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Preprint | bioRxiv | ID: ppbiorxiv-926477


BackgroundThe current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected. MethodsWe downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs. ResultsAn isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1{middle dot}05 x 10-2 (nucleotide substitutions/site/year, with 95% HPD interval being 6.27 x 10-4 to 2.72 x 10-2) for N, 5.34 x 10-3 (5.10 x 10-4, 1.28 x 10-2) for S, 1.69 x 10-3 (3.94 x 10-4, 3.60 x 10-3) for P, 1.65 x 10-3 (4.47 x 10-4, 3.24 x 10-3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic. ConclusionOur analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.

Indian J Med Res ; 129(6): 701-6, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19692753


BACKGROUND & OBJECTIVE: Fluoroquinolone has a broad spectrum of antimicrobial activity, and is widely used for gonorrhoea treatment. However, its efficacy can be compromised by the drug-resistance property of Neisseria gonorrhoeae isolates. Most resistant cases of N. gonorrhoeae are associated with mutations in the quinolone-resistance-determining-region (QRDR) within genes of gyrA and parC. This study was undertaken to describe resistance profile of N. gonorrhoeae to fluoroquinolones in Shanghai, P.R. of China, and also associated resistance mutations in gyrA and parC. METHODS: Eighty N. gonorrhoeae isolates were collected from Shanghai Skin Disease & Sexually Transmitted Disease Hospital or DongFang Hospital during April 2005 to April 2006 in Shanghai, P.R. of China. The minimum inhibitory concentrations (MIC) of fluoroquinolones for these isolates were determined by an agar dilution method. Mutation patterns within gyrA and parC were determined by direct sequencing or by using established restriction fragment length polymorphisms (RFLP) methods. RESULTS: Ninety five per cent (76 of 80) of isolates were resistant, 3.75 per cent (3 of 80) intermediate resistant, and 1.25 per cent (1 of 80) were sensitive to fluoroquinolone drug ciprofloxacin. Sequencing and RFLP analysis of gyrA and parC revealed that all resistant isolates had dual mutations of S91F and D95A/G/N in gyrA. Some isolates had an extra mutation within parC either of D86N, S87N or E91A/G. Mutation patterns for gyrA and parC were significantly (P<0.05) associated with MICs level. INTERPRETATION & CONCLUSION: Mutations of S91F and D95A/G/N in gyrA combined with S87N in parC was the most prevalent mutation pattern of fluoroquinolone resistant N. gonorrhoeae isolates. This mutation pattern was associated with a high level of quinolone resistance (MIC >16.0 microg/ml) which can serve as a maker for quinolone-resistance prediction in Shanghai, P.R. of China.

Antibacterianos , Farmacorresistência Bacteriana/genética , Fluoroquinolonas , Mutação , Neisseria gonorrhoeae , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , China , Fluoroquinolonas/farmacologia , Fluoroquinolonas/uso terapêutico , Humanos , Testes de Sensibilidade Microbiana , Neisseria gonorrhoeae/efeitos dos fármacos , Neisseria gonorrhoeae/genética , Polimorfismo de Fragmento de Restrição , Análise de Sequência de DNA