A Case Study of Applying Metagenomic Sequencing in Precise Epidemiology for the COVID-19 Pandemic - Sichuan Province, China, 2020.
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ABSTRACT:
SUBMITTER: Xu J
PROVIDER: S-EPMC8393149 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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: Not available
| S-EPMC7042184 | 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:Human infection with Chlamydia psittaci is rare but difficult to recognize. We report an outbreak of psittacosis among poultry processing workers in China. We applied metagenomic next-generation sequencing and identified Chlamydia psittaci reads from samples of all seven patients, four of which were subsequently confirmed by PCR. Epidemiological results suggested that the poultry processed in the factory was the possible source of human infection.
| 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:In order to understand the prevalence and genetic diversity of porcine deltacoronavirus (PDCoV) in diarrhoeal pigs in Sichuan province, 634 clinical samples were collected from individual pigs with diarrhoea in 13 regions of Sichuan province, China, from January 2017 and June 2019. The detection results showed that the infection rate of PDCoV was relatively low in diarrhoeal pigs, 13.25% (84/634), but the infection rate of PEDV (porcine epidemic diarrhea virus) was high, 32.18% (204/634). Coinfection with PEDV was common (55.95%, 47/84) in PDCoV-infected diarrhoeal pigs. Additionally, the chance of PDCoV infection was 2.77 times higher in suckling piglets than in sows, and about 3.30 times higher in spring and winter than in summer. PDCoV/PEDV coinfection was 75% less likely in sows than in suckling piglets. The complete genomes of four Sichuan PDCoV strains were sequenced and analysed. There were some insertion-deletion signatures in the whole genome sequences of four strains, including a 6-nt deletion in the non-structural gene 2 region, a 9-nt insertion in the non-structural gene 3 region, a 3-nt deletion in the S gene region, and a distinguishing 11-nt deletion in the 3'UTR region. Phylogenetic analysis based on complete genome sequences revealed that the PDCoV Sichuan strains were closely related to other Chinese PDCoV reference strains; however, phylogenetic analysis based on S gene sequences showed that the CH/SC/2019 strain clustered in a large clade with strains from the USA, Japan, and Korea. These data advance our understanding of the genetic diversity and evolutionary characteristics of PDCoV in China and may contribute to vaccine development.
| S-EPMC7474797 | biostudies-literature
Project description:Pleosporales is the largest and most morphologically diverse order in Dothideomycetes, including a large proportion of saprobic fungi. During the investigation of microfungi from decaying wood in Sichuan Province, several novel fungal taxa of asexual and sexual morphs were collected, identified, and well-described. Phylogenetic analyses based on SSU, ITS, LSU, RPB2 and TEF1α gene sequences suggested that these new taxa were related to Pleosporales and distributed in five families, viz. Amorosiaceae, Bambusicolaceae, Lophiostomataceae, Occultibambusaceae and Tetraplosphaeriaceae. The morphological comparison and molecular phylogeny evidence justify the establishment of six new taxa, namely Bambusicola guttulata sp. nov., Flabellascoma sichuanense sp. nov., Neoangustimassarina sichuanensis gen. et sp. nov., Occultibambusa sichuanensis sp. nov. and Pseudotetraploa bambusicola sp. nov. Among them, Neoangustimassarina was introduced as the second sexual morph genus in Amorosiaceae; Bambusicola guttulata, O. sichuanensis and P. bambusicola were isolated from bamboos, which contributed to the diversity of bambusicolous fungi. The detailed, illustrated descriptions and notes for each new taxon are provided, as well as a brief note for each family. The potential richness of fungal diversity in Sichuan Province is also discussed.
| S-EPMC9317281 | biostudies-literature
Project description:BackgroundEchinococcosis is a parasitic zoonosis caused by Echinococcus larvae parasitism causing high mortality. The Tibetan Region of Sichuan Province is a high prevalence area for echinococcosis in China. Understanding the geographic distribution pattern is necessary for precise control and prevention. In this study, a spatial analysis was conducted to explore the town-level epidemiology of echinococcosis in the Sichuan Tibetan Region and to provide guidance for formulating regional prevention and control strategies.MethodsThe study was based on reported echinococcosis cases by the end of 2017, and each case was geo-coded at the town level. Spatial empirical Bayes smoothing and global spatial autocorrelation were used to detect the spatial distribution pattern. Spatial scan statistics were applied to examine local clusters.ResultsThe spatial distribution of echinococcosis in the Sichuan Tibetan Region was mapped at the town level in terms of the crude prevalence rate, excess hazard and spatial smoothed prevalence rate. The spatial distribution of echinococcosis was non-random and clustered with the significant global spatial autocorrelation (I = 0.7301, P = 0.001). Additionally, five significant spatial clusters were detected through the spatial scan statistic.ConclusionsThere was evidence for the existence of significant echinococcosis clusters in the Tibetan Region of Sichuan Province, China. The results of this study may assist local health departments with developing better prevention strategies and prompt more efficient public health interventions.
| S-EPMC6214160 | biostudies-literature