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Objective:To investigate the phylogenetic and antigenic characteristics of hemagglutinin (HA) gene of influenza B/Victoria lineage (BV) viruses in Beijing during the 2021-2022 influenza surveillance season, and to analyze whether the circulating BV viruses match the vaccine strain.Methods:Pharyngeal swab specimens from influenza like-illness (ILI) cases in the 2021-2022 influenza surveillance season were collected from surveillance network labs in Beijing and cultured in MDCK cells and chicken embryo to isolate BV viruses. Nucleic acids of the viruses were extracted, and the HA gene was amplified and sequenced. The nucleotide and amino acid sequence identity of the HA gene was analyzed using MEGA5.0 software. A phylogenetic tree of HA gene was constructed using the maximum likelihood method. The N-glycosylation sites in HA were predicted online. Three-dimensional structure of HA was constructed using SWISS-MODEL homologous modeling. Hemagglutination inhibition (HI) test was performed to analyze the antigenicity of BV viruses.Results:A total of 402 BV viruses were collected and 58 strains with full-length HA gene sequences were chosen for further analysis. Compared with the HA gene of this year′s vaccine strain (B/Washington/02/2019), there were 27 amino acid mutations, 11 of which were located in four different antigenic determinants. The phylogenetic analysis revealed that three subgroups of 1A.3, 1A.3a1, and 1A.3a2 co-circulated in Beijing with 54 strains (54/58, 93.10%) clustered to the Clade 1A.3a2, two strains (2/58, 3.45%) clustered to the Clade 1A.3a1, and two strains (2/58, 3.45%) in the same subgroup (Clade 1A.3) as the vaccine component BV strain in 2021-2022. Compared with the vaccine strain (B/Washington/02/2019), two BV strains had an additional N-glycosylation site at residue 197, while the other 56 strains showed no change in N-glycosylation sites. Antigenic analysis showed that 35 BV strains (35/58, 60.34%) were antigenically similar to the vaccine strain and 23 strains (23/58, 39.66%) were low-response strains.Conclusions:Three subgroups of BV viruses co-circulated in Beijing during the 2021-2022 influenza surveillance season. The predominant subgroup was Clade 1A.3a2 (93.10%), showing a certain genetic distance with the vaccine strain (B/Washington/02/2019). Nearly 40% (39.66%) of the viruses were low-response strains. This study indicated that continuous monitoring of the variations of influenza epidemic strains and timely providing laboratory basis for screening vaccine component strains were the basic technical guarantee for coping with influenza pandemic.
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Objective:To clarify the M protein ( emm gene) types and drug susceptibility characteristic variations of Group A Streptococcus (GAS) in children in Beijing. Methods:The GAS strains isolated from throat swab samples of children diagnosed with scarlet fever and pharyngeal infection in scarlet fever etiology surveillance sentinel hospitals in 16 districts of Beijing in 2018, 2019 and 2021 were analyzed retrospectively.PCR amplification and sequencing were used for emm genotyping, and the minimum inhibitory concentrations (MIC) of 10 antibiotics were determined by the broth microdilution method.The data were analyzed using χ2 test and Fisher′ s exact method between groups. Results:A total of 557 GAS strains were collected, and 11 emm genotypes ( emm1, emm3, emm4, emm6, emm11, emm12, emm22, emm75, emm89, emm128, and emm212) were detected.Of 557 strains, 238 trains were of emm1 type (42.73%), 271 strains were of emm12 type (48.65%) and 48 strains were of other emm types (8.62%). The detection rates of emm1, emm12 and other emm type genes in 2018, 2019, and 2021 were [37.50% (105/280 strains), 57.14% (160/280 strains), 5.36% (15/280 strains)], [49.05% (129/263 strains), 39.54% (104/263 strains), 11.41% (30/263 strains)], and [28.57% (4/14 strains), 50.00% (7/14 strains), 21.43% (3/14 strains)], respectively.In children infected with emm12 in 2018 and 2019, there were more children under 6 years old than children over 6 years old (62.50% vs.46.88%, 46.36% vs.30.36%) (χ 2=7.182, 6.973; all P<0.05). Drug susceptibility testing results suggested that 225 randomly selected GAS strains were all 100.00% sensitive to 7 antibiotics including Penicillin, Levofloxacin, Meropenem, Linezolid, Cefotaxime, Cefepime and Vancomycin.The rates of resistance to Erythromycin, Tetracycline and Clindamycin were [88.57% (93/105 strains), 87.62% (92/105 strains), 86.67% (91/105 strains)], and [94.34% (100/106 strains), 94.34% (100/106 strains), 87.74% (93/106 strains)] in 2018 and 2019, respectively.The test strains were 100.00% (14/14 strains) resistant to the above 3 antibiotics in 2021.MIC 50 and MIC 90 values of Penicillin in 2018, 2019, and 2021 were (0.03 mg/L, 0.03 mg/L), (0.03 mg/L, 0.06 mg/L), and (0.06 mg/L, 0.06 mg/L), respectively.Among 225 GAS strains, 207 strains had drug resistance and were resistant to more than one drug.Specifically, 94.69% (196/207 strains) were resistant to Erythromycin, Tetracycline and Clindamycin.About 4.35% (9/207 strains) were resistant to both Erythromycin and Clindamycin.A total of 0.97% (2/207 strains) were resistant to Erythromycin and Tetracycline. Conclusions:The emm genotypes of GAS in children in Beijing are diverse in 2018, 2019 and 2021.The dominant genotypes are emm12 and emm1, and emm12 is the main epidemiological type.GAS strains maintain highly resistant to Erythromycin, Clindamycin and Tetracycline, and sensitive to Penicillin and other antibiotics.However, MIC 50 and MIC 90 of Penicillin shows an ascending trend.
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Objective@#To understand the antigenicity and genetic characterization of influenza B virus HA gene in B/Victoria-lineage virus (BV) in Beijing during 2017-2018.@*Methods@#Thirty BV virus strains isolated from MDCK cell culture by 17 laboratories in Beijing were collected. The antigenicity was analyzed by comparing with the vaccine strain recommended by WHO. The total viral nucleic acid was extracted and HA gene was amplified by RT-PCR and sequenced. The phylogenetic tree was constructed by HA and mutant sites were analyzed.@*Results@#Among 30 strains of BV, 23 strains (76.7%) were low-reactive strains, other 7 strains (23.3%) were related to the vaccine. The phylogenetic analysis showed that the HA gene of all 30 strains located in Clade 1A branch. In addition, amino acid mutations occurred in 8 sites, and 6 of them located in the antigen determining region.@*Conclusions@#There was a correlation between the high proportion of low-reactive antigenicity and 6 aa variation in antigenic determinants involved in HA region of BV influenza virus between 2017-2018, which provides an important laboratory basis for the recommendation of BV influenza vaccine.
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Objective: To establish a classified evaluation system for recognizing the levels of influenza epidemics and to explore the new reporting system on influenza epidemics. Methods: The following 3 indicators, including 1) the number of influenza-like illness, 2) positive rate of detection on influenza virus nucleic acids, and 3) the number of influenza outbreaks were chosen to calculate the synthetic index and to classify the grades of evaluation. Results: 209 weeks during 2013-2017 were classified into 5 grades: Grade 1 were 110 weeks (52.63%), Grade 2 were 47 weeks (22.49%), Grade 3 were 44 weeks (21.05%), Grade 4 were 8 weeks (3.83%), and Grade 5 were 0 week. Conclusion: This classified evaluation system provided simple, comprehensive and comparable reference indicators and used for the evaluation on influenza epidemics, also providing suggestions for influenza prevention and control accordingly.
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Humans , Beijing/epidemiology , Disease Outbreaks , Epidemics , Influenza, Human/epidemiology , Population Surveillance , Virus DiseasesABSTRACT
Objective: To analyze the characteristics of super-antigen (SAg) of group A Streptococcus pyogenes (GAS), isolated from patients with scarlet fever or pharyngeal infections in Beijing between 2015-2017. Methods: Throat swab specimens from patients with scarlet fever or pharyngeal infections were collected and tested for GAS. Eleven currently known SAg genes including SpeA, speC, speG, speH, speI, speJ, speK, speL, speM, smeZ and ssa were tested by real-time PCR while M protein genes (emm genes) were amplified and sequenced by PCR. Results: A total of 377 GAS were isolated from 6 801 throat swab specimens, with the positive rate as 5.5%. There were obvious changes noticed among speC, speG, speH and speK in three years. A total of 45 SAg genes profiles were observed, according to the SAgs inclusion. There were significant differences appeared in the frequencies among two of the highest SAg genes profiles between emm1 and emm12 strains (χ(2)=38.196, P<0.001; χ(2)=72.310, P<0.001). There also appeared significant differences in the frequencies of speA, speH, speI and speJ between emm1 and emm12 strains (χ(2)=146.154, P<0.001; χ(2)=52.31, P<0.001; χ(2)=58.43, P<0.001; χ(2)=144.70, P<0.001). Conclusions: Obvious changes were noticed among SAg genes including speC, speG, speH and speK from patients with scarlet fever or pharyngeal infections in Beijing between 2015-2017. SAg genes including speA, speH, speI and speJ appeared to be associated with the emm 1 and emm 12 strains. More kinds of SAg genes profiles were isolated form GAS but with no significant differences seen in the main SAg genes profiles, during the epidemic period.
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Female , Humans , Pregnancy , Antigens, Bacterial/genetics , Bacterial Outer Membrane Proteins , Bacterial Proteins , Beijing/epidemiology , China/epidemiology , Exotoxins , Membrane Proteins , Pharyngitis/microbiology , Pharynx/microbiology , Pregnancy Complications, Infectious/microbiology , Real-Time Polymerase Chain Reaction , Scarlet Fever/microbiology , Streptococcal Infections , Streptococcus pyogenes/isolation & purification , Superantigens/geneticsABSTRACT
Objective To establish a classified evaluation system for recognizing the levels of influenza epidemics and to explore the new reporting system on influenza epidemics.Methods The following 3 indicators,including 1) the number of influenza-like illness,2) positive rate of detection on influenza virus nucleic acids,and 3) the number of influenza outbreaks were chosen to calculate the synthetic index and to classify the grades of evaluation.Results 209 weeks during 2013-2017 were classified into 5 grades:Grade 1 were 110 weeks (52.63％),Grade 2 were 47 weeks (22.49％),Grade 3 were 44 weeks (21.05％),Grade 4 were 8 weeks (3.83％),and Grade 5 were 0 week.Conclusion This classified evaluation system provided simple,comprehensive and comparable reference indicators and used for the evaluation on influenza epidemics,also providing suggestions for influenza prevention and control accordingly.
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Objective To analyze the characteristics of super-antigen (SAg) of group A Streptococcus pyogenes (GAS),isolated from patients with scarlet fever or pharyngeal infections in Beijing between 2015-2017.Methods Throat swab specimens from patients with scarlet fever or pharyngeal infections were collected and tested for GAS.Eleven currently known SAg genes including SpeA,speC,speG,speH,speI,speJ,speK,speL,speM,smeZ and ssa were tested by real-time PCR while M protein genes (emm genes) were amplified and sequenced by PCR.Results A total of 377 GAS were isolated from 6 801 throat swab specimens,with the positive rate as 5.5％.There were obvious changes noticed among speC,speG,speH and speK in three years.A total of 45 SAg genes profiles were observed,according to the SAgs inclusion.There were significant differences appeared in the frequencies among two of the highest SAg genes profiles between emml and emml2 strains (x2=38.196,P＜0.001;x 2=72.310,P＜0.001).There also appeared significant differences in the frequencies of speA,speH,speI and speJ between emm 1 and emm 12 strains (x2 =146.154,P＜ 0.001;x2=52.31,P＜0.001;x2=58.43,P＜0.001;x2=144.70,P＜0.001).Conclusions Obvious changes were noticed among SAg genes including speC,speG,speH and speK from patients with scarlet fever or pharyngeal infections in Beijing between 2015-2017.SAg genes including speA,speH,speI and speJ appeared to be associated with the emm 1 and emm 12 strains.More kinds of SAg genes profiles were isolated form GAS but with no significant differences seen in the main SAg genes profiles,during the epidemic period.
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Objective@#To analyze the prevalence and drug resistance of mycoplasma pneumoniae in patients with community-acquired pneumonia during 2011-2015 in Beijing.@*Methods@#Totally 2 272 mycoplasma pneumoniae samples were collected from patients with community-acquired pneumonia in 5 sentinel hospitals during 2011-2015. Mycoplasma pneumoniae were detected by real-time PCR. 142 copies of positive samples with Ct value under 30 were cultured to get the strains so that the genotypes based on the P1 gene sequence and the drug resistance based on the in vitro drug resistance test could be conducted. χ2 test was used to compare the detection rates of mycoplasma pneumoniae among different age groups and different onset-phase.@*Results@#The positive rate of mycoplasma pneumoniae was 13.6%(308 cases). The positive rate in groups aging (5-14), (15-24) and ≥60 years old were separately 24.4% (67/275), 24.4% (38/156) and 3.9% (28/727) (χ2=1.22, P<0.001). The annual detection rate of mycoplasma pneumoniae in 2011-2015 were 14.6% (73/501), 10.2% (36/353), 26.4% (101/383), 10.3% (41/398), 9.0% (57/637),respectively (χ2=72.65, P<0.001). Seasonally, the peak of positive rate was between October and December (17.5%, 122/699) and the lowest positive rate was between April and June (8.6%, 43/502). 36 strains were isolated from 142 swabs and 23 (63.9%) were P1-Ⅰ and 13 (36.1%) were P1-Ⅱ by genotyping. All isolates were susceptible to the fluoroquinolones (levofloxacin, ciprofloxacin, and gatifloxacin) and tetracycline. All P1-Ⅱ strains were susceptible to macrolides while most of the P1-Ⅰ strains (22 strains) were macrolide-resistant.@*Conclusion@#People aging (5-14) and (15-24) years old were more susceptible to mycoplasma pneumoniae in patients with community-acquired pneumonia in Beijing between 2011 and 2015. The highest positive rate of mycoplasma pneumoniae was in 2013 and the case distributed in all seasons. The major popular genotype was P1-Ⅰ, whose strains were mostly macrolide-resistant.
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Objective To reveal the genetic distribution of group A streptococcus progeny(GAS)isolated from children with re-spiratory tract infection in Beijing in 2015.Methods The throat swabs were collected from children with clinical diagnosis of scarlet fever and pharyngeal infection during May to July,2015.16 pediatric outpatient departments or pediatric emergency department of hospitals located in 16 districts of Beijing were enrolled in this study.PCR amplification and gene sequencing were employed.The encoding mature M protein gene(emm)distribution in different condition was compared and analyzed.Results A total of 247 GAS were isolated,including 73(29.6%,73/247)isolates from cases with scarlet fever and 174(70.4%,174/247)isolates from cases with pharyngeal infection.Among all isolates,six genotypes of emm were identified,including emm12(53.4%,132/247),emm1(44. 1%,109/247)and others(emm22,emm75,emm131 and emm241,2.5%,6/247).The significant difference of emm distribution with age was observed in this study:emm1 isolates were dominant in children aged 6-12,whereas emm12 isolates were dominant in chil-dren aged 1-5(P<0.05).While the emm distribution showed no significant difference in groups with different location,gender,and disease pattern(P>0.05).Conclusion Emm1 and emm12 were the circulating genotype of GAS in Beijing children,2015.Moreo-ver,the difference of distribution between emm1 and emm12 was proved in this study.
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Objective To investigate the genetic characteristic of whole-genome of influenza A/H3N2 viruses in severe acute respiratory infection cases in Beijing area.Methods From 2014 to 2016,the viral RNA was extracted from 32 strains isolated from SARI cases,then sequenced by Ion Torrent PGM Sequencer.The phylogeny and molecular features of whole-genome were analyzed by Mega and Consurf software.Results The HA gene of tested strains isolated in 2014-2015 influenza season belonged to lineage 3C.3a and 3C.2a,while those isolated in 2015-2016 influenza season belonged to cluster 3C.2a.Moreover,compared with the vaccine strains,7 variant amino acids of protein of HA1 were identified,and two of them were located in antigenic sites.All isolates were sensitive to neuraminidase inhibitors while showed resistance to blockers for M2 ion channel.Conclusion The phylogenetic features of isolates studied in this study are similar with that of current circulating strains.However,the difference between isolates and vaccines should not be overlooked.
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<p><b>OBJECTIVE</b>To understand the distribution of emm gene types related to group A streptococcus-caused scarlet fever among children in Beijing and to analyze the relationship between the mutation of the emm types and scarlet fever.</p><p><b>METHODS</b>Nasopharyngeal swab samples were collected from the scarlet fever cases diagnosed in 36 hospitals in Beijing to isolate the GAS strains from May to July, betgween 2011 and 2014. Genotyping of emm gene was performed with PCR and N-terminal gene fragments of M protein were sequenced. Data of all the scarlet fever cases in Beijing that reported through the National Notifiable Infectious Disease Surveillance System (NNIDSS) , were gathered and analyzed.</p><p><b>RESULTS</b>Among the collected 2 161 nasopharyngeal swabs, 762 GAS strains were identified (35.3%). In addition, 7 emm types were detected, in which emm12 accounted for 69.4% (529/762) , emm1 accounted for 29.8% (227/762) , and other five types (emm 11, 22, 75, 89, and 128) accounted for 0.8% (6/762) , respctively. Compared with the emm types detected between 2011 and 2014, emm12, emm1 and other types accounted for 82.2% (295/359) , 16.7% (60/359) and 1.1% (4/359, including emm11, 22 and 89) in 2011 respectively.emm12, emm1 and emm75 accounted for 77.3% (123/163) , 23.9% (39/163) and 0.6% (1/163) respectively in 2012. emm12 and emm1 accounted for 50.7% (38/75) and 49.3% (37/75) in 2013 while emm12, emm1 and emm128 accounted for 44.2% (73/165) , 55.2% (91/165) and 0.6% (1/165) respectively in 2014. The differences of the constitution of emm types from 2011 to 2014 appeared statistically significant (P<0.001). In 2011 and 2012, major type appeared as emm12, but in 2014, emm1 became predominant. A total of 6 152 cases were reported in 2011, while 2 908, 2 048 and 3 918 cases were reported in 2012, 2013 and 2014 respectively. Age specific differences were noticed in the distribution of emm types GAS strains in 2011, with the number of emm12 strains detected higher in 1-5 year olds than in age group > 5 years (P<0.05). There were area specific differences in distribution of emm types of GAS strains seen in 2011 and 2013. In 2011, the number of emm1 strains detected in urban area was higher than in suburb area (P<0.05). However, in 2013, the number of emm1 strains detected in suburb area was seen higher than in urban area (P< 0.05).</p><p><b>CONCLUSION</b>GAS with emm12 and GAS emm1 appeared interchangeably predominant in Beijing from 2011 to 2014. Changes in predominant emm types seemed also related to the trends of incidence rates on scarlet fever.</p>
Subject(s)
Child , Humans , Antigens, Bacterial , Bacterial Outer Membrane Proteins , Beijing , Epidemiology , Carrier Proteins , Genotype , Mutation , Scarlet Fever , Epidemiology , Genetics , Streptococcus pyogenes , Classification , GeneticsABSTRACT
Objective To explore the relationship between superantigen and M protein gene (emm)-types genes of Group A Streptococcus pyogenes (GAS) isolated from patients with scarlet fever in Beijing from May 2012 to July 2013 .Methods GAS was isolated from specimens of patients with scarlet fever . Superantigen genes (speA ,speB ,speC ,speF ,speG ,speH ,speI ,speJ ,speL ,speK ,speM ,ssa ,and smeZ) ,and emm gene were amplified by polymerase chain reaction .Rate and proportion were compared by chi-square test .Results Of the 423 GAS strains isolated from patients with scarlet fever from 2012 to 2013 ,most of the isolates possessed speB (97 .6% ) ,speC (99 .8% ) ,speF (98 .3% ) ,speG (99 .8% ) , smeZ (94 .1% ) and ssa (88 .4% ) ,and some of them possessed speH (54 .6% ) ,speI (53 .4% ) ,speA (45 .2% ) and speJ (43 .5% ) ,but very few isolates possessed speK (2 .4% ) ,speL (1 .4% ) and speM (1 .7% ) .Type emm12 (59 .5% ) and type emm1 (37 .4% ) were the main types of GAS .Most of the emm12-type isolates possessed speH (84 .8% ) and speI (84 .0% ) compared with only 4 .0% of speH and 3 .4% of speI in type emm1 .Most of type emm1 possessed speA (95 .3% ) and speJ gene (94 .6% ) compared with only 17 .3% of speA and 14 .8% of speJ in type emm12 .The superantigen genes profiles were significant different between emm 1-type and emm 12-type isolates (P< 0 .05) .Conclusion Type emm1 and type emm12 are epidemic strains in patients with scarlet fever from 2012 to 2013 in Beijing ,and emm gene-types are associated with superantigen genes profiles .
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Objective To screen a sensitive method for detecting respiratory viruses from three different methods of singleplex conventional PCR , multiplex conventional PCR and multiplex real-time RT-PCR.Methods Parallel examination of 17 respiratory viruses was performed on 73 throat swab specimens collected from patients with upper respiratory tract infection by the three methods .The detection rates of dif-ferent respiratory viruses were used as evaluating indicator for the three methods .Results The numbers of respiratory viruses detected by singleplex conventional PCR , multiplex conventional PCR and multiplex real-time PCR were 56, 41 and 87, respectively.Conclusion The multiplex real-time RT-PCR might be used for the detection of respiratory viruses in laboratory as its high detection rate in comparison with the other two methods .
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PURPOSE: To evaluate the feasibility for gold immunochromatographic assay (GICA) in rapid detection of influenza virus A infection. MATERIALS AND METHODS: Seventy-three patients were enrolled. All patients contributed nasopharyngeal secretions and paired serum samples. Nasopharyngeal secretions was used for colloidal gold immunochromatographic rapid assay for influenza A virus immediately after the collection of specimen. Paired serum samples were used for the hemagglutination inhibition assay at the Centers for Disease Control and Prevention influenza network laboratory in Beijing. RESULTS: Compare GICA test to hemagglutination inhibition (HI) assay, the Kappa value was 0.402 and the p value in the paired chi2 test was higher than 0.05. Therefore, the difference was not statistically significant. The sensitivity of GICA was 50.0% and the specificity was 90.2%, and the negative predictive value was 90.2%. CONCLUSION: The sensitivity for Influenza A antigen detection by using GICA is relatively low, the specificity is relatively satisfactory.
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Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Antigens, Viral/blood , Gold Colloid , Chromatography, Affinity/methods , Influenza A virus/immunology , Influenza, Human/diagnosis , Reagent Kits, Diagnostic , Sensitivity and SpecificityABSTRACT
No abstract available.
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To screen and identify the possible pathogen of the firstly confirmed human case of avian influenza A in Beijing, the throat swabs and tracheal aspirates of this case were collected and the H5N1 viral nucleotide was tested with real time RT-PCR. The certification of result, screening of other pathogens in respiratory tract and sub-typing of influenza viruses were made by using re-sequencing microarray. It was found that the H5N1 viral nucleic acid was positive in the tracheal aspirate of this case by means of detection with real time RT-PCR and the specific sequence of the non-structural protein (NS) gene of H5N1 virus was obtained through the detection with re-sequencing clip. Through the comparative study with the sequence in Genbank, it was proved to be the H5N1 nucleic acid of avian influenza viruses and excluded the possibility of infections with 30 subtypes of influenza viruses and 33 other respiratory tract pathogens. It is apparent that the pathogen detection with re-sequencing clip shows the high sensitivity and specificity and it plays an important role in the pathogen screening and identification for the firstly confirmed human case of avian influenza A in Beijing.
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<p><b>OBJECTIVE</b>To establish the RT-PCR method to type the influenza virus.</p><p><b>METHODS</b>After amplifying the virus by cell culture, we carried out RT-PCR by using two pairs typing primers and four pairs subtyping primers to detect the influenza virus.</p><p><b>RESULTS</b>In those 23 samples which had cytopathologic changes, there were 10 positive strains detected by RT-PCR assay including seven A type (six H3N2 subtype and one H1N1 subtype) and three B type.</p><p><b>CONCLUSION</b>This method is rapid, specific and sensitive and possesses great value for practical application in the surveillance of influenza virus.</p>