Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 417
Filter
1.
J Virol ; 96(10): e0024122, 2022 05 25.
Article in English | MEDLINE | ID: covidwho-1868711

ABSTRACT

In this study, 232 class I Newcastle disease viruses (NDVs) were identified from multiple bird species at nationwide live bird markets (LBMs) from 2017 to 2019 in China. Phylogenetic analysis indicated that all 232 isolates were clustered into genotype 1.1.2 of class I on the basis of the fusion (F) gene sequences, which were distinct from the genotypes identified in other countries. Most of the isolates (212/232) were shown to have the typical F gene molecular characteristics of class I NDVs, while a few (20/232) contained mutations at the site of the conventional start codon of the F gene, which resulted in open reading frames (ORFs) altered in length. The isolates with ACG, CTA, and ATA mutations showed different levels of increased virulence and replication capacity, suggesting that these viruses may be transitional types during the evolution of class I NDVs from avirulent to virulent. Further evaluation of biological characteristics with recombinant viruses obtained by reverse genetics demonstrated that the ATG located at genomic positions 4523 to 4525 was the authentic start codon in the F gene of class I NDV, and the specific ATA mutations which contributed to the expression of F protein on the surface of infected cells were the key determinants of increased replication capacity and virulence. Interestingly, the mutation at the corresponding site of genotype II LaSota of class II had no effects on the virulence and replication capacity in chickens. Our results suggest that the alteration of virulence and replication capacity caused by specific mutations in the F gene could be a specific characteristic of class I NDVs and indicate the possibility of the emergence of virulent NDVs due to the persistent circulation of class I NDVs. IMPORTANCE The available information on the distribution, genetic diversity, evolution, and biological characteristics of class I Newcastle disease viruses (NDVs) in domestic poultry is currently very limited. Here, identification of class I NDVs at nationwide live bird markets (LBMs) in China was performed and representative isolates were characterized. A widespread distribution of genotype 1.1.2 of class I NDVs was found in multiple bird species at LBMs in China. Though most isolates demonstrated typical molecular characteristics of class I NDVs, a few that contained specific mutations at the site of the conventional start codon of the fusion gene with increased virulence and replication capacity were identified for the first time. Our findings indicate that the virulence of class I NDVs could have evolved, and the widespread transmission and circulation of class I NDVs may represent a potential threat for disease outbreaks in poultry.


Subject(s)
Newcastle Disease , Poultry Diseases , Animals , Chickens/virology , China/epidemiology , Codon, Initiator , Commerce , Epidemiological Monitoring/veterinary , Genotype , Newcastle Disease/epidemiology , Newcastle disease virus/genetics , Phylogeny , Poultry/virology , Poultry Diseases/epidemiology , Virulence/genetics
2.
Viruses ; 14(5)2022 04 20.
Article in English | MEDLINE | ID: covidwho-1792408

ABSTRACT

Coronavirus disease 2019 (COVID-19) pandemic has caused immeasurable impacts on the health and socioeconomic system. The real-time identification and characterization of new Variants of Concern (VOCs) are critical to comprehend its emergence and spread worldwide. In this sense, we carried out a national epidemiological surveillance program in Brazil from April to October 2021. Genotyping by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and sequencing were performed to monitor the dynamics and dissemination of VOCs in samples from 15 federative units. Delta VOC was first detected on June 2021 and took sixteen weeks to replace Gamma. To assess the transmissibility potential of Gamma and Delta VOCs, we studied the dynamics of RT-qPCR cycle threshold (Ct) score in the dominance period of each variant. The data suggest that Delta VOC has a higher transmission rate than Gamma VOC. We also compared relevant symptom patterns in individuals infected with both VOCs. The Delta-infected subjects were less likely to have low oxygen saturation or fatigue, altered results on chest computed tomography, and a propensity for altered X-rays. Altogether, we described the replacement of Gamma by Delta, Delta enhanced transmissibility, and differences in symptom presentation.


Subject(s)
COVID-19 , SARS-CoV-2 , Brazil/epidemiology , COVID-19/epidemiology , Epidemiological Monitoring , Humans , SARS-CoV-2/genetics
3.
Front Public Health ; 10: 711938, 2022.
Article in English | MEDLINE | ID: covidwho-1775960

ABSTRACT

Leptospirosis is a globally disseminated zoonotic disease with no national surveillance systems. On the other hand, surveillance is crucial for improving population health, and surveillance systems produce data that motivates action. Unfortunately, like many other countries, Ecuador put in place a monitoring system that has never been tested. The goal of this study was to use scenario tree modeling to assess the sensitivity of Ecuador's current national surveillance system to human leptospirosis as the basis for an economic assessment of the system. We created a decision-tree model to analyze the current system's sensitivity. The inputs were described as probabilities distributions, and the model assessed the program's sensitivity as an output. The model also considers the geographical and weather variations across Ecuador's three continental regions: Andean, Amazonia, and the Coast. Several data sources were used to create the model, including leptospirosis records from Ecuador's Ministry of Public Health, national and international literature, and expert elicitation, all of which were incorporated in a Bayesian framework. We were able to determine the most critical parameters influencing each scenario's output (CSU) sensitivity through sensitivity analysis. The Coast region had the best sensitivity scenario, with a median of 0.85% (IC 95% 0.41-0.99), followed by the Amazonia with a median of 0.54% (CI 95% 0.18-0.99) and the Andes with a median of 0.29% (CI 95% 0.02-0.89). As per the sensitivity study, the most influential criteria on the system's sensitivity were "Attendance or probability of going to a health center" and "probability of having symptoms," notably for the Coast and Amazonia Regions.


Subject(s)
Epidemiological Monitoring , Leptospirosis , Animals , Bayes Theorem , Ecuador/epidemiology , Humans , Leptospirosis/epidemiology , Zoonoses
5.
Pediatr Infect Dis J ; 41(2): 91-96, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1722660

ABSTRACT

BACKGROUND: Invasive bacterial infection (IBI) remains a major burden of mortality and morbidity in children. As coronavirus disease 2019 (COVID-19) emerged, stringent nonpharmaceutical interventions (NPIs) were applied worldwide. This study aimed to evaluate the impact of NPIs on pediatric IBI in Korea. METHODS: From January 2018 to December 2020, surveillance for pediatric IBIs caused by 9 pathogens (S. pneumoniae, H. influenzae, N. meningitidis, S. agalactiae, S. pyogenes, S. aureus, Salmonella species, L. monocytogenes and E. coli) was performed at 22 hospitals throughout Korea. Annual incidence rates were compared before and after the COVID-19 pandemic. RESULTS: A total of 651 cases were identified and the annual incidence was 194.0 cases per 100,000 in-patients in 2018, 170.0 in 2019 and 172.4 in 2020. Most common pathogen by age group was S. agalactiae in infants < 3 months (n = 129, 46.7%), S. aureus in 3 to < 24 months (n = 35, 37.2%), Salmonella spp. in 24 to < 60 months (n = 24, 34.8%) and S. aureus in children ≥ 5 years (n = 128, 60.7%). Compared with 2018 to 2019, the incidence rate in 2020 decreased by 57% for invasive pneumococcal disease (26.6 vs. 11.5 per 100,000 in-patients, P = 0.014) and 59% for Salmonella spp. infection (22.8 vs. 9.4 per 100,000 in-patients, P = 0.018). In contrast, no significant changes were observed in invasive infections due to S. aureus, S. agalactiae and E. coli. CONCLUSIONS: The NPIs implemented during the COVID-19 pandemic reduced invasive diseases caused by S. pneumoniae and Salmonella spp. but not S. aureus, S. agalactiae and E. coli in children.


Subject(s)
Bacterial Infections/classification , Bacterial Infections/epidemiology , Communicable Disease Control/methods , COVID-19/prevention & control , Child , Child, Preschool , Epidemiological Monitoring , Hospitals , Humans , Incidence , Infant , Republic of Korea/epidemiology , Retrospective Studies , SARS-CoV-2
7.
Microbiol Spectr ; 10(1): e0251321, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1707792

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide. Many variants of SARS-CoV-2 have been reported, some of which have increased transmissibility and/or reduced susceptibility to vaccines. There is an urgent need for variant phenotyping for epidemiological surveillance of circulating lineages. Whole-genome sequencing is the gold standard for identifying SARS-CoV-2 variants, which constitutes a major bottleneck in developing countries. Methodological simplification could increase epidemiological surveillance feasibility and efficiency. We designed a novel multiplex real-time reverse transcriptase PCR (RT-PCR) to detect SARS-CoV-2 variants with S gene mutations. This multiplex PCR typing method was established to detect 9 mutations with specific primers and probes (ΔHV 69/70, K417T, K417N, L452R, E484K, E484Q, N501Y, P681H, and P681R) against the receptor-binding domain of the spike protein of SARS-CoV-2 variants. In silico analyses showed high specificity of the assays. Variants of concern (VOC) typing results were found to be highly specific for our intended targets, with no cross-reactivity observed with other upper respiratory viruses. The PCR-based typing methods were further validated using whole-genome sequencing and a commercial kit that was applied to clinical samples of 250 COVID-19 patients from Taiwan. The screening of these samples allowed the identification of epidemic trends by time intervals, including B.1.617.2 in the third Taiwan wave outbreak. This PCR typing strategy allowed the detection of five major variants of concern and also provided an open-source PCR assay which could rapidly be deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, P.1, and B.1.617.2 variants and of four Omicron mutations on the spike protein (ΔHV 69/70, K417N, N501Y, P681H). IMPORTANCE COVID-19 has spread globally. SARS-CoV-2 variants of concern (VOCs) are leading the next waves of the COVID-19 pandemic. Previous studies have pointed out that these VOCs may have increased infectivity, have reduced vaccine susceptibility, change treatment regimens, and increase the difficulty of epidemic prevention policy. Understanding SARS-CoV-2 variants remains an issue of concern for all local government authorities and is critical for establishing and implementing effective public health measures. A novel SARS-CoV-2 variant identification method based on a multiplex real-time RT-PCR was developed in this study. Five SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, and Omicron) were identified simultaneously using this method. PCR typing can provide rapid testing results with lower cost and higher feasibility, which is well within the capacity for any diagnostic laboratory. Characterizing these variants and their mutations is important for tracking SAR-CoV-2 evolution and is conducive to public infection control and policy formulation strategies.


Subject(s)
COVID-19/virology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/classification , COVID-19/epidemiology , Epidemiological Monitoring , Humans , Mutation , Pandemics , Public Health , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics , Taiwan , Whole Genome Sequencing
8.
Science ; 375(6582): 703-704, 2022 Feb 18.
Article in English | MEDLINE | ID: covidwho-1701253

ABSTRACT

As pandemic restrictions lift, virus tracking and preparation for next variant may suffer.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Endemic Diseases , Communicable Disease Control , Epidemiological Monitoring , Humans , Masks
9.
Eur Rev Med Pharmacol Sci ; 26(3): 1020-1027, 2022 02.
Article in English | MEDLINE | ID: covidwho-1699173

ABSTRACT

OBJECTIVE: Microorganisms present a global public health problem and are the leading cause of hospital-acquired infections. Therefore, it is essential to study the prevalence of microorganisms in hospital environments. The conclusion from such a study can contribute to identify the areas most likely to be contaminated in a hospital and appropriate measures that can decrease the exposure risk. MATERIALS AND METHODS: The prevalence of microorganisms in hospital air was examined in different departments by obtaining air samples with an impactor before and during the SARS-CoV-2 pandemic. A total of 2145 microorganisms were identified, and the corresponding data were jointly analyzed by area, sampling period, and concentration. RESULTS: The most frequently detected microorganisms in hospital air were Staphylococcus, Micrococcus, Neisseria, and fungi, and the more polluted departments were the hemodialysis department, respiratory department, treatment room, and toilet. Significant differences were found between the concentration of bacteria and fungi before and during the pandemic, which could be related to multiple environmental conditions. Furthermore, SARS-CoV-2 was negative in all the air samples. CONCLUSIONS: Overall, this study confirmed the existence and dynamic characteristics of airborne microorganisms in a hospital. The results contribute to the adaptation of specific measures which can decrease the exposure risk of patients, visitors, and staff.


Subject(s)
Air Microbiology , Bacteria/isolation & purification , Fungi/isolation & purification , Hospitals , Air Pollution, Indoor , Bacteria/classification , Environmental Monitoring , Epidemiological Monitoring , Fungi/classification , Hospital Departments , Pandemics , SARS-CoV-2
12.
Curr Med Sci ; 42(1): 226-236, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1603118

ABSTRACT

OBJECTIVE: The annual influenza epidemic is a heavy burden on the health care system, and has increasingly become a major public health problem in some areas, such as Hong Kong (China). Therefore, based on a variety of machine learning methods, and considering the seasonal influenza in Hong Kong, the study aims to establish a Combinatorial Judgment Classifier (CJC) model to classify the epidemic trend and improve the accuracy of influenza epidemic early warning. METHODS: The characteristic variables were selected using the single-factor statistical method to establish the influencing factor system of an influenza outbreak. On this basis, the CJC model was proposed to provide an early warning for an influenza outbreak. The characteristic variables in the final model included atmospheric pressure, absolute maximum temperature, mean temperature, absolute minimum temperature, mean dew point temperature, the number of positive detections of seasonal influenza viruses, the positive percentage among all respiratory specimens, and the admission rates in public hospitals with a principal diagnosis of influenza. RESULTS: The accuracy of the CJC model for the influenza outbreak trend reached 96.47%, the sensitivity and specificity change rates of this model were lower than those of other models. Hence, the CJC model has a more stable prediction performance. In the present study, the epidemic situation and meteorological data of Hong Kong in recent years were used as the research objects for the construction of the model index system, and a lag correlation was found between the influencing factors and influenza outbreak. However, some potential risk factors, such as geographical nature and human factors, were not incorporated, which ideally affected the prediction performance to some extent. CONCLUSION: In general, the CJC model exhibits a statistically better performance, when compared to some classical early warning algorithms, such as Support Vector Machine, Discriminant Analysis, and Ensemble Classfiers, which improves the performance of the early warning of seasonal influenza.


Subject(s)
Epidemiological Monitoring , Influenza, Human/epidemiology , Machine Learning , Models, Statistical , Hong Kong , Humans
13.
Environ Health Perspect ; 129(4): 45002, 2021 04.
Article in English | MEDLINE | ID: covidwho-1673983

ABSTRACT

BACKGROUND: Wastewater testing offers a cost-effective strategy for measuring population disease prevalence and health behaviors. For COVID-19, wastewater surveillance addresses testing gaps and provides an early warning for outbreaks. As U.S. federal agencies build a National Wastewater Surveillance System around the pandemic, thinking through ways to develop flexible frameworks for wastewater sampling, testing, and reporting can avoid unnecessary system overhauls for future infectious disease, chronic disease, and drug epidemics. OBJECTIVES: We discuss ways to transform a historically academic exercise into a tool for epidemic response. We generalize lessons learned by a global network of wastewater researchers around validation and implementation for COVID-19 and opioids while also drawing on our experience with wastewater-based epidemiology in the United States. DISCUSSION: Sustainable wastewater surveillance requires coordination between health and safety officials, utilities, labs, and researchers. Adapting sampling frequency, type, and location to threat level, community vulnerability, biomarker properties, and decisions that wastewater data will inform can increase the practical value of the data. Marketplace instabilities, coupled with a fragmented testing landscape due to specialization, may require officials to engage multiple labs to test for known and unknown threats. Government funding can stabilize the market, balancing commercial pressures with public good, and incentivize data sharing. When reporting results, standardizing metrics and contextualizing wastewater data with health resource data can provide insights into a community's vulnerability and identify strategies to prevent health care systems from being overwhelmed. If wastewater data will inform policy decisions for an entire community, comparing characteristics of the wastewater treatment plant's service population to those of the larger community can help determine whether the wastewater data are generalizable. Ethical protocols may be needed to protect privacy and avoid stigmatization. With data-driven approaches to sample collection, analysis, and interpretation, officials can use wastewater surveillance for adaptive resource allocation, pandemic management, and program evaluation. https://doi.org/10.1289/EHP8572.


Subject(s)
COVID-19 , Epidemiological Monitoring , SARS-CoV-2/isolation & purification , Waste Water/virology , Humans , Pandemics , United States
15.
PLoS One ; 17(1): e0262868, 2022.
Article in English | MEDLINE | ID: covidwho-1643287

ABSTRACT

A serological COVID-19 Multiplex Assay was developed and validated using serum samples from convalescent patients and those collected prior to the 2020 pandemic. After initial testing of multiple potential antigens, the SARS-CoV-2 nucleocapsid protein (NP) and receptor-binding domain (RBD) of the spike protein were selected for the human COVID-19 Multiplex Assay. A comparison of synthesized and mammalian expressed RBD proteins revealed clear advantages of mammalian expression. Antibodies directed against NP strongly correlated with SARS-CoV-2 virus neutralization assay titers (rsp = 0.726), while anti-RBD correlation was moderate (rsp = 0.436). Pan-Ig, IgG, IgA, and IgM against NP and RBD antigens were evaluated on the validation sample sets. Detection of NP and RBD specific IgG and IgA had outstanding performance (AUC > 0.90) for distinguishing patients from controls, but the dynamic range of the IgG assay was substantially greater. The COVID-19 Multiplex Assay was utilized to identify seroprevalence to SARS-CoV-2 in people living in a low-incidence community in Ithaca, NY. Samples were taken from a cohort of healthy volunteers (n = 332) in early June 2020. Only two volunteers had a positive result on a COVID-19 PCR test performed prior to serum sampling. Serological testing revealed an exposure rate of at least 1.2% (NP) or as high as 5.7% (RBD), higher than the measured incidence rate of 0.16% in the county at that time. This highly sensitive and quantitative assay can be used for monitoring community exposure rates and duration of immune response following both infection and vaccination.


Subject(s)
Antibodies, Viral/chemistry , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/blood , COVID-19/epidemiology , COVID-19 Serological Testing/standards , Coronavirus Nucleocapsid Proteins/chemistry , Epidemiological Monitoring , Female , Humans , Immunoglobulin A/chemistry , Immunoglobulin A/immunology , Immunoglobulin G/chemistry , Immunoglobulin G/immunology , Immunoglobulin M/chemistry , Immunoglobulin M/immunology , Male , Middle Aged , New York/epidemiology , Phosphoproteins/chemistry , Phosphoproteins/immunology , Protein Interaction Domains and Motifs , Recombinant Proteins/chemistry , Recombinant Proteins/immunology , SARS-CoV-2/classification , Sensitivity and Specificity , Spike Glycoprotein, Coronavirus/chemistry
17.
PLoS One ; 17(1): e0262170, 2022.
Article in English | MEDLINE | ID: covidwho-1637228

ABSTRACT

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Genes, Viral , Pandemics/prevention & control , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Sequence Analysis, RNA/methods , Spike Glycoprotein, Coronavirus/genetics , Base Sequence , Brazil/epidemiology , COVID-19/virology , Diagnostic Tests, Routine/methods , Electrophoresis, Agar Gel/methods , Epidemiological Monitoring , Humans , Mutation , RNA, Viral/genetics , RNA, Viral/isolation & purification
19.
Emerg Microbes Infect ; 11(1): 168-171, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1623181

ABSTRACT

HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.


Subject(s)
Common Cold/epidemiology , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/genetics , Genome, Viral , Genotype , Pneumonia, Viral/epidemiology , Base Sequence , Bayes Theorem , Child , Child, Hospitalized , Child, Preschool , China/epidemiology , Common Cold/pathology , Common Cold/transmission , Common Cold/virology , Coronavirus Infections/pathology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Coronavirus OC43, Human/classification , Coronavirus OC43, Human/pathogenicity , Epidemiological Monitoring , Female , Humans , Infant , Male , Monte Carlo Method , Mutation , Phylogeny , Pneumonia, Viral/pathology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Recombination, Genetic
20.
Sci Rep ; 11(1): 23562, 2021 12 07.
Article in English | MEDLINE | ID: covidwho-1623168

ABSTRACT

During the winter months of 2020/2021 a wave of multisystem inflammatory syndrome in children (MIS-C) emerged in Poland. We present the results of a nationwide register aiming to capture and characterise MIS-C with a focus on severity determinants. The first MIS-C wave in Poland was notably high, hence our analysis involved 274 children. The group was 62.8% boys, with a median age of 8.8 years. Besides one Asian, all were White. Overall, the disease course was not as severe as in previous reports, however. Pediatric intensive care treatment was required for merely 23 (8.4%) of children, who were older and exhibited a distinguished clinical picture at hospital admission. We have also identified sex-dependent differences; teenage boys more often had cardiac involvement (decreased ejection fraction in 25.9% vs. 14.7%) and fulfilled macrophage activation syndrome definition (31.0% vs. 15.2%). Among all boys, those hospitalized in pediatric intensive care unit were significantly older (median 11.2 vs. 9.1 years). Henceforth, while ethnicity and sex may affect MIS-C phenotype, management protocols might be not universally applicable, and should rather be adjusted to the specific population.


Subject(s)
COVID-19/complications , Systemic Inflammatory Response Syndrome/diagnosis , Systemic Inflammatory Response Syndrome/epidemiology , Adolescent , Age Factors , COVID-19/diagnosis , COVID-19/epidemiology , Child , Child, Preschool , Cohort Studies , Epidemiological Monitoring , Female , Humans , Incidence , Infant , Intensive Care Units, Pediatric , Male , Mucocutaneous Lymph Node Syndrome/complications , Mucocutaneous Lymph Node Syndrome/diagnosis , Mucocutaneous Lymph Node Syndrome/epidemiology , Poland/epidemiology , Prevalence , Registries , SARS-CoV-2 , Severity of Illness Index , Sex Factors
SELECTION OF CITATIONS
SEARCH DETAIL