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In Zherong county, Fujian province, the black spot of Pseudostellaria heterophylla often breaks out in the rainy season from April to June every year. As one of the main leaf diseases of P. heterophylla, black spot seriously affects the yield and quality of the medicinal material. To identify and characterize the pathogens causing black spot, we isolated the pathogens, identified them as a species of Alternaria according to Koch's postulates, and then tested their pathogenicity and biological characteristics. The results showed that the pathogens causing P. heterophylla black spot were A. gaisen, as evidenced by the similar colony morphology, spore characteristics, sporulation phenotype, and the same clade with A. gaisen on the phylogenetic tree(the maximum likelihood support rate of 100% and the Bayesian posterior probability of 1.00) built based on the tandem sequences of ITS, tef1, gapdh, endoPG, Alta1, OPA10-2, and KOG1077. The optimum conditions for mycelial growth of the pathogen were 25 ℃, pH 5-8, and 24 h dark culture. The lethal conditions for mycelia and spores were both treatment at 50 ℃ for 10 min. We reported for the first time the A. gaisen-caused black spot of P. heterophylla. The results could provide a theoretical basis for the diagnosis and control of P. heterophylla leaf spot diseases.
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Bayes Theorem , Phylogeny , Caryophyllaceae , Alternaria , MyceliumABSTRACT
ObjectiveTo determine the pathogenic characteristics and genotype of two outbreaks of herpangina in children in Dapeng New District， Shenzhen， in May 2021. MethodsA total of five throat swabs from children in the two outbreaks of herpangina were collected and examined for common enteroviruses by real-time PCR. The VP1 region was further amplified by nested RT-PCR. The CLUSTAL W program in MEGA7 software was used to conduct the alignment and reconstruct a phylogenetic tree. ResultsThe pathogen causing the 2 cluster outbreaks of herpangina was coxsackievirus A4 （CVA4）. The sequences of CVA4 VP1 genes revealed that a nucleotide identity of 92% between the strains in the two outbreaks. The three CVA4 strains isolated in kindergarten A had the closest phylogenetic relationship with that isolated in Shenzhen in 2018（MN840533）， with the nucleotide identity of 98.11%. The two strains in kindergarten B had the closest phylogenetic relationship with CVA4 strain isolated in Sichuan in 2018（MW178763）， with the nucleotide identity of 97.88%. The phylogenetic tree showed that all five CVA4 strains in this study belonged to the C2 genotype. ConclusionThe C2 genotype of CVA4 is the causative agent in both outbreaks of herpangina.
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Objective@#To know the pre-treatment drug resistance ( PDR ) status of newly reported human immunodeficiency virus type 1 ( HIV-1 ) infected individuals in Wenzhou, so as to provide guidance for antiretroviral therapy ( ART ). @*Methods@# Totally 232 plasma samples of newly reported HIV-1 infected individuals who had not received ART were collected in Wenzhou in 2019. Virus ( HIV-1 ) RNA was extracted, followed by reverse transcription PCR and nested PCR to amplify the pol region and sequence. Resistance mutations and resistance to non-nucleoside reverse transcriptase inhibitors ( NNRTIs ), nucleoside reverse transcriptase inhibitors ( NRTIs ) and protease inhibitors ( PIs ) was analyzed.@*Results@#The pol region sequences from 199 infected patients were obtained and the incidence of PDR was 8.04% ( 16/199 ). Eight genotypes were detected, including circulating recombinant forms ( CRFs ) CRF07_BC ( 47.24%, 94/199 ) and CRF01_AE ( 29.15%, 58/199 ) which were the dominant types. Two unique recombinant forms ( URFs ) were detected, namely URF( CRF01_AE/BC ) and URF( B/C ) . Thirty-one cases ( 15.58% 31/199 ) had drug-resistant mutations. For NNRTIs, NRTIs and PIs, 20 cases ( 64.52% ) , 2 cases ( 6.45% ) and 9 cases ( 29.03% ) with drug resistance mutations were detected, respectively. The resistance mutations to NNRTIs included K101E, K103N/R, V106I, E138K, V179D/E/T, Y181C, G190A and H221Y. Four cases each had two resistance mutations to NNRTIs. The resistance mutations to NRTIs were V75M and M184V. The resistance mutations to PIs were M46I, L33F and Q58E. For the newly released NNRTI drug Doravirine ( DOR ), two cases were found to have mutations of resistance. @*Conclusions@#The incidence of PDR among newly reported HIV-1 patients in Wenzhou is 8.04%, mainly caused by NNRTIs drug-resistant mutation. Resistance to the new drug DOR has emerged. The surveillance of drug resistance should continue to be strengthened.
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Objective:Due to the limitation of traditional identification methods of Chinese medicinal materials， the study established a rapid method to identify Persicae Semen mixed with Armeniacae Semen Amarum by allele-specific polymerase chain reaction （PCR）. Method:By comparing the ribosomal DNA internal transcribed spacer （ITS） gene sequences of Persicae Semen and Armeniacae Semen Amarum， single nucleotide polymorphism （SNP） sites were searched and specific primers were designed. Different Persicae Semen and Armeniacae Semen Amarum samples were amplified by PCR， the effects of annealing temperature， primer concentration and cycle number on the PCR reaction system were optimized， and the specificity and detection limit of this method were investigated. In addition， the established PCR method was used to detect the samples of Persicae Semen mixed with different proportion of Armeniacae Semen Amarum from different sources and producing areas. Result:A specific PCR method for identifying Persicae Semen mixed with Armeniacae Semen Amarum was established. When the annealing temperature was 63 ℃ and the number of primer cycles was 30， only Armeniacae Semen Amarum could be amplified with 432 bp specific band， while Persicae Semen samples did not have this band. The minimum detection limit of this method for Armeniacae Semen Amarum was 0.2 ng， and the detection limit for Armeniacae Semen Amarum adulterated in Persicae Semen was 1%. Conclusion:The established allele-specific PCR method can accurately detect whether there is Armeniacae Semen Amarum in Persicae Semen， which can provide experimental basis for the quality control of Persicae Semen and guarantee the safety of its clinical use.
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OBJECTIVE: To study the gene sequence characteristics of hantavirus in Heilongjiang Province in order to find out the reasons for the changes of clinical characteristics of hemorrhagic fever with renal syndrome in Heilongjiang Province in recent years.METHODS: Totally 110 rat lung specimens,121 blood specimens from patients diagnosed with mild or atypical HFRS and 100 blood specimens from patients diagnosed with typical HFRS in the First Affiliated Hospital of Harbin Medical University and the Seventh Hospital of Qiqihar City from 2005 to 2015 were collected. The gene sequences were obtained by nucleic acid extraction, RT-NestPCR, and gene sequencing. Explore the possible reasons for the changes in clinical characteristics of HFRS by comparing the obtained sequences with previous strains, homology analysis, building phylogenetic trees of M gene, and finding out the law of nucleotide and amino acid loci changes. RESULTS: TM gene of twenty-six mild or atypical HFRS patients were successfully amplified, including 14 cases of HTN type and 12 cases of SEO type; M gene of twenty-two typical HFRS patients were amplified, including 19 cases of HTN type and 3 cases of SEO type. Compared with the standard strain 76-118, the nucleotide homology of hantavirus from mild or atypical HFRS patients, typical HFRS patients and mice was 74.4%-89.2%, 87.4%-90.3% and 88.1%-88.5%. Comparing hantavirus gene sequence from mice and from patients, the nucleotide homology was 79.7-99.1%. Hljh38 and Hljh39 from patients were significantly different from the other strains. They were the same subtype as Amur virus because they had high homology with Amur strains H5 and H8205(94.9%-97.6%). The deduced amino acids showed some variations compared with the standard strains, but no obvious variation law was observed. CONCLUSION: The reason for the changes of clinical characteristics of hemorrhagic fever with renal syndrome in Heilongjiang province is related to the change of viral type. There are also variations of hantavirus and amino acid, but the relationship between specific variation law and clinical manifestations needs to be further verified.
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Catabacter hongkongensis is an anaerobic gram-positive coccobacillus that was first isolated in Hong Kong. It is infectious and causes high mortality in patients with rare but underlying diseases. Alistipes indistinctus is an anaerobic gram-negative coccobacillus. This bacterium is a common member of the human intestinal microbiota. We report a case of C. hongkongensis and A. indistinctus isolated from blood cultures of a patient with acute appendicitis. A 35-year-old female patient with no specific medical history was admitted to the hospital due to abdominal pain, vomiting, nausea, and diarrhea experienced on the day before admission. On admission, laboratory tests revealed leukocytosis, neutropenia, and elevated C–reactive protein and procalcitonin levels. Following an abdominal computed tomography showing acute appendicitis with suspected perforation, emergency surgery was performed. Growth was observed in two anaerobic blood culture bottles after four days. After further culturing of the bacteria on Brucella Blood Agar, two types of bacteria were obtained. The two bacterial isolates, one gram-positive and one gram-negative, were unable to be identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Thus, 16S rRNA gene sequence analysis was performed, resulting in identification of the bacteria as C. hongkongensis and A. indistinctus. The patient was administered antibiotics and discharged two days after surgery. Although MALDI-TOF MS enables fast and accurate identification of bacteria, C. hongkongensis and A. indistinctus were not listed in the spectral library, and 16S rRNA gene sequence analysis was useful for identifying the two bacteria.
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Adult , Female , Humans , Abdominal Pain , Agar , Anti-Bacterial Agents , Appendicitis , Bacteria , Brucella , Diarrhea , Emergencies , Gastrointestinal Microbiome , Genes, rRNA , Hong Kong , Leukocytosis , Mass Spectrometry , Mortality , Nausea , Neutropenia , Sequence Analysis , VomitingABSTRACT
Objective To assess the significance of screening for inherited metabolic diseases in the treatment and diagnosis of infantile cholestatic hepatopathy,and to analyze the biochemical changed character‐istics of patients who were diagnosed with gene mutations. Methods From January 2016 to January 2017,69 children who were diagnosed as intrahepatic cholestasis in the Pediatric Gastroenterology Department of Shengjing Hospital Affiliated to China Medical University were enrolled. The medical history,physical exami‐nation,biochemical test and genetic metabolism screening results were recorded. Results Sixty‐seven cases of 69 children made tandem mass spectrometry(MS/MS),gas chromatography‐mass spectrometry(GC/MS) or genetic testing. Compared with the normal hereditary metabolic disease screening group, the abnormal group had higher levels of alkaline phosphatase,total bilirubin,direct bilirubin,and total bile acid,the differ‐ence was statistically significant (P<0. 05). The most common abnormal in MS/MS were elevation of free carnitines and arginine,citrulline,methionine,and the most common abnormal in GC/MS were elevation of 3‐hydroxyl propionic acid,4‐hydroxyl phenyllactic acid,4‐hydroxyl phenylacetic acid. In 6 children with posi‐tive genetic test results,the MS/MS and GC/MS of 4 neonatal intrahepatic cholestasis caused by citrin defi‐ciency showed aminoacidemia(citrullinemia,tyrosinemia) and elevations of urine organic acids. Five muta‐tions of SLC25A13 gene were found in the neonatal intrahepatic cholestasis caused by citrin deficiency pa‐tients,including IVS6+5G >A,851del4,IVS11 +1G >A,851 854de and 852 855del. The main clinical manifestations of progressive familial intrahepatic cholestasis type 2 ( PFIC2) were cholestatic jaundice and pruritus,γ‐glutamyl transpeptidase was normal,and with the c. 667C>T defection in the ABCB11 gene. The TALDO1 gene mutation type of one transaldolase deficiency was c. 716G>A and c. 854dupA heterozygous mutation. Conclusion MS/MS and GC/MS play a vital role in the early identification of cholestasis caused by genetic and metabolic disorders. Genetic testing can provide accurate diagnosis for rare genetic metabolic diseases.
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Objective To investigate rickettsiae infection from host animals and vector arthropods in some areas of Yunnan Province. Methods Rat clip and cage traps were used to capture mice. Chiggers from body surface of mice and ticks from body surface of farm cattle were collected. DNAs were extracted from mice spleens, chiggers and ticks. Rickettsiae groEL segment were amplified by nested-polymerase chain reaction (nPCR), sequenced to analyze the homology with other known sequences. Results A total of 410 samples were collected for rickettsiae groEL segment detection with nPCR and 19 samples (4.63%) showed positive for rickettsiae groEL segment . Among them, 2.68%(11/410)were positive for Orientia tsutsugamsushi (Ot) groEL segment, and 1.22%(5/410)were positive for spotted fever group rickettsia (SFGR) groEL segment, and 0.49%(2/410)were positive for rickettsia mooseri (Rm) groEL segment, and 0.24%(1/410)were positive for rickettsia endosymbiont(Re) groEL segment. When analyzed the homology with other known sequences, 11Ot strains with 93.6%-100% similarities among them in this study shared the highest similarity with other Ot strains from GenBank respectively, reached up to 96.1%-100%; The groEL segments of 5 SFGR strains with 92.1%-99.5% similarities among them in this study shared highest similarity with other SFGR strains from other GenBank respectively, reached up to 98.9%-100%; In this study groEL segments of 2 Rm strains all showed 100% similarity with Wilmington strain (GenBank No:AE017197); One groEL segment of Re showed 98.9% similarity with Re strain (GenBank No:EU435143). Conclusion There were kinds of rickettsiaes infection in host animals and vector arthropods in Yunnan Province, so the monitoring and prevention of the Rickettsiosis should be strengthened.
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Objective To analyze the genetic structure and recombination characteristics of a new-ly discovered HIV-1 unique recombinant strain in Yunnan Province. Methods During a test for drug-resist-ant HIV genotypes in Yunnan Province in 2016, a recombinant fragment was found in the pol region of a HIV-1 strain isolated from a patient. Two overlapping segments of the HIV-1 genome were amplified by RT-PCR, and then the products were sequenced. Recombination analysis was performed using RIP, jpHMM and SimPlot3. 5 software. A phylogenetic tree was constructed for homology analysis by Neighbor-joining method using MEGA6. 06 software. Results A nearly full-length HIV-1 gene sequence with 8590 bp in length was obtained. Breakpoint analysis indicated that the sequence consisted of CRF01_AE and fragments of B and C subtypes. CRF01_AE was used as the backbone with B and C subtype fragments inserted. The positions were 791 to 1171 for CRF01_AE, 1172 to 2652 for C subtype fragment, 2653 to 2977 for B subtype frag-ment, and 2978 to 9380 for CRF01_AE using HIV-1 HXB2 as the reference strain. Conclusions Some new strains formed by cross-recombination of CRF01_AE and B and C subtypes were discovered in Yunnan Province in recent years. It was found that the recombination pattern of the newly discovered strain was com-plex, suggesting that close attention should be paid to the changes in epidemic trends, which was of great im-portance to understand the current prevalence and epidemic trends of HIV-1.
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Objective@#To understand the epidemiological characteristics of outbreaks and analyze the genetic characteristics of the whole genome of influenza H3N2 virus among avian-human-swine, and to elaborate the source of influenza virus.@*Methods@#The epidemic information was collected using the case investigation, the pharyngeal swab samples from influenza-like-illness cases were detected by real-time PCR and virus isolation. The phylogeny and molecular features of whole-genome were analyzed with EditSeq and MEGA 5.05 software.@*Results@#The prevalence rate of this outbreak was 34.88%, 15 samples of throat swabs were collected, the positive rate of nucleic acid detection was 73.33%, 5 strains of seasonal influenza A (H3N2) influenza viruses were isolated. The phylogenetic analysis showed the eight gene segments of the isolated influenza viruses belonged to the same cluster with 2015-2016 influenza vaccine strain A/Switzerland/9715293/2013(H3N2), and no recombination was found. Compared with vaccine strain, 14 variant amino acids of protein of HA were identified, and 8 of them were located in antigenic sites. All strains were sensitive to neuraminidase inhibitors while they showed resistance to blockers of M2 ion channel. The glycosylation sites analysis showed that two new glycosylation sites NRT151-153 and NAT245-247were added.@*Conclusions@#The outbreak was caused by seasonal influenza A (H3N2) virus which had an antigenic drift and no genetic avian-human-swine recombination was found.
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We investigated epidemiological characteristic of scrub typhus in Yongshan County,Yunnan Province,China. The serum samples were collected from the patients with fever for detecting the antibody against Orientia tsutsugamsushi (Ot) by colloidal gold immunoassay assay.Rat traps were used to capture rodents.The spleen tissues of the captured rodents were detected by nested-polymerase chain reaction for rickettsia groEL segment.The groEL segments were sequenced and analyzed the homology with the other known sequences.Thirty-four scrub typhus cases were found in Yongshan County,Yunnan Prov-ince from May 2015 to October 2015.Among them,21 cases were confirmed by laboratory tests and 13 cases were clinical di-agnosis diseases.Of these patients,32.35% of the cases occurred in June.The 32.35% were in the group of the 40-49 year-old,and 79.41% were farmers,94.12% exhibited eschar or skin ulcer(31.25% were observed in groin of these cases),and rash developed in 50%.In 39 spleen tissue samples of Rattus flavipectus,9 samples showed positive for groEL gene Ot,but gro-EL gene of Typhus group rickettsia and spotted fever group rickettsia were negative.Sequence analysis showed that YSP30 was closely related to some Saitama related strains of Ot,such as HSB1,FAR1 and UAP4,while the other 8 strains were closely related to some Karp related strains of Ot,such as UT213,UT221 and SH205.It was confirmed that the Yongshan County was the natural foci of scrub typhus by the serological and molecular biological detections.There are Karp and Saitama genotype related Ots in the natural foci.
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Objective The sequence characteristics and polymorphism of the UL141 gene may help find the pathogenesis of human cytomegalovirus (HCMV) infection.This study was to charac-terize the sequences of HCMV UL141 in low-passage clinical isolates in Guangzhou . Methods We collected urine samples from 10 in-fants with clinically confirmed HCMV infection in the Guangzhou are-a, isolated low-passage clinical virus strains and identified them by multiplex PCR.We performed amplification, cloning, identification and sequencing of the HCMV UL141 gene and searched the GenBank for its homologous sequences followed by sequence analysis . Results The HCMV UL141 gene was found to have 2 open reading frames( ORF) , UL141a and UL141b, composed of 315 and 1017 nucleotides and included in the GenBank with the sequence numbers of DQ180372 and DQ180371, respectively.The full length of the UL141 gene in the low-passage HCMV clinical strain (D3) was 1277 bp, the coding protein consisting of 338 amino acid residues , and the full lengths of the ORFs UL 141a and UL141b were 315 bp and 1017 bp, respectively, with relatively conservative DNA sequences .Mutations were identified in 46 sites with base substitution but no insertion or deletion .The modification sites in all the isolated strains were relatively conservative after translation of the HCMV UL 141 coding protein.The isoelectric points of the UL141 protein were 8.36-8.68 for all the clinical isolates. Conclusion Polymorphism exists in the UL141 gene and its amino acid sequences of the HCMV low-passage clinical strains isolated from infants in Guangzhou , which has shed some light on the function of the ULl 41 protein and pathogenesis of HCMV infection .
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We investigated the complete genome characteristic of the Hantaan virus strain AYW89-15 isolated in Jiangxi Province,China.Primers were designed and were used to amplify the complete S,M and L segments by RT-PCR.The PCR product were then cloned and sequenced,the gene sequences were analyzed with DNAStar and MEGA6.0 software.Result showed that the complete gene sequence was 11 848 nucleotides in length,the S,M and L segments were 1 699 nt,3 616 nt and 6 533 nt respectively,encoding 429,1 133 and 2 151 amino acids respectively.The sequence identities between stain AYW89-15 and other Hantaan virus were 79.7％-87.3％ at the nucleotide level and 92.3％-98.4％ at the amino acid level.Phylogenetic analysis of HV showed AYW89-15 belonged to a new HTNV lineage.AYW89-15 was a new subtype of HTNV that exists in Jiangxi Province.
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To understand pathogen spectrum of nontuberculosis Mycobacteria (NTM) and the dominant NTM in Gansu Province and provide the scientific basis for the effective prevention and treatment of NTM diseases,875 Mycobacteria isolates were collected from 2012 to 2014 in Lanzhou Pulmonary Hospital,NTM species were identified by means of PNB/TCH differentiate medium and 16S rRNA gene sequence analysis respectively.Forty-six isolats of NTM were identied from 875 PNB/TCH.Then with 16S rRNA gene sequence analysis,the NTM strains were identified to 3 strains of Nocadia and 43 strains of NTM,including M.intracellulare,M.kansasii,M.avium,M.senegalense,M.gordonae,M.szulgai,M.peregrinumand M.fortuitum.Among them,there were 31 strains of M.intracellulare,which accounted for 72.09％ of the total number of NTM strains.The dominant nontuberculosis Mycobacteria in Gansu Province were mainly M.intracellulare.The application of molecular biology can rapidly and accurately identify the species of nontuberculosis Mycobacteria,and can provide relevant evidence for clinical diagnosis and therapy.
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Objective The sequence characteristics and polymorphism of the UL141 gene may help find the pathogenesis of human cytomegalovirus (HCMV) infection.This study was to charac-terize the sequences of HCMV UL141 in low-passage clinical isolates in Guangzhou . Methods We collected urine samples from 10 in-fants with clinically confirmed HCMV infection in the Guangzhou are-a, isolated low-passage clinical virus strains and identified them by multiplex PCR.We performed amplification, cloning, identification and sequencing of the HCMV UL141 gene and searched the GenBank for its homologous sequences followed by sequence analysis . Results The HCMV UL141 gene was found to have 2 open reading frames( ORF) , UL141a and UL141b, composed of 315 and 1017 nucleotides and included in the GenBank with the sequence numbers of DQ180372 and DQ180371, respectively.The full length of the UL141 gene in the low-passage HCMV clinical strain (D3) was 1277 bp, the coding protein consisting of 338 amino acid residues , and the full lengths of the ORFs UL 141a and UL141b were 315 bp and 1017 bp, respectively, with relatively conservative DNA sequences .Mutations were identified in 46 sites with base substitution but no insertion or deletion .The modification sites in all the isolated strains were relatively conservative after translation of the HCMV UL 141 coding protein.The isoelectric points of the UL141 protein were 8.36-8.68 for all the clinical isolates. Conclusion Polymorphism exists in the UL141 gene and its amino acid sequences of the HCMV low-passage clinical strains isolated from infants in Guangzhou , which has shed some light on the function of the ULl 41 protein and pathogenesis of HCMV infection .
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Aims: The aim of this study was to isolate and identify the yeast and mold strains from the starter and to investigate their amylolytic activity. Methodology and results: Thirty-two yeasts were isolated from ten samples of look-paeng khao-mak, a traditional starter culture in the production of khao-mak (sweet rice) in several places in Thailand. All isolates were identified based on their morphological and biochemical characteristics including the sequencing of D1/D2 domain of large subunit (26S) ribosomal DNA analyses. They were identified as Saccharomycopsis fibuligera (9 isolates), Candida rugosa (2 isolates), C. tropicalis (1 isolate), Clavispora lusitaniae (1 isolate), Wickerhamomyces anomalus (15 isolates) and Meyerozyma guilliermondii (4 isolates). All isolates of S. fibuligera showed high amylolytic activity. One-hundred isolates of mold were isolated from twenty-one samples of look-paeng khao-mak. They were belonged to Amylomyces sp. (42 isolates), Rhizopus sp. (30 isolates), Mucor sp. (12 isolates) and Penicillium sp. (16 isolates) based on their morphological characteristics. Four isolates, LK4-1, LK8-2, LK12-5 and LK17-1 showed amylase activity ranged from 32.24 to 39.74 unit/mL by dinitrosalicylic acid (DNSA) method. The isolates LK4-1, LK8-2 and LK12-5 were identified as Amylomyces rouxii and LK17-1 was Rhizopus microsporus based on their morphological characteristics and the ribosomal RNAencoding DNA (rDNA) internal transcribed spacer (ITS) sequences. Conclusion, significance and impact study: The characterization and evaluation of yeast and mold species based on their phenotypic and genetic characteristics including their amylase activity will be useful for the diversity and sweet rice production.
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Triazoles are the most widely used antifungal drugs in clinic with broad spectrum and high efficacy,which targets sterol 14α-demethylase (CYP51),an enzyme expressed by the gene EGR11,which is a key enzyme in the fungi ergos-terol biosynthesis.On the one hand,the CYP51 belongs to a transmembrane protein.It is difficult to get the exact functional structure conformation which becomes a big challenge for the development of new drugs.On the other hand,it becomes con-sensus that EGR11 exon mutation cause CYP51 structural change is one of the major reasons for antifungal drugs resistance. Therefore,study of the structural changes toward the antifungal drug resistance is quite important.The review authors have summarized the research progress on CYP51 over the recent years.
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Objective To detect the genotype of hepatitis C virus(HCV)in chronic hepatitis C(CHC)infection patients using gene sequence method and observe the distributive characteristic of HCV genotype in Hubei.Methods A total of 447 HCV-RNA-positive plasma samples were collected from chronic hepatitis C patients in Infectious Diseases Department of Renmin Hospital of Wuhan University from February 2013 to July 2015.Then NS5B region gene sequence of HCV genome were de-tected by Sanger sequencing method and compared with HCV genotype in NCBI genebank database for analyzing HCV geno-type.Results A total of 11 kinds of genotypes were detected,including genotypes 1a,1b,2a,3a,3b,6a,6b,1b/2a,1b/2k,6a/1b and 6d/6k,respectively.Detection cases of various genotypes were respectively 7 cases (1.57%),325 cases (72.71%),67 cases (14.99%),7 cases (1.57%),20 cases (4.47%),14 cases (3.13%),2 cases (0.45%),2 cases (0.45%),1 case (0.22%),1 case (0.22%)and 1 case (0.22%).Conclusion Genotype 1b was the major type of HCV-RNA genotype,fol-lowed by 2a,also other genotypes existed,which prompted that the prevalence of HCV genotype was diversity in Hubei.
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The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of multiple gene sequence analysis based on genes of DNA repair pathway was used to compare bacterial genomes. Housekeeping and DNA repair genes were searched in 872 completely sequenced bacterial genomes. Seven DNA repair and housekeeping genes from distinct metabolic pathways were selected, aligned, edited and concatenated head-to-tail to form a super-gene. Results showed that the multiple gene sequence analysis using DNA repair genes had better resolution at class level than the housekeeping genes. As housekeeping genes, the DNA repair genes were advantageous to separate bacterial groups at low taxonomic levels and also sensitive to genes derived from horizontal transfer.
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Objective To compare Vitek2 Compact and Walkaway 40 in the identification of Brucella.Methods Used Vitek2 Compact and Walkaway 40 automated microbial identification system to identify clinical isolates and compared with the de-tection of 16S rRNA gene sequences analysis.Results The clinical isolates was identified as Bergeyella zoohelcum or Moraxella by Walkaway 40 and as Brucella melitensis by Vitek2 Compact.16S RNA sequence analysis of the isolate,the se-quence was identical to the sequences of 16S rRNA of Brucella,which excluded the possibility of B.zoohelam and Moraxel-la .Determined that the isolate was B.melitensis.Conclusion Vitek 2 Compact can accurately identified Brucella.Use molec-ular methods to corroborate when the isolates was identified as Brucella by Vitek 2 Compact,this method can greatly im-prove the detection rate of brucellosis and reduce the possibility of misdiagnosis.Walkaway 40 cannot accurately identified Brucella,Misidentification of Brucella can result in wrong treatment of the patient and let the staff in the risk of laboratory-acquired infection.Recommend laboratory should be cautious reporting in the identified B.zoohelam or Moraxella by Walk-away 40 and use Vitek2 Compact or molecular methods for review.