Next-generation Sequencing Study of Pathogens in Serum from Patients with Febrile Jaundice in Sierra Leone / 生物医学与环境科学（英文）

OBJECTIVE@#People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus (YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice.@*METHODS@#In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV-negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice.@*RESULTS@#The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus (89.58%), Epstein-Barr virus (55.21%), hepatitis C virus (34.38%), rhinovirus (28.13%), hepatitis A virus (20.83%), coxsackievirus (10.42%), Ebola virus (8.33%), hepatitis E virus (8.33%), lyssavirus (4.17%), leptospirosis (4.17%), chikungunya virus (2.08%), Crimean-Congo hemorrhagic fever virus (1.04%), and hepatitis B virus (1.04%).@*CONCLUSION@#The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.

Single nucleotide polymorphisms characteristics of the Yersinia Pestis in China / 中国地方病学杂志

Objective To study the single nucleotide polymorphisms (SNP) characteristics of Yersinia pestis strains from different natural foci in China.Methods Genome-wide comparison was done to find SNP sites by the Mummer program among 9 Yersinia pestis genome which was downloaded from NCBI.Then 13 genic fragments including 19 SNP sites were amplified by PCR and sequenced in 133 Yersinia pestis strains,and the results were cluster analyzed with the BioNumerics software.Results Three thousand seven hundred and eighty sequence variation sites were found by genome-wide comparison.Using the different combinations of SNP sites,UPGMA cluster analysis revealed obvious geographic regional and eco-aggregation characteristics of Yersinia pestis strains isolated from China.Conclusions As relatively stable genetic markers,SNP can better reflect the genome characteristics of Yersinia pestis in different plague natural foci of China.

Comparison of Yersinia pestis genomes from a new natural foci in China / 中国地方病学杂志

Objective Measurement and analysis of the complete genome sequences of Yersinia Pestis from a new plague natural foci and adjacent foci in China, to know the genetic relationship among the epidemic strain isolated in Yulong (D 106004) and Jianchuan strains (D 182038) and the Tibetan strain ( Z 176003 ). Methods Three complete genome sequences were sequenced using the whole-genome shotgun and Solexa method and comparative genomics analysis was done among the three sequences. Genome comparative analysis among the coding sequences was done by BLAST software, SNPs finding was done by the program, genome rearrangements were analyzed using MAUVE software. Results All of the genomes of Yersinia pestis strains D182038, D106004 and Z176003 consist of a single circular chromosome and three virulence plasmids, pMT1, pCD1 and pPCP1. They had similar characteristics in chromosome and plasmid features, and there were no significant difference in coming sequence (CDS) of the cluster of orthologous groups of proteins (COG) functional classification and the number of insertion sequence in the three strains (x2 =3.03, 0.257, all P ＞ 0.05). The comparative genomics results showed that the three bacteria had 2882 genes with 100％ homology, of 3636 genes predicted in D106004, 2994 were identical with D182038's and 3113 with Z176003's, and of which 240 had 90％ homology with D182038's and 200 with Z176003 's. Synonymous single nucleotide polymorphisms(sSNPs) were 59 and 68, and non-synonymous SNPs(nsSNPs) were 104 and 203 between strains D106004 and Z176003/D182038. There were 11 segments rearrangements between D106004 and Z176003, which was less than 16 segments rearrangements between D106004 and D182038. ConclusionsThe three strains are highly homologous, the Yulong strain has more similarity with Tibet strain than with Jianchuan strain, the strain from Yulong foci may be evolved from Tibet foci.

Public health situation and needs assessment after Wenchuan earthquake in Anxian, Sichuan province / 中华预防医学杂志

<p><b>OBJECTIVE</b>To explore the public health situation and needs in Anxian after Wenchuan earthquake so as to make an effective strategy for disease control and prevention.</p><p><b>METHODS</b>69 concentrated settlements with 100 residents were investigated. Probability proportion to size was adopted for sampling of 2200 residents from 687 scattered households (about 440 000 scattered residents). The content of this survey included drinking water, food hygiene, environment sanitation, planning immunity and medical health service, disease surveillance and so on. SPSS 16.0 was used for data analysis, and statistical interpretation was used to describe the results.</p><p><b>RESULTS</b>90.9% (31/66) resettled residents in Anxian lived in tents, 7.6% (5/66) lived in the movable-plate house, 93.3% (621/666) scattered households lived in tents and 71.9% (446/621) of them lived in tents which were built by residents themselves; the rate of drinking water disinfection in resettlement sites and scattered households were 97.1% (66/68) and 94.6% (650/687); 12.8% scattered residents had mouldy or food; 50% of resettlement sites raised animals; 43.6% (17/39) medical station didn't have bacterin inoculation service; 66.7% (10/15) lacked sufficient disinfection equipment; register rate was 50.0% (33/66) and report rate of symptoms and infectious diseases was 56.1% (37/66).</p><p><b>CONCLUSION</b>There was still some risk of enteric and vector-borne diseases in Anxian, therefore, some tailored measures should be very important.</p>

Mental health assessment among scattered residents after Wenchuan earthquake in Anxian, Sichuan province / 中华预防医学杂志

<p><b>OBJECTIVE</b>To explore the mental health status of residents scattered living in Anxian after Wenchuan earthquake so as to provide scientific basis for further mental health intervention.</p><p><b>METHODS</b>A face to face interview was conducted among the scattered residents with designed questionnaire, which had three parts of the physical and emotional reaction, the relax methods and the social care and supports expected. Two-stage probability proportional to size (PPS) sample method was performed to sample 2184 from 0.44 million scattered residents in Anxian. On the basis of statistical description, mental health of different characteristics groups was compared.</p><p><b>RESULTS</b>Three main symptoms of posttraumatic stress disorders in 2184 residents (11.23+/-3.44) were higher than the 103 fire victims in Hunan in 2003 (10.06+/-3.26), three factor scores of SCL-90 (5.76+/-1.74) were higher than normal in 1998 repair mode (n=23 891) (4.72+/-1.44), and the statistical difference was observed (t=10.77, P<0.05; t=706.04, P<0.05). Comparing the mental health of different groups, some significant differences were found by age, gender and education background.</p><p><b>CONCLUSION</b>The earthquake disaster brought prevalent physical and emotional reaction. Elderly people, female, junior students need mental intervention immediately. Therefore, strengthen the mental education and assistance (especially in high risk groups) would be of more significance.</p>

Estimating rapid detection of F1 antigen of Yersinia pestis with gold-immunochromatography / 中国地方病学杂志

Objective To develop a rapid test for the detection of F1 antigen of Yersinia Pestis based on gold-immunochromatography.Methods F1 antibodies were coupled with colloidal gold to prepare collidal gold reagent,which was used to detect F1 antibodies based on double antigen sandwich.The collidal gold reagent was estimated for its sensitivity specificity and stablity in labs and 1798 samples were detected in 17 surveillance spots.Results The reagent was sensitive to 0.0010 g/L F1 antigens.The reagens kept stable when it had been placed at 4℃ or room-temperature for 12 months and did not react to Yersinia pseudotuberculosis and Yersinia enterolitica.In 17 surveillance labs the reagent was used to test 1798 viscera samples from animal.resulting an accordance rate of 97.11%(1746/1798)to bacterial culture and 96.83%(1741/1798)accordance to reverse indirect hemagglutination assay(RIHA),showing a higher detection rate[9.23%(166/1798)]compared with RIHA[6.79%(122/1798)]and bacterial culture[6.28%(113/1798)].Conclusions The collidal gold reagent,sensitive and specific in diagnosing Yersinia pestis infection of both human and animals,is a rapid method in surveillance spot.

Study on the application and evaluation of methods for gene and antigen detection in plague surveillance program / 中华流行病学杂志

<p><b>OBJECTIVE</b>To apply and evaluate new methods regarding specific gene and antigen detection in plague surveillance program.</p><p><b>METHODS</b>1798 samples from natural foci of plague were tested, using internal quality control multiple-polymerase chain reaction, F1 antigen marked by immuno chromatographic assay and enzyme linked immunosorbent assay. Culture of Yersinia pestis and reverse indirect hemagglutination assay were used as reference diagnostic methods.</p><p><b>RESULTS</b>The overall positive rate of culture on Yersinia pestis together with gene and antigen detection was 7.34%, showing an 16.81% increase when comparing to 6.28% using Yersinia pestis culture method alone. The rate of coincidence was 97.13%.</p><p><b>CONCLUSION</b>The new standard being used for specific gene and antigen detection could increase the positive rate of diagnosis on plague.</p>

Molecular biological characteristics and genetic significance of Yersinia pestis in China / 中华流行病学杂志

<p><b>OBJECTIVE</b>To understand the molecular biological characteristics in order to analyse the genetic background of Yersinia pestis in China.</p><p><b>METHODS</b>Primary datum on ribotyping, pulsed field gene electrophoresis (PFGE), random amplified polymorphic DNA (RAPD) and insertion sequence (IS) of Yersinia pestis were used and under cluster analysis. Genetic interval and various methods of recognized molecular feature between different strains were evaluated.</p><p><b>RESULTS</b>Ribotypes the PFGE types seemed to be corresponding. Stains from Microtus fuscus and area in Tibet Zhongba belonged to 7 copy rRNA gene and the genetic interval were the far more with 6 copy rRNA gene stains, and not definite with RAPD, but with many exceptions. The genetic interval between strains were showed by resemble value.</p><p><b>CONCLUSION</b>Yersinia pestis in China had its own manifold, particular molecular biological characteristics due to natural barriers, geographical complex, circumstances in Tianshan Mountains and Gandise Mountains areas. Yersinia pestis were limited to separateness, evoluted only in certain areas to form a great many gene types.</p>

Genetic analysis of Yersinia pestis strains isolated in China / 中华流行病学杂志

<p><b>OBJECTIVE</b>The strains of Yersinia pestis isolated in different period and different natural foci in China were analyzed.</p><p><b>METHODS</b>Traditional and molecular biological methods were used. Rhamnose fermentation, rRNA gene copy number, nitrite reduction, and the glycerol fermentation were important characters for typing, and pulse field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) profile could reflect the genetic distance between the strains.</p><p><b>RESULTS</b>The strains could be divided into 15 genetic types by those 6 characters with each of them covered an isolated geographical territories.</p><p><b>CONCLUSION</b>The characters of strains were described; the genetic relationship of different types, their evolution, and the forming and shift of plague natural foci were analyzed.</p>