A Case Study of Applying Metagenomic Sequencing in Precise Epidemiology for the COVID-19 Pandemic - Sichuan Province, China, 2020.
Ontology highlight
ABSTRACT:
SUBMITTER: Xu J
PROVIDER: S-EPMC8393149 | biostudies-literature | 2020 Nov
REPOSITORIES: biostudies-literature
Publications
A Case Study of Applying Metagenomic Sequencing in Precise Epidemiology for the COVID-19 Pandemic - Sichuan Province, China, 2020.
Xu Jianan J Wang Ye Y Li You Y Yang Huiping H Pan Ming M Liu Jian J Shi Lina L Feng Yuliang Y Liu Li L Li Jin J Zhang Li L He Shusen S
China CDC weekly 20201101 47
Similar Datasets
Project description:BACKGROUND: Porcine torovirus (PToV) is a member of the genus Torovirus which is responsible for gastrointestinal disease in both human beings and animals with particular prevalence in youth. Torovirus infections are generally asymptomatic, however, their presence may worsen disease consequences in concurrent infections with other enteric pathogens. METHODS: A total of 872 diarrheic fecal samples from pigs of different ages were collected from 12 districts of Sichuan Province in the southwest of China. RT-PCR was done with PToV S gene specific primers to detect the presence of PToV positive samples. M gene specific primers were used with the PToV positive samples and the genes were sequenced. A phylogenetic tree was constructed based on the M gene nucleotide sequences from the 19 selected novel Sichuan strains and 21 PToV and BToV M gene sequences from GenBank. RESULTS: A total of 331 (37.96%, 331/872) samples were found to be positive for PToV and the highest prevalence was observed in piglets aged from 1 to 3 weeks old. Through phylogenetic inference the 40 PToV M gene containing sequences were placed into two genotypes (I & II). The 19 novel Sichuan strains of genotype I showed strong correlations to two Korean gene sequences (GU-07-56-11 and GU-07-56-22). Amino-acid sequence analysis of the 40 PToV M gene strains revealed that the M gene protein was highly conserved. CONCLUSIONS: This study uncovered the presence of PToV in Sichuan Province, and demonstrated the need for continuous surveillance PToV of epidemiology.
| S-EPMC4064267 | biostudies-literature
Project description:Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits the immune function of the macrophage and T-cell lymphatic systems, and has caused huge economic losses to the porcine breeding industry. Molecular epidemiological investigation of PCMV is important for prevention and treatment, and this study is the first such investigation in Sichuan Province, Southwest China. A PCMV positive infection rate of 84.4% (865/1025) confirmed that PCMV is widely distributed in Sichuan Province. A phylogenetic tree was constructed based on the PCMV glycoprotein B gene (gB) nucleotide and amino acid sequences from 24 novel Sichuan isolates and 18 other PCMV gB sequences from Genbank. PCMV does not appear to have evolved into different serotypes, and two distinct sequence groups were identified (A and B). However, whether PCMV from this region has evolved into different genotypes requires further research. Analysis of the amino acid sequences confirmed the conservation of gB, but amino acid substitutions in the major epitope region have caused antigenic drift, which may have altered the immunogenicity of PCMV.
| S-EPMC3675093 | biostudies-literature
Project description:ObjectivesTo investigate the period prevalence of complex wounds among the overall inpatients, and the impact of complex wounds on inpatient health expense and length of hospital stay (LOS).DesignAn observational study.Setting6056 healthcare institutions across Sichuan province in China.ParticipantsThis study included 4 033 763 people admitted to healthcare institutions during 1 September 2018 and 31 December 2018.ResultsThe point prevalence of complex wounds was 4.07 per 1000 among inpatients in Sichuan. The most common complex wounds were pressure ulcers (1.47 per 1000 among inpatients). Older, male, Han ethnic groups and retired people were most likely to suffer from complex wounds. The median LOS was longer for those with complex wounds as their main condition of treatment compared with all-cause admissions in Sichuan (12 days compared with 7 days; p<0.001). The median cost of care for people with complex wounds was higher than for admission for any cause (¥6500.18 compared with ¥3337.16; p<0.001). People with pressure ulcers had the longest LOS, while people with ulcers related to diabetes incurred the highest costs.ConclusionsComplex wounds, especially pressure ulcers, are common in Sichuan province and their presence is associated with significantly longer lengths of hospital stay and higher medical costs. Additionally, this study only included admitted inpatients during the sampling time period, hence the prevalence of complex wounds may be underestimated. The high prevalence rate and heavy direct and indirect disease burden of complex wounds indicate that health policies for early detection and prevention of complex wounds in elders are urgently needed.
| S-EPMC7651747 | biostudies-literature
Project description:Q fever is a zoonotic disease caused by infection with Coxiella burnetii (C. burnetii). Due to its atypical symptoms and the absence of specific detection methods, Q fever is underdiagnosed commonly. Herein, we report a case of Q fever confirmed by metagenomic next-generation sequencing (mNGS) in March 2024 in Guangdong Province, China. The patient initially experienced fever and was admitted to hospital six days later. Despite a series of laboratory tests conducted at the hospital, the pathogen remained undetermined. Ten days after admission, mNGS revealed that the patient was infected with C. burnetii. The patient subsequently underwent treatment with doxycycline and recovered well. Epidemiological investigation revealed that the patient had been exposed to sheep infected with C. burnetii without any protective measures in Jiangxi Province, China. Based on the comprehensive results of mNGS, exposure history, clinical manifestations and treatment response, the patient was confirmed as a Q fever case. As a neglected and underestimated illness, Q fever necessitates an elevation in awareness among medical staff and the public. The public should be encouraged to take personal protective measures when exposed to livestock. Further research is needed to explore the rational application of mNGS in the diagnosis of uncommon and unknown diseases.
| S-EPMC11895022 | biostudies-literature
Project description: Not available
| S-EPMC7042184 | biostudies-literature
Project description:BackgroundThe re-emergence of scrub typhus in the southern provinces of China in recent decades has been validated, thereby attracting the attention of public health authorities. There has been a spatial and temporal expansion of scrub typhus in Hainan Province, but the epidemiological characteristics, environmental drivers, and potential high-risk areas for scrub typhus have not yet been investigated.ObjectiveThe aims of this study were to characterize the spatiotemporal epidemiology of scrub typhus, identify dominant environmental risk factors, and map potential risk areas in Hainan Province from 2011 to 2020.MethodsThe spatiotemporal dynamics of scrub typhus in Hainan Province between 2011 and 2020 were analyzed using spatial analyses and seasonal-trend decomposition using regression (STR). The maximum entropy (MaxEnt) model was applied to determine the key environmental predictors and environmentally suitable areas for scrub typhus, and the demographic diversity of the predicted suitable zones was evaluated.ResultsDuring 2011-2020, 3260 scrub typhus cases were recorded in Hainan Province. The number of scrub typhus cases increased continuously each year, particularly among farmers (67.61%) and individuals aged 50-59 years (23.25%) who were identified as high-risk groups. A dual epidemic peak was detected, emerging annually from April to June and from July to October. The MaxEnt-based risk map illustrated that highly suitable areas, accounting for 25.36% of the total area, were mainly distributed in the northeastern part of Hainan Province, where 75.43% of the total population lived. Jackknife tests revealed that ground surface temperature, elevation, cumulative precipitation, evaporation, land cover, population density, and ratio of dependents were the most significant environmental factors.ConclusionIn this study, we gained insights into the spatiotemporal epidemiological dynamics, pivotal environmental drivers, and potential risk map of scrub typhus in Hainan Province. These results have important implications for researchers and public health officials in guiding future prevention and control strategies for scrub typhus.
| S-EPMC10665174 | biostudies-literature
Project description:BackgroundPorcine astrovirus (PoAstV) is widely distributed worldwide, and is highly prevalent among piglets with or without diarrhea, existing as at least five distinct lineages (PoAstV1-PoAstV5) within the genus Mamastrovirus. However, our knowledge of the diversity and epidemiology of PoAstV in China is limited.ResultsIn this study, fecal samples from 21/120 (17.5 %) domestic pigs, including 18/100 (18 %) diarrheic and 3/20 (15 %) healthy pigs, and from 1/9 (11.1 %) healthy wild boars tested in Sichuan Province were positive for PoAstV on reverse transcription-PCR. Of the 22 positive samples, 13.6 % were positive for PoAstV only, whereas 40.9 % also contained Porcine epidemic diarrhea virus (PEDV), 22.7 % also contained porcine group A rotavirus (PRoVA), and 22.7 % also contained PEDV and PRoVA. A phylogenetic analysis of the RdRp gene revealed genetic heterogeneity among the PoAstV sequences and two lineages were detected in this study, with PoAstV-2 predominant. PoAstV-5 was detected in wild boars for the first time.ConclusionsPoAstV infections exist in Sichuan Province regardless of the disease status in the pig population, either alone or in combination with other enteric viruses, and may be associated with diarrhea.
| S-EPMC4704384 | biostudies-literature
Project description: Not available
| S-EPMC10699661 | biostudies-literature
Project description:ObjectiveRecently, China has experienced a considerable influence of the COVID-19 pandemic on the local people's health and economy. Hence, the current research aims to investigate the psychological and socioeconomic impact of COVID-19 on rural communities in the Sichuan Province of China.MethodsA total of 499 participants (village representatives of Sichuan Province) were approached to partake in a cross-sectional online survey and share their experience regarding the ongoing pandemic. The descriptive statistics and ordinary least squares (OLS) regression were used to analyse the data.ResultsOur analysis revealed that the pandemic has significantly affected local people psychologically, leading to socioeconomic vulnerability. Notably, we find that local households are worried about their income losses regardless of their socioeconomic status (40%-43%), level of income (37%-43%) and industry involvement (38%-43%). However, as income increases, the level of stress decreases. The results further show that government transfer payment is a significant factor in reducing stress due to its reliable and uninterrupted income flow. Contrary to our proposition, the pandemic stress was less observed, which might be because of people's trust in government and effective antiepidemic countermeasures to contain the disease.ConclusionThis study finds that COVID-19 has a significant impact on local people's health, psychology and income. This study is one of the first to provide empirical evidence regarding the early health and socioeconomic effects of COVID-19 at the household level in rural communities, which are very important to devise policies to ease the outbreak and prevent further losses at the local community level.
| S-EPMC8359857 | biostudies-literature
Project description:A new orchid species, Hemipiliaavisoides, is described from Songpan County and Maoxian County, Sichuan Province, China. Morphologically, H.avisoides is most similar to H.hui, but can be distinguished by the combination of its involute middle lip lobe that is smaller than the lateral lobes, floral bracts that are 5 mm long and are always shorter than the ovary, a leaf that is appressed to the substrate and is adaxially green with white lines along 7-9 principal veins and the subterranean stem with a solitary sheath at its base. The floral morphology of H.avisoides is presented by utilising in vivo micro-CT scanning and 3D visualisation.
| S-EPMC9836486 | biostudies-literature