1.Phylogenetic and antigenic analysis on hemagglutinin gene of influenza B virus (Victoria) in 2023-2024 surveillance season in Beijing
Guilan LU ; Jiachen ZHAO ; Weixian SHI ; Li ZHANG ; Yimeng LIU ; Zhaomin FENG ; Ying SUN ; Daitao ZHANG ; Xiaomin PENG
Chinese Journal of Experimental and Clinical Virology 2024;38(4):415-421
Objective:To disclose phylogenetic and antigenic characteristics of hemagglutinin (HA) gene of influenza B virus (Victoria) (BV) in the 2023-2024 influenza surveillance season in Beijing, and understand the matching with influenza vaccine component strain.Methods:Pharyngeal swab specimens from influenza like-illness (ILI) in the 2023-2024 influenza surveillance season were collected from surveillance network labs in Beijing and BV strains were isolated through MDCK or chicken embryo culture. After extracting nucleic acid, HA gene was amplified and sequenced. The nucleotide and amino acid sequence identity were conducted and the maximum likelihood method in Mega 5.0 software was used to construct the phylogenetic tree of HA gene. N-glycosylation sites of HA were performed online. Furthermore, three-dimensional structure of HA was available from SWISS-MODEL homologous modeling. Hemagglutination inhibition (HI) tests were performed to analyze antigenic characteristics of HA of BV strains.Results:Fifty-four BV strains were randomly selected to be analyzed further. Compared with the HA gene of this influenza season vaccine strain (B/Austria/1359417/2021), there are three amino acid mutations among all BV strains, two of which are located in two different antigenic determinants. Furthermore, the phylogenetic tree analysis revealed that only one subgroup of 1A.3a.2 was circulating simultaneously. All BV strains are located in Clade 1A.3a.2 subgroup, and in the same subgroup with that of the vaccine component BV strain in 2023-2024. All BV strains have the same glycosylation sites as that of the vaccine component BV strain in 2023-2024. Antigenic analysis showed that all BV strains were antigenically similar with its vaccine strain.Conclusions:In the 2023-2024 influenza surveillance season, the prevalent BV strains in the population in Beijing city are located in Clade 1A. 3a. 2 subgroup. The antigen matching between BV epidemic strains and vaccine BV components is relatively high during this surveillance season.
2.Phylogenetic and antigenic analysis of HA gene of influenza virus B (Victoria) in Beijing during 2021-2022 surveillance season
Guilan LU ; Shujuan CUI ; Jiachen ZHAO ; Yimeng LIU ; Weixian SHI ; Zhaomin FENG ; Yang PAN ; Daitao ZHANG ; Peng YANG ; Quanyi WANG ; Xiaomin PENG
Chinese Journal of Microbiology and Immunology 2023;43(8):619-626
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.
3.Preliminary investigation and analysis on the epidemic situation of Redondoviridae in Beijing
Jiachen ZHAO ; Yimeng LIU ; Lin ZOU ; Xiaomin PENG ; Guilan LU ; Cheng QIAN ; Shujuan CUI ; Daitao ZHANG ; Weixian SHI
Chinese Journal of Experimental and Clinical Virology 2023;37(2):135-139
Objective:To understand the epidemic situation of Redondoviridae in Beijing and analyze its epidemiologic characteristics.Methods:Pharyngeal swab samples of healthy people and patients with acute respiratory infection in Beijing, including influenza like cases and severe acute respiratory infection (SARI) cases in hospitals were collected. Real time PCR was used to detect the nucleic acid of Redondoviridae. The positive samples were amplified and sequenced to analyze their species. The age and sex distribution of patients and species distribution of Redondoviridae were obtained through statistical analysis. Multiplex PCR was used to detect other common respiratory pathogens in the positive samples of Redondoviridae in influenza like cases and SARI cases, and the pathogenicity of Redondoviridae was analyzed.Results:The positive rates of Redondoviridae in healthy people and acute respiratory infection cases were 20.48% (189/923) and 11.23% (43/390), respectively, with a statistically significant difference ( P<0.05). The positive rate of male was higher than that of female in the healthy population, and the positive rate of the elderly group was higher than that of the adult group and the underage group, with a statistically significant difference ( P<0.05). The positive rate of male patients with acute respiratory tract infection was higher than that of female patients, but there was no significant difference. The proportion of Vientovirus in the positive samples of Redondoviridae was higher than that of Brisavirus, and the difference was statistically significant ( P<0.05). Among the throat swabs of respiratory tract infection cases, 43 were positive for Redondoviridae, of whom 24 were not detected for other pathogens. Conclusions:Redondoviridae widely exists in healthy people of all age groups in Beijing, and is also found in acute respiratory infection cases. The positive rate of Redondoviridae is different in different ages and genders. Both Vientovirus and Brisavirus were detected, and the proportion of Vientovirus was significantly higher than Brisavirus.
4.Epidemic characteristics and hemagglutinin gene variation of influenza A(H3N2) in Beijing, 2022—2023
Jiachen ZHAO ; Yimeng LIU ; Xiaomin PENG ; Guilan LU ; Shujuan CUI ; Ying SUN ; Daitao ZHANG ; Weixian SHI
Chinese Journal of Experimental and Clinical Virology 2023;37(6):606-612
Objective:To characterize the epidemic of influenza in Beijing from 2022 to 2023 and the variation of gene and antigenicity of hemagglutinin (HA) of influenza A H3N2 virus, so as to provide scientific basis for influenza prevention and control in Beijing.Methods:Statistical analysis was carried out on the result of influenza pathogenic monitoring in Beijing from week 14, 2022 to week 20, 2023, and 79 strains of influenza A H3N2 virus were selected at different time and population sources, and their genetic variation and evolution characteristics were analyzed through HA gene amplification sequencing and antigenicity analysis.Results:From week 14, 2022 to week 20, 2023, 24 244 throat swabs of influenza like cases were collected in Beijing, and 4 987 influenza virus nucleic acid positive cases were detected, including 2 749 influenza A H3N2 positive cases, with a detection rate of 11.34%. Among the 79 strains, 50 strains (63.29%) showed low response, 94.44% of the strains from August to November 2022 had low response, and 54.10% of the strains from February to March 2023 had low response, with a statistically significant difference ( χ2=8.079, P=0.004). Compared with the vaccine strain A/Darwin/9/2021, the HA gene sequence of 79 strains of influenza A H3N2 showed nucleotide similarity of 97.47% to 98.47% and amino acid similarity of 97.05% to 98.17%. Genetic evolution analysis showed that the 18 strains isolated from August to November 2022 were all distributed in the 3C.2a1b.2a.1a.1 branch, while the 61 strains isolated from February to March 2023 all belonged to the 3C.2a1b.2a.3a.1 branch. Compared with the vaccine strain, there were multiple site mutations distributed at multiple antigenic determinants and receptor binding sites in A, B, C, D, and E. All strains had potential glycosylation sites of 8NST, 22NGT, 38NAT, 45NSS, 63NCT, 126NWT, 133NGT, 246NST, 285NGS, 483NET, while one strain missed 165NVT glycosylation sites; 55 strains between February and March 2023 missed 122NES glycosylation sites. Conclusions:The HA gene locus of influenza A H3N2 virus detected in Beijing from week 14, 2022 to week 20, 2023 showed multiple mutations, continuous monitoring of this subtype variation is crucial.
5.Dosimetry of organs at risk between involved field radiation and extended field radiation in patients with thoracic esophageal cancer
Cheng YUAN ; Mingrui LIU ; Linxin SHI ; Weixian SHAO ; Qiang WANG ; Aonan DU ; Wen ZHANG ; Jianwei SUN ; Hui MIAO
Chinese Journal of Radiological Health 2022;31(2):210-213
Objective To study the irradiation dose of organs at risk (OAR) in involved field radiation and extended field radiation in patients with thoracic esophageal cancer who received intensity modulated radiotherapy (IMRT). Methods A total of 40 patients with thoracic esophageal cancer were treated with IMRT. The involved field, extended field, and OAR were outlined to generate IMRT plans. The conformity index (CI) and homogeneity index (HI) of planning target volume (PTV) and the irradiation parameters of OAR were evaluated for the two plans. Paired t-test was used for comparison of irradiation parameters. Results The PTV of both plans received the prescribed dose. There were no significant differences in CI and HI of PTV between the two groups (P = 0.317, 0.130). There were significant differences in average lung dose, lung V5, lung V20, lung V30, spinal cord Dmean, heart Dmean, heart Dmax, heart V30, heart V40, and heart V60 between the two groups (P < 0.01). Conclusion Compared with the extended field, the involved field can reduce the irradiation dose of ORA in patients with thoracic esophageal cancer, thus reducing the risk of radiation.
6.Analysis of emm genotypes and drug susceptibility characteristic variations of Group A Streptococcus in children in Beijing
Jiachen ZHAO ; Yimeng LIU ; Xiaomin PENG ; Shujuan CUI ; Guilan LU ; Weixian SHI ; Chunna MA ; Fu LI ; Daitao ZHANG ; Quanyi WANG ; Peng YANG
Chinese Journal of Applied Clinical Pediatrics 2022;37(21):1645-1650
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.
7.Establishment of a nested PCR assay for the detection of 2019 novel coronavirus and its preliminary application
Weixian SHI ; Zhaomin FENG ; Shujuan CUI ; Yang PAN ; Cheng QIAN ; Ruolei XIN ; Peng YANG ; Quanyi WANG ; Daitao ZHANG ; Zhiyong GAO
Chinese Journal of Experimental and Clinical Virology 2022;36(2):214-218
Objective:To establish a nested PCR method to detect the 2019 novel coronavirus (2019-nCoV), as a supplement to the real-time fluorescent PCR method, and discuss the preliminary application value of this method in clinical diagnosis.Methods:According to the conservative sequences of the 2019-nCoV gene, the nested PCR primers including N gene and S gene, were designed on line. By optimizing the nested PCR reaction systems, the qualitative detection was established by testing N gene and sequencing its PCR product while the preliminary type identification was established by testing S gene and sequencing its PCR product. The sensitivity was evaluated by the gradient dilution of 2019-nCoV positive samples’ nucleic acid and the specificity was evaluated by detecting the human coronavirus OC43, 229E, HKU1, NL63, influenza virus positive samples. The established method was applied to 15 samples with Ct >33 and 15 samples with Ct <33 screened by real-time fluorescent PCR, and the positive amplification result were sequenced and analyzed to verify the result. Results:The established nested PCR method could amplify specific bands of 355 bp N gene fragment and 449 bp S gene fragment. No amplifications occurred in other human coronaviruses samples including 229E、OC43、HKU1、NL63 or in influenza virus samples including H3N2, H1N1(pdm) and B. The minimum detection limit of the N gene fragment could reach Ct value about 37.21. Among the 30 COVID-19 positive samples, the N gene positive coincidence rate detected by nested PCR was 100% (30/30); the S gene positive coincidence rate reached 60% (18/30). 28 samples’ sequences of N gene fragment were completely consistent with 2019-nCoV by BLAST, and the characteristic result of site mutations of 12 samples’ S gene was obtained. Conclusions:A nested PCR method for the specific detection of 2019-nCoV was established, and some characteristic mutations on S gene could be analyzed by sequencing the PCR amplified products. It could be used as a supplement to the real-time fluorescent PCR method.
8. Antigenicity and genetic characterization of HA gene in influenza B/Victoria-lineage virus in Beijing 2017-2018
Xiaomin PENG ; Shujuan CUI ; Jiashen ZHAO ; Yang PAN ; Daitao ZHANG ; Yimeng LIU ; Guilan LU ; Weixian SHI ; Quanyi WANG ; Peng YANG
Chinese Journal of Experimental and Clinical Virology 2019;33(4):337-341
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.
9.Investigation of the sedative effect of dexmedetomidine compound midazolam under different formula
Junli SI ; Yongyong SHI ; Weixian ZHAO ; Jianbin XIAO ; Jinhe DENG
The Journal of Practical Medicine 2017;33(16):2747-2749
Objective To investigate the sedative effects of different doses of dexmedetomidine with mid-azolam in spinal anesthesia. Methods 130 cases of spinal anesthesia were randomly divided into 2 groups,group D1 and group D2,with 65 cases in each group. Patients in 2 groups were given midazolam and dexmedetomidine with different doses. The heart rates ,blood pressure ,SpO2 ,Narcotrend value and Ramsay sedation scores were recorded at mutiple time points. The working time ,maintaining time of sedative effect ,and adverse reactions were compared between 2 groups. Results MAP,HR and NT decreased significantly in 2 groups(P < 0.05,respec-tively). The keeping time was relatively longer in group D1 compared with group D2(P<0.05). The working time was faster in group D2 compared with group D1. The rate of bradycardia in group D2 was relatively higher than that in group D1. Conclusion Good sedative effect can be obtained by drug in 2 groups. Group D1,with midazolam 0.05 mg/kg+dexmedetomidine 0.3μg/kg,may have a certain advantage in anaesthesia in the spinal canal.
10.Whole-genome analysis for 32 influenza A(H3N2) viruses in severe acute respiratory infection cases
Yang PAN ; Yi ZHANG ; Peng YANG ; Weixian SHI ; Xiaomin PENG ; Shujuan CUI ; Daitao ZHANG ; Guilan LU ; Jiachen ZHAO ; Quanyi WANG
International Journal of Laboratory Medicine 2017;38(17):2367-2370
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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