Epidemic Virus Research Articles

Spatiotemporal Trends in Human Immunodeficiency Virus Epidemics in Nigeria: A Systematic Review Protocol

The scourge of the Human Immunodeficiency Virus infection is not abating fast as expected despite the many strategies put in place by various stakeholders. Geographical variations in its distribution have been implicated in its slow decline in sub-Saharan Africa, and Nigeria carries the highest burden in West Africa with subnational variations in 2019. This may negatively impact the implementation of interventions if not properly targeted. Geospatial technique is very important for spatial identification of hotspots and clusters which makes it easy to implement strategies, allocate scares resources, interventions and programs to achieve a success in the fight against the epidemics. It is on this note that the researcher is set to conduct this systematic review to assess trends in human immunodeficiency virus epidemics in Nigeria. The protocol will follow the preferred reporting items for systematic review and meta-analysis (PRISMA-P) 2020 guideline. The protocol was registered with the International Prospective Register for Systematic Reviews (PROSPERO) with registration number CRD42023488081. Articles would be retrieved electronically through database such as PubMed, Medline, Scopus, web of Science citation index, Google Scholar, and the open grey. Search period would be December 15th 2023 to June 15th, 2024 for related published articles. Two researchers will independently review articles for inclusion and if there are any disagreements, a third researcher would be called. Risk of bias would be assessed using New Castle Ottawa Scale and JBI critical appraisal checklist. Furthermore, statistical analysis will be conducted using the Review Manager Version 5.4. In conclusion, the Identification of clusters/hotspots helps the targeted allocation of scares resources, implementation of interventions and programs more efficiently and effectively. This strategy combined with the already existing ones, is a sure way to win the fight against the HIV epidemics.

Antigenic analysis of the influenza B virus hemagglutinin protein

Influenza B viruses (IBVs) primarily infect humans and are a common cause of respiratory infections in humans. Here, to systematically analyze the antigenicity of the IBVs Hemagglutinin (HA) protein, 31 ​B/Victoria and 19 ​B/Yamagata representative circulating strains were selected from Global Initiative of Sharing All Influenza Data (GISAID), and pseudotyped viruses were constructed with the vesicular stomatitis virus system. Guinea pigs were immunized with three doses of vaccines (one dose of DNA vaccines following two doses of pseudotyped virus vaccines) of the seven IBV vaccine strains, and neutralizing antibodies against the pseudotyped viruses were tested. By comparing differences between various vaccine strains, we constructed several pseudotyped viruses that contained various mutations based on vaccine strain BV-21. The vaccine strains showed good neutralization levels against the epidemic virus strains of the same year, with neutralization titers ranging from 370 to 840, while the level of neutralization against viruses prevalent in previous years decreased 1–10-fold. Each of the high-frequency epidemic strains of B/Victoria and B/Yamagata not only induced high neutralizing titers, but also had broadly neutralizing effects against virus strains of different years, with neutralizing titers ranging from 1000 to 7200. R141G, D197 ​N, and R203K were identified as affecting the antigenicity of IBV. These mutation sites provide valuable references for the selection and design of a universal IBV vaccine strain in the future.

Multiplex reverse transcription recombinase polymerase amplification combined with lateral flow biosensor for simultaneous detection of three viral pathogens in cattle

Bovine viral diarrhea virus (BVDV), bovine epidemic fever virus (BEFV), and bovine respiratory syncytial virus (BRSV) cause respiratory symptoms in cattle. The absence of rapid, precise, and easily accessible diagnostic methods poses difficulties for herders and veterinary epidemiologists during outbreaks of major infectious animal diseases. Considering the mixed infection of viruses, a multiple-detection method, reverse transcription recombinase polymerase amplification (mRT-RPA) combined with a lateral flow biosensor (LFB), was established to simultaneously detect the three pathogens. This technique is based on the specific binding of three differently labeled RT-RPA products (DNA sequences) to antibodies on the three test lines of the LFB, achieving multiplex detection through the presence or absence of coloration on the LFB test lines. The fluorescence values of the LFB test lines are recorded by a test strip reader. The mRT-RPA-LFB assay completes detection at a constant temperature of 41 °C within 33 min. The limits of detection (LODs) for BVDV, BEFV and BRSV were 2.62 × 101, 2.42 × 101 and 2.56 × 101 copies/μL, respectively. No cross-reactivity was observed with the other six bovine viruses. The developed method showed satisfactory intra- and inter-assay precision, and the average coefficients of variation were ranged from 2.92 % to 3.99 %. The diagnostic sensitivity and specificity were 98.11 % and 100 %, respectively, which were highly consistent with the RT-qPCR assay, and the kappa value was 0.988 (95 % confidence interval, CI). In general, the mRT-RPA-LFB assay has the potential to become a powerful tool for rapid screening of cattle diseases because of its advantages such as fast detection speed, convenient operation, strong specificity, and high sensitivity.

Exploring antiviral effect and mechanism of Jinye Baidu granules（JYBD）against influenza A virus through network pharmacology and in vitro and invivo experiments

Ethnopharmacological relevanceJinye Baidu granules (JYBD) have been used to treat acute respiratory tract infections and demonstrated clinical efficacy for the treatment of emerging or epidemic respiratory viruses such as SARS-CoV-2 and influenza virus. Aim of the studyThis study is to investigate the antiviral effect of JYBD against influenza A viruses (IAV) in vitro and in vivo and elucidate its underlying mechanism. Materials and methodsUltra-high-performance liquid chromatography connected with Orbitrap mass spectrometer (UHPLC-Orbitrap MS) was employed to describe the chemical profile of JYBD. The potential pathways and targets involved in JYBD against IAV infection were predicted by network pharmacology. The efficacy and mechanism of JYBD were validated through both in vivo and in vitro experiments. Moreover, combination therapy with JYBD and the classic anti-influenza drugs was also investigated. ResultsA total of 126 compounds were identified by UHPLC-Orbitrap MS, of which 9 compounds were unambiguously confirmed with reference standards. JYBD could significantly inhibit the replication of multiple strains of IAV, especially oseltamivir-resistant strains. The results of qRT-PCR and WB demonstrated that JYBD could inhibit the excessive induction of pro-inflammatory cytokines induced by IAV infection and regulate inflammatory response through inhibiting JAK/STAT, NF-κB and MAPK pathways. Moreover, both JYBD monotherapy or in combination with oseltamivir could alleviate IAV-induced severe lung injury in mice. ConclusionsJYBD could inhibit IAV replication and mitigate virus-induced excessive inflammatory response. Combinations of JYBD and neuraminidase inhibitors conferred synergistic suppression of IAV both in vitro and in vivo. It might provide a scientific basis for clinical applications of JYBD against influenza virus infected diseases.

Integration of Google Trends Data in Predicting New HIV Cases in Western Visayas, the Philippines

Recent studies have demonstrated the capacity of Internet search data to be used for monitoring and tracking infectious diseases. Given that the Philippines has one of the most rapidly expanding human immunodeficiency virus (HIV) epidemics in the globe, it is imperative to enhance the local surveillance and prediction of HIV by utilizing easily accessible web data such as Google Trends. This study aims to [1] evaluate the advantages of utilizing Google Trends data (GTD) in predicting new monthly HIV diagnoses in the Western Visayas and [2] determine the suitable modeling approach that effectively utilizes this tool in forecasting HIV cases in the region. Data on new monthly HIV cases from January 2012–December 2022 in Western Visayas was requested from the Department of Health Region VI Office and HIV-related internet search data was obtained from Google Trends. Data imputations were applied to mitigate the effects of COVID-19 on HIV data. The results of the traditional seasonal autoregressive integrated moving average (SARIMA) model were compared with the results of the neural network autoregression (NNAR) model using cross-validation via rolling forecast origin. GTD have a moderately weak but significant association with HIV case numbers in Western Visayas. NNAR models outperformed the traditional SARIMA models in terms of mean absolute percentage error, mean absolute error, and root mean squared error. The use of Google search data in NNAR models improved the predictive accuracy of the forecasts when using moving average imputation as a replacement for outliers. However, this does not accurately represent the overall NNAR process, as the linear interpolation replacements did not yield comparable outcomes. This study showed that, if suitable models are adopted, utilizing HIV-related web data has the potential to produce real-time surveillance systems for HIV monitoring and forecasting. This presents an opportunity to enhance local surveillance in the country not just for HIV but also for other infectious diseases such as tuberculosis and dengue. Internet search data is free and readily available, and public health agencies can adopt this type of modeling, even with limited funding; however, further study is advised.

Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

Despite intensive study, much remains unknown about the dynamics of seasonal influenza virus epidemic establishment and spread in the United States (US) each season. By reconstructing transmission lineages from seasonal influenza virus genomes collected in the US from 2014 to 2023, we show that most epidemics consisted of multiple distinct transmission lineages. Spread of these lineages exhibited strong spatiotemporal hierarchies and lineage size was correlated with timing of lineage establishment in the US. Mechanistic epidemic simulations suggest that mobility-driven competition between lineages determined the extent of individual lineages' geographical spread. Based on phylogeographic analyses and epidemic simulations, lineage-specific movement patterns were dominated by human commuting behavior. These results suggest that given the locations of early-season epidemic sparks, the topology of inter-state human mobility yields repeatable patterns of which influenza viruses will circulate where, but the importance of short-term processes limits predictability of regional and national epidemics.

Epidemic influenza virus nucleoprotein gene incorporated into vaccine influenza virus strain genome to optimize systemic and local T-cell immune response against live attenuated influenza vaccine

Introduction. Optimization of the vaccine-induced T-cell repertoire is one of the strategies to expand the spectrum of protective potential for live attenuated influenza vaccine (LAIV). LAIV cross-protective properties can be improved by introducing the nucleoprotein (NP) gene derived from epidemic parental virus into vaccine strain genome, i.e. by replacing the classical 6:2 genome formula with 5:3. The main objective of the present study was to detail evaluation for virus-specific systemic and tissue-resident memory T-cells subsets in mice immunized with seasonal H1N1 LAIV of the genome formula 6:2 and 5:3. Materials and methods. Two H1N1 LAIV strains with varying NP genes (LAIV 6:2 and LAIV 5:3) were generated using reverse genetics techniques. C57BL/6J mice were immunized intranasally with the vaccine candidates, twice, 3 weeks apart. Cells from the spleen and lung tissues were isolated 7 days after booster immunization to be stimulated with whole H1N1 influenza virus for assessing cytokine-producing memory CD44+CD62L– T-cells as well as expression of CD69 and CD103 surface markers using flow cytometry. Humoral murine serum immunity against H1N1 virus was assessed by ELISA. Results. The LAIV 5:3 vs classical 6:2 vaccine strain carrying the epidemic parental NP gene induced significantly more pronounced humoral immune response against recent influenza virus. The group of mice immunized with LAIV 5:3 demonstrated higher levels of virus-specific CD4+ and CD8+ effector memory T cells (TEM) in the spleen, including a subset of polyfunctional (IFNγ+TNFα+IL-2+) CD4+ TEM, compared to LAIV 6:2 group. Virus-specific memory T cell levels in lung tissues after immunization with LAIV 5:3 vs LAIV 6:2 also tended to increase, but no significant difference in stimulated tissue-resident CD69+CD103– and CD69+CD103+ T cells between the groups were found. Conclusion. Modification of the seasonal LAIV strain genome for updating its epitope composition allowed to enhance the virus-specific T-cell immune response both at systemic level and in lung tissues, thereby shoeing that the effectiveness of the vaccine against circulating influenza viruses can be potentially increased.

Protective Factors, Stress and Anxiety Effects on the Resilience Levels of Healthcare Workers

Objective: This study investigated how protective factors, stress and anxiety levels affect the resilience levels of healthcare workers (HCWs) throughout the COVID-19 pandemic. Specific aims included examining whether resilience levels among HCWs vary significantly based on demographic variables. Methods: A total of 303 HCWs from two training and research hospitals completed the survey. Protective Factors for Resilience Scale (PFRS), The Stress and Anxiety to Viral Epidemics–9 Items Scale, and Brief Resilience Scale were used as data collection tools. Confirmatory factor analysis, reliability analyses, construct validity analysis, discriminant validity analysis, structural equation modelling, t-test and ANOVA were conducted respectively. Results: Only the impact of the individual sub-factor of PFRS on the resilience level of HCWs was positive and significant (b=.847, t= 8.670, p

Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution.

The coevolutionary dynamics of lytic viruses and microbes with CRISPR-Cas immunity exhibit alternations between sustained host control of viral proliferation and major viral epidemics in previous computational models. These alternating dynamics have yet to be observed in other host-pathogen systems. Here, we address the breakdown of control and transition to large outbreaks with a stochastic eco-evolutionary model. We establish the role of host density-dependent competition in punctuated virus-driven succession and associated diversity trends that concentrate escape pathways during control phases. Using infection and escape networks, we derive the viral emergence probability whose fluctuations of increasing size and frequency characterize the approach to large outbreaks. We explore alternation probabilities as a function of non-dimensional parameters related to the probability of viral escape and host competition. Our results demonstrate how emergent feedbacks between host competition and viral diversification render the host immune structure fragile, potentiating a dynamical transition to large epidemics.

A Systematic Review of the Efficacy of Full-Scale Simulation Exercises in Enhancing Hospital Disaster Preparedness

Introduction: A full-scale simulation exercise is a comprehensive drill designed to replicate a real-world emergency scenario, thereby identifying the strengths and weaknesses in current practices. The overarching goal is to enhance healthcare system resilience through improved protocols, as highlighted in this systematic review tailored for researchers. The study aims specifically to assess the impact of full-scale simulations on enhancing hospital disaster plans. Methodology: Following PRISMA guidelines, this systematic review investigates the impact of full-scale simulation exercises on hospital disaster preparedness. The focus was on hospital staff involved in disaster and emergency preparedness training. The primary intervention was the execution of full-scale simulation exercises, and our research included various study designs, including randomised controlled trials and observational study designs. A comprehensive electronic database search was conducted, spanning PubMed, Scopus, Web of Science, and the Cochrane Central Register of Controlled Trials, from inception until October 9, 2023. The risk of bias was assessed using NIH tools. Results: The literature search yielded 2398 results, with 28 publications finally included in the systematic review. Summarising a broad range of disaster preparedness simulation exercises with a specific focus on full-scale simulation (FSS), the studies consistently demonstrated a positive impact on participants' skills, as well as identifying safety issues in hospital settings. Moreover, they revealed that simulations effectively addressed crucial areas for improvement in disaster response, including communication breakdowns, equipment deficiencies, and flaws in emergency plans. The studies utilised a multidimensional approach to evaluation metrics, encompassing non-technical skills, communication, teamwork, decision-making, and operational readiness. The exercises varied in duration from 30 minutes to multi-day simulations, covering a diverse range of disaster scenarios, such as mass casualties, viral epidemics, large aviation accidents, and terrorist attacks. Conclusion: Full-scale simulation exercises are a preparatory learning tool to test facility and staff readiness for complex emergencies. This systematic review focused on the different exercise scenarios used to address critical aspects of disaster response such as communication breakdowns, equipment deficiencies, and flaws in emergency plans. The scenarios and their duration were varied, and involved a multidimensional approach to evaluation. Such exercises enhance critical thinking and problem-solving skills, increase familiarity with potential emergencies, and build confidence in making judgments in real-world situations. In our opinion, there is a need for further programs that align simulation exercises with community resources for better preparedness in the face of public health disasters.

Variability in the Timing of Respiratory Syncytial Virus Epidemics in Guatemala, 2008-2018.

The description of local seasonality patterns in respiratory syncytial virus (RSV) incidence is important to guide the timing of administration of RSV immunization products. We characterized RSV seasonality in Guatemala using the moving epidemic method (MEM) with absolute counts of RSV-associated acute respiratory infections (ARI) from hospital surveillance in Santa Rosa and Quetzaltenango departments of Guatemala. From Week 17 of 2008 through Week 16 of 2018, 8487 ARI cases tested positive for RSV by rRT-PCR. Season onsets varied up to 5 months; early seasons starting in late May to early August and finishing in September to November were most common, but late seasons starting in October to November and finishing in March to April were also observed. Both epidemic patterns had similar durations ranging from 4 to 6 months. Epidemic thresholds (the levels of virus activity that signal the onset and end of a seasonal epidemic) calculated prospectively using previous seasons' data captured between 70% and 99% of annual RSV detections. Onset weeks differed by 2-10 weeks, and offset weeks differed by 2-16 weeks between the two surveillance sites. Variability in the timing of seasonal RSV epidemics in Guatemala demonstrates the difficulty in precisely predicting the timing of seasonal RSV epidemics based on onset weeks from past seasons and suggests that maximal reduction in RSV disease burden would be achieved through year-round vaccination and immunoprophylaxis administration to at-risk infants.

Development of a Recombinant Live Attenuated Influenza Vaccine Virus Expressing Pneumococcal Surface Antigen A as a Strategy for Combined Protection Against Influenza and Bacterial Coinfection Caused by Streptococcus pneumoniae

Introduction Bacterial superinfection with Streptococcus pneumoniae following the influenza virus infection complicates the course of the disease and is a major cause of mortality during influenza virus epidemics. The effectiveness of licensed polysaccharide vaccines is limited by the serotypes included in the vaccine and possible immune tolerance during revaccination. Pneumococcal surface protein A (PspA), which includes conserved regions and has at least two functions in pathogen virulence, is considered a promising target for the development of new-generation vaccines, including gene-engineering constructions. Therefore, the development of an influenza virus vector-based vaccine expressing conserved bacterial proteins seems to be a promising strategy for designing combined vaccines against influenza and bacterial pathogens. Methods A recombinant live attenuated influenza virus (LAIV) expressing PspA fragment in a modified hemagglutinin was rescued on the A/Leningrad/134/17/57 (H2N2) backbone. This recombinant virus was assessed for its growth characteristics in vitro, as well as for its immunogenicity and protective capacity, using a mouse model of influenza-bacterial coinfection. Results The rescued recombinant LAIV/HA+PspA virus was genetically stable after sequential passaging in embryonated chicken eggs and possessed an attenuated phenotype similar to the classical LAIV strain. The LAIV/HA+PspA bivalent vaccine-induced IgG antibodies specific to both influenza virus and S. pneumoniae and provided complete protection of vaccinated mice against lethal influenza infection, as well as a 40% survival rate for lethal homologous and heterologous influenza infection complicated by concomitant bacterial infection with S. pneumoniae. Conclusion The presented design of a recombinant influenza virus carrying immunogenic fragments of a bacterial pathogen can be considered a promising strategy for the combined protection of vaccinated individuals against influenza and its bacterial complications, and further in-depth studies of such recombinant viruses in preclinical studies are warranted.

Children's Hospital Resource Utilization During the 2022 Viral Respiratory Surge.

Multiple viral respiratory epidemics occurred concurrently in 2022 but their true extent is unclear. To aid future surge planning efforts, we compared epidemiology and resource utilization with prepandemic viral respiratory seasons in 38 US children's hospitals. We performed a serial cross-sectional study from October 2017 to March 2023. We counted daily emergency department (ED), inpatient, and ICU volumes; daily surgeries; viral tests performed; the proportion of ED visits resulting in revisit within 3 days; and proportion of hospitalizations with a 30-day readmission. We evaluated seasonal resource utilization peaks using hierarchical Poisson models. Peak volumes in the 2022 season were 4% lower (95% confidence interval [CI] -6 to -2) in the ED, not significantly different in the inpatient unit (-1%, 95% CI -4 to 2), and 8% lower in the ICU (95% CI -14 to -3) compared with each hospital's previous peak season. However, for 18 of 38 hospitals, their highest ED and inpatient volumes occurred in 2022. The 2022 season was longer in duration than previous seasons (P < .02). Peak daily surgeries decreased by 15% (95% CI -20 to -9) in 2022 compared with previous peaks. Viral tests increased 75% (95% CI 69-82) in 2022 from previous peaks. Revisits and readmissions were lowest in 2022. Peak ED, inpatient, and ICU volumes were not significantly different in the 2022 viral respiratory season compared with earlier seasons, but half of hospitals reached their highest volumes. Research on how surges impact boarding, transfer refusals, and patient outcomes is needed as regionalization reduces pediatric capacity.

A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome

AbstractSequence changes in viral genomes generate protein sequence diversity that enables viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. The massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. An alignment‐free approach removes various restrictions posed by an alignment‐dependent approach for studying sequence diversity. The publicly available tool, UNIQmin, offers an alignment‐free approach for studying viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed four‐part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment‐free at any rank of the taxonomy lineage, using the recent global public health threat Monkeypox virus (MPX) sequence data as a case study. The protocol enables a systematic bioinformatics approach to study sequence diversity across taxonomic lineages, which is crucial for our future preparedness against viral epidemics. This is particularly important when data are abundant, freely available, and alignment is not an option. © 2024 Wiley Periodicals LLC.Basic Protocol 1: Tool installation and input file preparationBasic Protocol 2: Generation of a minimal set of sequences for a given datasetBasic Protocol 3: Comparative minimal set analysis across taxonomic lineage ranksBasic Protocol 4: Factors affecting the minimal set of sequences

Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses.

Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

Comparative analysis of the incidence and mortality of COVID-19 in Korean end-stage kidney disease patients: hemodialysis, peritoneal dialysis, and transplantation.

Patients with end-stage kidney disease (ESKD) are more susceptible to viral epidemics and are known to have higher incidence and death rates of coronavirus disease 2019 (COVID-19) compared to the general population. We determined COVID-19 incidence and mortality among chronic hemodialysis (HD), peritoneal dialysis (PD), and kidney transplantation (KT) patients in Korea. We conducted a retrospective cohort study and data regarding Korean ESKD adults (aged ≥18 years) were obtained from the National Health Insurance Service of Korea from October 2020 to December 2021. We examined and compared the incidence of COVID-19-related infections and deaths among the patients receiving HD, PD, and KT. Of all ESKD patients, 85,018 (68.1%) were on HD, 8,399 (6.7%) on PD, and 31,343 (25.1%) on KT. The COVID-19 incidence was 1.3% for HD, 1.2% for PD, and 1.5% for KT. COVID-19 mortality was 16.3% for HD, 12.2% for PD, and 4.7% for KT. PD patients had a lower incidence of infection compared to HD patients (odds ratio [OR], 0.76; 95% confidence interval [CI], 0.607-0.93), but KT patients had a significantly higher risk of infection (OR, 1.28; 95% CI, 1.13-1.44). Compared with HD, the risk of COVID-19-related death was not different for PD patients but was significantly lower for KT patients (hazard ratio, 0.55; 95% CI, 0.35-0.88). COVID-19 incidence was lower in PD patients than in HD patients, but mortality was not different between them. KT was associated with a higher risk of COVID-19 infection but lower mortality compared to HD.

Comparison of the Stress and Anxiety to Viral Epidemic-9 and SAVE-6 scales among healthcare workers in Peru.

Peru is a country that has a high incidence of viral outbreaks and epidemics, which is why it is necessary to validate a scale that measures anxiety and stress in professionals who are on the front lines of these events. Therefore, our objective was to validate the Peruvian-Spanish version of the Stress and Anxiety to Viral Epidemics-9 items (SAVE-9) scale and to concurrently compare its validity and internal consistency with the SAVE-6 scale among healthcare workers (HCWs). We conducted a cross-sectional study based on data collected from a self-reported survey in paper-and-pencil format between April and July 2023. A total of 203 HCWs participated in the research. We developed a confirmatory factor analysis (CFA) and item response theory (IRT). We calculated Cronbach's α coefficient and McDonald's ω to assess the internal consistency of the scales. The results show that SAVE-9 (a two-factor model) and SAVE-6 (a one-factor model) provided an excellent fit in the confirmatory factor analysis. Both scales demonstrated strong internal consistency (Cronbach's α 0.85 and 0.86, respectively). Significant correlations were found between the SAVE-9 and SAVE-6 scales and Generalized Anxiety Disorder-7 items scale (r = 0.44 and r = 0.38, respectively, p < 0.001) as well as the Patient Health Questionnaire-9 items (r = 0.39 and r = 0.35, respectively, p < 0.001). The optimal cutoff points for SAVE-9 and SAVE-6 were identified for assessing anxiety, aligned with a GAD-7 score ≥5 points. The Peruvian-Spanish SAVE-9 and SAVE-6 scales are reliable and valid rating scales to assess the anxiety response of HCWs in response to viral epidemics. Though COVID-19 is diminished, these scales will be useful for other viral epidemics in the future.

Early assessment of viral respiratory epidemics for the 2023/2024 season based on community laboratory surveillance network in France

Early assessment of viral respiratory epidemics for the 2023/2024 season based on community laboratory surveillance network in France

U-CAN-seq: A Universal Competition Assay by Nanopore Sequencing.

RNA viruses quickly evolve subtle genotypic changes that can have major impacts on viral fitness and host range, with potential consequences for human health. It is therefore important to understand the evolutionary fitness of novel viral variants relative to well-studied genotypes of epidemic viruses. Competition assays are an effective and rigorous system with which to assess the relative fitness of viral genotypes. However, it is challenging to quickly and cheaply distinguish and quantify fitness differences between very similar viral genotypes. Here, we describe a protocol for using reverse transcription PCR in combination with commercial nanopore sequencing services to perform competition assays on untagged RNA viruses. Our assay, called the Universal Competition Assay by Nanopore Sequencing (U-CAN-seq), is relatively cheap and highly sensitive. We used a well-studied N24A mutation in the chikungunya virus (CHIKV) nsp3 gene to confirm that we could detect a competitive disadvantage using U-CAN-seq. We also used this approach to show that mutations to the CHIKV 5' conserved sequence element that disrupt sequence but not structure did not affect the fitness of CHIKV. However, similar mutations to an adjacent CHIKV stem loop (SL3) did cause a fitness disadvantage compared to wild-type CHIKV, suggesting that structure-independent, primary sequence determinants in this loop play an important role in CHIKV biology. Our novel findings illustrate the utility of the U-CAN-seq competition assay.

High-resolution and real-time wastewater viral surveillance by Nanopore sequencing

Wastewater genomic sequencing stands as a pivotal complementary tool for viral surveillance in populations. While long-read Nanopore sequencing is a promising platform to provide real-time genomic data, concerns over the sequencing accuracy of the earlier Nanopore versions have somewhat restrained its widespread application in wastewater analysis. Here, we evaluate the latest improved version of Nanopore sequencing (R10.4.1), using SARS-CoV-2 as the model infectious virus, to demonstrate its effectiveness in wastewater viral monitoring. By comparing amplicon lengths of 400 bp and 1200 bp, we revealed that shorter PCR amplification is more suitable for wastewater samples due to viral genome fragmentation. Utilizing mock wastewater samples, we validated the reliability of Nanopore sequencing for variant identification by comparing it with Illumina sequencing results. The strength of Nanopore sequencing in generating real-time genomic data for providing early warning signals was also showcased, indicating that as little as 0.001 Gb of data can provide accurate results for variant prevalence. Our evaluation also identified optimal alteration frequency cutoffs (>50 %) for precise mutation profiling, achieving >99 % precision in detecting single nucleotide variants (SNVs) and insertions/deletions (indels). Monitoring two major wastewater treatment plants in Hong Kong from September 2022 to April 2023, covering over 4.5 million population, we observed a transition in dominant variants from BA.5 to XBB lineages, with XBB.1.5 being the most prevalent variants. Mutation detection also highlighted the potential of wastewater Nanopore sequencing in uncovering novel mutations and revealed links between signature mutations and specific variants. This study not only reveals the environmental implications of Nanopore sequencing in SARS-CoV-2 surveillance but also underscores its potential in broader applications including environmental health monitoring of other epidemic viruses, which could significantly enhance the field of wastewater-based epidemiology.