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Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

mLife 2022年第3期1卷 311-322页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu Research Institute of Public Health Nankai UniversityTianjinChina TEDA Institute of Biological Sciences and Biotechnology Nankai UniversityTianjinChina Engineering and Research Center for Microbial Functional Genomics and Detection Ministry of EducationNankai UniversityTianjinChina State Key Laboratory for Infectious Disease Prevention and Control Chinese Center for Disease Control and PreventionNational Institute for Communicable Disease Control and PreventionBeijingChina Research Units of Discovery of Unknown Bacteria and Function Chinese Academy of Medical SciencesBeijingChina

The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal ***,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 *** this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 *** possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation *** a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation ***,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons *** addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐***,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.

关键词： de novo mutation evolutionary trends mutation characteristics mutation frequency SARS‐CoV‐2

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Ecology of antibiotic resistant vibrios in traditional shrimp farming system(bhery)of West Bengal,India

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Journal of Coastal Life Medicine 2013年第4期 265-272页

作者： Leesa Priyadarsani Thangapalam Jawahar Abraham Department of Aquatic Animal Health Faculty of Fishery SciencesWest Bengal University of Animal and Fishery SciencesKolkata–700094West BengalIndia

Objective:To study the ecology of antibiotic resistant bacteria with emphasis on sucrose negative vibrios in water and sediments samples of traditional shrimp farming system(bhery)in West Bengal,***:The vibrios were isolated from traditional shrimp farm samples on thiosulphate citrate bile salt sucrose agar and sucrose negative bacterial strains were used as biomarkers to assess the frequency of antibiotic ***:The incoming water brought presumptive vibrios ranging from 5.50×10^(1)to 1.00×10^(3)mL in to the bhery,and there appeared to build up vibrios in the culture system with days of culture,as there was about 9 fold increase in *** levels of vibrios were observed to be moderately higher in outlet water and ranged between 4.15×10^(2)and 4.15x10^(3)*** counts of vibrios in pond sediment was found to be 1.00x10^(2)-4.90×10^(3)g;while in inlet(2.00×10^(2)-4.20×10^(4)g)and outlet(3.00×10^(2)-6.85×10^(3)g)their levels were observed to be higher than the pond *** different Vibrio species were encountered in traditional shrimp culture system and all vibrios were sensitive to chloramphenicol,followed by ciprofloxacin and gatifloxacin(98.24%),gentamicin(95.61%)and other *** multiple antibiotic resistance(MAR),i.e.,resistance to at least two antibiotics,was noticed among 43.85%of the sucrose negative vibrios and 41.86%of the sucrose negative *** vibrios harveyi strains exhibited *** no antibiotic was used in the bhery,the prevalence of MAR in 44%of the sucrose negative vibrios and nonvibrios is a cause of *** MAR index was higher in inlet water and sediment *** MAR observed in biomarker strains of pond water and sediment(40%)was comparable to those of inlet samples,thus confirming the fact that incoming water was the major source of antibiotic resistant ***:It seems that the shrimp culture in bhery does not favour the proliferation and spread of antibiotic res

关键词： Traditional shrimp farming Penaeus monodon Vibrio spp. Biomarkers Antibiotic resistance mutation frequency R-plasmid

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Determination of MBL Gene by Using PCR-RFLP and the Study on the Association of Plasma Concentrations of Mannose Binding Protein in Healthy Individuals of Han and Mongolian Population

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Journal of Microbiology and Immunology 2004年第2期2卷 140-144页

作者：贾天军李萍张庶民刘洁赵铁军张进顺雷殿良翟登高李河民 Hebei North University Zhangjiakou 075029 China National Institute for the Control of Pharmaceutical and Biological Products (NICPBP) Beijing 100050 China

The aim of this study was to analyze the point mutation of the exon 1 at codon 54 of the mannose (or mannan)-binding lectin (MBL) gene in healthy individuals of Chinese Hans and Mongolian population, and to find out any association between the plasma levels of MBL and the gene mutation frequency in both groups of individuals. Blood samples were collected randomly from 56 healthy individuals of Chinese Hans and 37 Mongolian. The detection of the point mutations of the MBL gene was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and detections for plasma levels of MBL were determined by using MBL ELISA kits. A MBL PCR method of assay was established with high specificity, and good reproducibility. By optimizing the PCR condition, the optimal annealing temperature was 55℃, and the lowest detection limit was 160 pg. No bands were found in non-specificity samples (HAV, HBV, HCV and TB), and the sequences of PCR products were the same as the expected ones. Also a MBL PCR-RFLP was established. Upon electrophoresis of the digested products in 3% agarose gel, there were 3 patterns: in which 2 bands correspond to molecule weight 232 bp and 93 bp; 1 band, corresponds to molecule weight 325 bp and 3 bands correspond to molecule weight 325 bp, 232 bp and 93 bp, respectively. Three bands of 325 bp, 232 bp and 93 bp of point mutations were found at codon 54 of MBL coding gene. Frequencies in healthy Han and Mongolian population were 0.2321 and 0.1757 respectively. The average plasma MBL concentration was 1998.750 μg/L, with SD of 1505.152 in 56 healthy Han population and 2525.676 μg/L, with SD of 1955.188 in 37 Mongolian. A negative correlation between MBL concentration and gene mutation frequency was found in healthy Han population. frequency of point mutation was 1.00 when the MBL concentrations were below 100 μg/L; frequency of point mutation was 0.4524 when the concentration was 100 μg/L to 1000 μg/L; and the frequency of point mutati

关键词： MBL PCR-RFLP Hans Mongolian mutation frequency Concentration

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Transcription-coupled repair pathway in UVC-induced SupF gene mutation in Tet-on 293 cell line

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Journal of Medical Colleges of PLA(China) 2008年第2期23卷 76-80页

作者： Li Jin Song Bo Chen Zhiwen Zeng Yijun Zhou Huchuan Wei Quanfang Yang Jin Urinary Surgery Research Institute Southwest Hospital Third Military Medical University Chongqing 400038 China Department of Biochemistry College of Medicine Third Military Medical University Chongqing 400038 China

Objective： To explore the role of transcription-coupled repair （TCR） pathway in the UVC-induced SupF gene mutation in Tet-on 293 cell line, we designed and constructed a Tet-responsive plasmid DNA pTCR-C1, and utilized this pTCR-C 1 plasmid to obtain the mutation frequency of SupF reporter gene induced by UVC in Tet-on 293 cell line. Methods： SupF gene was cloned into a Tet-responsive plamid pBI-L, which include a bidirectional Tet-responsive promoter, and was named pTCR-C1. The pTCR-C1 plasmid was transfected into Tet-on 293 cell line, and the mutation frequency of SupF reporter gene was detected in the presence and absence of DOX. Results： The pTCR-C1 plasmid was identified with the methods of restriction digestion and DNA sequencing. The mutation frequency of SupF reporter gene in the presence of DOX was higher than in the absence of DOX. Conclusion： The TCR pathway takes part in the UVC-induced SupF gene mutation in Tet-on 293 cell line.

关键词： Transcription-coupled repair SupF gene Tet-on mutation frequency

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