better than high-dose in both single and combined treatments. This study provides a comprehensive landscape and optimization strategy for druggable VTHPs, constructing an innovative and potent pipeline to discover novel antiviral host proteins and repositioned drugs, which may facilitate their delivery to clinical application in translational medicine to combat fatal and spreading viral infections.


Subject(s)
Antiviral Agents , Influenza A virus , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Dextromethorphan , Humans , Influenza A virus/genetics
19.
Viruses ; 14(1)2021 12 29.
Article in English | MEDLINE | ID: covidwho-1628815

ABSTRACT

Outbreaks of influenza, caused by the influenza A virus (IAV), occur almost every year in various regions worldwide, seriously endangering human health. Studies have shown that host non-coding RNA is an important regulator of host-virus interactions in the process of IAV infection. In this paper, we comprehensively analyzed the research progress on host non-coding RNAs with regard to the regulation of IAV replication. According to the regulation mode of host non-coding RNAs, the signal pathways involved, and the specific target genes, we found that a large number of host non-coding RNAs directly targeted the PB1 and PB2 proteins of IAV. Nonstructural protein 1 and other key genes regulate the replication of IAV and indirectly participate in the regulation of the retinoic acid-induced gene I-like receptor signaling pathway, toll-like receptor signaling pathway, Janus kinase signal transducer and activator of transcription signaling pathway, and other major intracellular viral response signaling pathways to regulate the replication of IAV. Based on the above findings, we mapped the regulatory network of host non-coding RNAs in the innate immune response to the influenza virus. These findings will provide a more comprehensive understanding of the function and mechanism of host non-coding RNAs in the cellular anti-virus response as well as clues to the mechanism of cell-virus interactions and the discovery of antiviral drug targets.


Subject(s)
Host-Pathogen Interactions , Influenza A virus/genetics , Influenza, Human/immunology , RNA, Untranslated , Virus Replication , Antiviral Agents/immunology , Cell Cycle , Humans , Immunity, Innate , Influenza, Human/virology , MicroRNAs , RNA, Circular , Signal Transduction
20.
Curr Opin Virol ; 53: 101198, 2022 04.
Article in English | MEDLINE | ID: covidwho-1615552

ABSTRACT

Influenza viruses are simultaneously supported and antagonized by factors within the host cell. This close relationship is the theoretical basis for future antivirals that target the host rather than the virus itself, a concept termed host-directed therapeutics. Genetic screening has led to the identification of host factors capable of modulating influenza virus infections, and these factors represent candidate targets for host-directed antiviral strategies. Despite advances in understanding host targets, however, there are currently no host-directed interventions for influenza viruses in clinical use. In this brief review, we discuss some host factors identified in knockout/knockdown and overexpression screens that could potentially be targeted as host-directed influenza intervention strategies. We further comment on the feasibility of changing gene expression in the respiratory tract with RNA delivery vectors and transient CRISPR-mediated gene targeting.


Subject(s)
Influenza A virus , Influenza, Human , Orthomyxoviridae , Antiviral Agents/therapeutic use , Host-Pathogen Interactions , Humans , Influenza A virus/genetics , Influenza, Human/drug therapy
SELECTION OF CITATIONS
SEARCH DETAIL