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Objective:To study the characteristics and evolution of the whole genome sequence of an imported Chikungunya virus (CHIKV) case in Tianjin, China, and to provide a scientific basis for the surveillance and control of CHIKV.Methods:The serum specimen of CHIKV was collected at Tianjin Second People's Hospital, on November 4th, 2019, and the viral RNA was extracted. Eleven overlapping primers were used to amplify the complete genome of CHIKV by RT-PCR. The amplification products were then subjected to next generation sequencing (NGS) using Illumina Miniseq platform.Results:The complete genome sequence of the Tianjin CHIKV obtained had similarities ranging from 92.72% to 99.86% with other Chinese isolates. Phylogenetic analysis indicated that the Tianjin CHIKV belonged to the Indian Ocean Lineage (IOL), East/Central/South African (ECSA) cluster, consistent with most strains from China. The Tianjin CHIKV is most similar (99.74%) to a Pakistan strain. Compared with the reference strain S27, 37 non-structural and 28 structural protein amino acid substitutions had been detected in Tianjin CHIKV genome, including two key site mutations, E1-D284E and E2-I211T, in accordance with other strains in the ECSA cluster. Besides, Tianjin CHIKV possessed two point virulent residues at position 12 and 82 in E2, and also a nsP3-R524Opal nonsense mutation.Conclusions:Tianjin CHIKV showed stronger virulence and greater transmissibility in Aedes albopictus. Therefore, the surveillance and monitoring of CHIKV in China should be strengthened.
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Objective@#To describe the epidemiological characteristics of a cluster of COVID-19 cases reported in Baodi district of Tianjin as of 18 February, 2020, which might be associated with the exposure in a local department store, and provide suggestions for prevention and control strategy development.@* Methods@#The basic characteristics, time and area distributions, clinical manifestations, epidemiological history and transmission mode of the COVID-19 cases associated with the department store exposure were analyzed.@* Results@#A total of 40 COVID-19 cases were associated with the department store exposure, accounting for 75.47% of the total confirmed cases (53 cases) reported in Baodi district. The cases were mainly at the age of 60 years or older (35.00%) and farmers (40.00%). The main clinical manifestations included fever (95.00%), cough (35.00%), and diarrhea (15.00%). The proportion of confirmed severe cases was 32.50%. The incidence curve showed that the incidence peak occurred on 31 January, 2020. Among the 40 cases, 6(15.00%) were department store employees, 19(47.50%) were customers and 15(37.50%) were close contacts (secondary cases). The first case occurred on 21 January, 2020, this case was a department store employee who had a purchasing history at whole sale markets in other provinces and cities before the onset, and 3 employees were still on duty after symptom onsets. The median of the incubation period of customer cases was 6 days, and the median of the interval between onset and medical treatment of customer cases was 7 days.@* Conclusion@#This was a cluster epidemic of COVID-19, which might be associated with the exposure in the department store. By now, the current prevention and control measures have achieved satisfied effects.
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Objective:To retrospectively analyze the test results of novel coronavirus (2019-nCoV) in different samples (throat swab, sputum and feces) collected from recovered COVID-19 patients in order to provide a more reliable basis for discharge and reduce the risk of recurrence after discharge.Methods:Throat swabs and sputum were sampled in pairs from 78 patients before discharge and sampled in pairs twice from 54 cases with an interval of 1-5 d. Real-time fluorescence quantitative RT-PCR was used to detect the virus in the two types of samples. Throat swab, sputum and fecal samples of six patients were tested for 2019-nCoV during follow-up.Results:The detection rate of viral nucleic acid was 46.15% in throat swabs and 50.00% in sputum samples. Test results of the second paired samples showed that the detection rate of viral nucleic acid was 25.93% in throat swabs and 46.30% in sputum samples, and the difference between the two types of samples was statistically significant ( P<0.05). During follow-up, 2019-nCoV nucleic acid could be detected in the fecal samples of the six patients, but not in their throat swab and sputum samples. Their fecal samples remained positive up to 52 d. Conclusions:In the late convalescence, the respiratory symptoms of COVID-19 patients gradually disappeared with the improvement of clinical symptoms. Moreover, the virus might enter the gastrointestinal tract from respiratory tract, and could long-term exist in recovered patients and be excreted in feces. In order to reduce the rate of missed detection and avoid false negative results, it was suggested to test the viral nucleic acid in different types of samples before a COVID-19 patient was discharged.
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Objective:To study the characteristics and influence factors of laboratory test results of confirmed COVID-19 cases in Tianjin.Methods:Sample collection was conducted based on the standard operating procedure. Tianlong automatic magnetic bead nucleic acid extraction reagent was used for RNA extraction. Real-time RT-PCR was performed using four approved COVID-19 nucleic acid detection kits. Related epidemiological data of the cases were collected. One-way analysis of variance and non-parametric test for inter-group differences analysis were conducted using SPSS25.0 software.Results:A total of 162 PCR tests were completed for novel coronavirus nucleic acid detection in 123 confirmed COVID-19 cases. Eleven PCR results were positive for a single target gene and 10 of which were positive for nucleocapsid protein (N) gene. Nineteen cases were tested with two kinds of nucleic acid detection kits and the results of different detection kits were different. Different types of samples were collected form 13 cases for nucleic acid detection and the results showed that the Ct value of sputum sample was lower than that of throat swab sample. No significant difference in Ct values of throat swab samples was observed among patients with different clinical symptoms ( PCt-N=0.797, PCt-ORF1a/b=0.551). The 123 cases were divided into different groups according to the time interval between the onset date and the date of the first positive detection of viral nucleic acid. No significant difference in Ct values of throat swab samples was observed among different time interval groups ( PCt-N=0.373, PCt-ORF1a/b=0.058). Conclusions:Sputum samples were better than upper respiratory tract samples for viral nucleic acid detection. The sensitivity of N gene detection was higher, but re-sampling was needed when the result was positive for the single target N gene. Appropriate detection kits should be selected according to the actual needs, and samples should be collected at multiple time points, in multiple types and form multiple sites for detection.
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Objective:To investigate the drug resistance and pathogenic mechanism of a uropathogenic Escherichia coli (UPEC) strain UPEC132 at the genome-wide level. Methods:The susceptibility of UPEC132 strain to 16 antimicrobial agents was determined by minimum inhibitory concentration (MIC) assay. The UPEC132 strain was genotyped by multilocus sequence typing (MLST). The three-generation sequencing platform was used to sequence and assemble the whole genome of the UPEC132 strain. Drug resistance and virulence gene function annotations were predicted by Prodigal software and screened by using genome database. Genome sequences of the UPEC132 strain and 23 other UPEC strains collected from GenBank were phylogenetically analyzed, and a phylogenetic tree was constructed by RAxML software.Results:The UPEC132 strain was resistant to ampicillin, ampicillin/sulbactam, tetracycline, erythromycin, chloramphenicol and cefazolin. Its genotype was ST10522 by MLST. The whole genome of the UPEC132 strain included one complete genome (chromosome) and two plasmid sequences. The sequence sizes of the chromosome and plasmids 1 and 2 were 5 234 468 bp, 117 139 bp and 101 356 bp, and the guanine-cytosine (GC) content was 50.48%, 49.05%, and 54.04%, respectively. There were 4 856, 140 and 116 genes annotated in the chromosome and plasmids 1 and 2, respectively. Drug resistance genes were mainly distributed in the chromosomal genome, mainly including the multidrug resistance efflux pump gene clusters. Only blaTEM-1 and tetG genes were carried in the plasmid 2. Virulence genes were also mainly distributed in the chromosome genome, including nine pilus adhesins, five iron uptake systems and three secretory toxins. Gene clusters encoding Afa and type Ⅳ fimbriae were located on plasmids 1 and 2, respectively. The phylogenetic tree showed that the UPEC132 strain was not in the same branch with either of the 23 UPEC strains. Conclusions:The UPEC132 strain belonged to ST10522, which was a newly named ST type of Escherichia coli and first reported at home and abroad. The genome-wide genetic information of the UPEC132 strain was fully revealed. The multidrug resistance genes and virulence genes carried by the UPEC132 strain were associated with its drug resistance and pathogenicity.