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Evolutionary dynamics of the severe acute respiratory syndrome coronavirus.2 genomes

Medical Review 2022年第1期2卷 3-22页

作者： Zhaohui Qian Pei Li Xiaolu Tang Jian Lu Institute of Pathogen Biology Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100871China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100176China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China

The coronavirus.disease 2019(COVID-19)pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health.As severe acute respiratory syndrome coronavirus.2(SARS-CoV-2),the causative agent of COVID-19,has evolved,thousands of single nucleotide variants(SNVs)have been identified across the viral genome.The roles of individual SNVs in the zoonotic origin,evolution,and transmission of SARS-CoV-2 have become the focus of many studies.This review summarizes recent comparative genomic analyses of SARS-CoV-2 and related coronavirus.s(SC2r-CoVs)found in non-human animals,including delineation of SARS-CoV-2 lineages based on characteristic SNVs.We also discuss the current understanding of receptor-binding domain(RBD)evolution and characteristic mutations in variants of concern(VOCs)of SARS-CoV-2,as well as possible co-evolution between RBD and its receptor,angiotensin-converting enzyme 2(ACE2).We propose that the interplay between SARS-CoV-2 and host RNA editing mechanisms might have partially resulted in the bias in nucleotide changes during SARS-CoV-2 evolution.Finally,we outline some current challenges,including difficulty in deciphering the complicated relationship between viral pathogenicity and infectivity of different variants,and monitoring transmission of SARS-CoV-2 between humans and animals as the pandemic progresses.

关键词： molecular evolution population genetics severe acute respiratory syndrome coronavirus.2 variant virus.

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Qualitative, quantitative and structural analysis of non-coding regions of classical swine fever virus.genome

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Chinese Science Bulletin 2001年第15期46卷 1251-1258页

作者： XIAO Ming ZHU Zhizhan ZHANG Chuyu Institute of Virology College of Life SciencesWuhan UniversityWuhan 430072China Department of Physics Wuhan UniversityWuhan 430072China

Classical swine fever virus.(CSFV) is the pathogen of the swine fever. Understanding of the replication and expression of its genome is the basis for research of the pathogenicity for CSFV and development of antiviral drug. The noncoding regions (NCRs) of CSFV are the main regulatory regions for replication and expression. Qualitative, quantitative and structural analysis of 3’ NCRs and 5’ NCRs was done in order to locate the regulatory region in the NCRs and to character the NCRs. The sites, conserved sequences and structural elements related to the initiation of replication and expression were extracted from 17 3’ NCRs and 56 5’ NCRs. Those cis-elements may be initial recognition sites for replication, binding sites for transcription factors of host cell and interacting sites for initiation of protein synthesis, based on which a mechanism for the replication and expression of CSFV was brought forth. This research offers the direction for further experiment and lays down a basis for the research on

关键词： classical swine fever virus noncoding regions RNA replication information content pestivirus plus-strand RNA virus.

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Fruit bats as anatural reservoir of zoonotic virus.s

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Chinese Science Bulletin 2003年第12期48卷 1179-1182页

作者： JIA Guangle ZHANG Ying WU Tinghe ZHANG Shuyi WANG Yinan Institute of Zoology Chinese Academy of SciencesBeijing 100080China Shanxi Agricultural University Taigu 030801China

As a natural reservoir of manifold zoonotic virus.s, fruit bats have been involved in at least three emerging zoonoses in recent years. This paper aims to intro-duce the epidemiological characteristics of these diseases emerged in the Australasian region between 1994 and 1999, transmission pathways of the newly discovered virus.s and the relationship between the changed entironment of fruit bats and occurrences of these emerging diseases and provide a clue for the epidemiological investigations of SARS.

关键词： fruit bat natural reservoir zoonotic virus.

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Construction of polyhedrin-positive recombinant virus.ith expression of truncated δ-endotoxin fromBacillus thuringiensis in insect cell

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Chinese Science Bulletin 1996年第7期41卷 597-603页

作者：王福山黄永秀齐义鹏刘子夜杨远征 Institute of Virology Wuhan University Wuhan 430072 China

Baculovirus.s have been widely used as biological agents because of their specificpathogenicity for target insect and harmlessness to mammals, birds and plants as well asadvantages with persistence and epidemics as pestcides. A major drawback for morewide-spread use of these virus.s is their low virulenee and slow speed of action, which re-stricted their use. No enhancement in pathogenicity of recombinant virus.s was observedwith insertion of the Bacillus thuringiensis full-length endotoxin cryIA(c) and cryIA(b) geneinto the AcNOV (Autographa californica nuclear polyhedrosis virus. genome under the con-trol of polyhedrin gene promoter. The reason may be that protoxin, full-length genesproduct of recombinant virus.in infected insect cells, which was short of insect gut alkalienvironment, cannot be degraded into active toxic polypeptide. Expression level of 3’

关键词： Bacillus thuringiensis δ-endotoxin polyhedrin gene expression recombinant virus.

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Chinese tomato yellow leaf curl virus.-a new species of geminivirus

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Science China(Life Sciences) 1998年第4期41卷 337-343页

作者：刘玉乐蔡健和李冬玲秦碧霞田波

Chinese tomato yellow leaf curl virus.(TYLCV CHI) and other geminivirus.s were analysed with 20 monoclonal antibodies. It was shown that TYLCV CHI is serologically close to Chinese tabacco leaf curl virus.(TbLCV CHI). The fragment of TYLCV CHI DNA including the common region (CR), N terminal of coat protein gene and AV1 gene was amplified by PCR and cloned, and its DNA sequence was determined. These results showed that TYLCV CHI is different from other known geminivirus.s in the world, and is a new whitefly transmitted geminivirus.

关键词： Chinese tomato yellow leaf curl virus geminivirus new virus.

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A modified hepatitis B surface antigen carrying both preS1 and preS2 epitopes

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Science China(Life Sciences) 1998年第1期41卷 56-63页

作者：惠静毅李光地孔玉英汪垣

The DNA fragments coding for preS2(120 146) and preS1(21 47) amplified by PCR were fused to both 5′ and 3′ ends of S gene at the position of amino acid 223. The fusion gene was placed downstream of the promoter P7.5 of the universal vaccinia viral vector pGJP 5 and the recombinant vaccinia virus.vS2SS1 was then selected by \%in vivo\% homogeneous recombination. Fusion protein S2SS1 could be expressed in the mammalian cells infected with vS2SS1. The investigation of expression, secretion, antigenicity and particle assembly of the S2SS1 protein demonstrated that S2SS1 protein could be assembled into particles which presented preS1, preS2 and S antigenicity and be efficiently secreted from the cells. It also showed that the level of its expression and secretion approached to that of the S protein expressed by the recombinant vaccinia virus.

关键词： hepatitis B surface antigen (HBsAg) preS1 and preS2 epitopes fusion protein particle recombi nant vaccinia virus.

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An efficient method of constructing homologous recom binant baculovirus.with PCR-amplified fragments

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Science China(Life Sciences) 2003年第4期46卷 431-437页

作者：侯松旺陈新文王汉中胡志红 Joint-lab of Invertebrate Virologyand Key Laboratory of Molecular Virology WuhanInstitute of Virology Chinese Academy of Sciences KeyLaboratory of Agricultural Microbiology Ministry of Agriculture HuazhongAgricultureUniversityWuhan430072China

This paper describes a rapid method of constructing homologous recombinant baculovirus.in E. coli with PCR-amplified fragments. By using this method, the traditional steps of constructing transfer vector are omitted. The method is based on phage l red system which can promote the recombination between the homologous fragments with the length above 36 bp. Taking HaSNPV as an example, this paper describes the rapid recombination process by using chloramphenicol resistance gene (CmR) to replace orf135 in HaSNPV genome. A pair of primers with length of 60 bp was synthesized, in which 40 bp was homologous to the each end sequence of orf135, and the rest 20 bp was homologous to the each end sequence of CmR. By using these primers, a linear fragment containing the complete CmR gene between 40 bp of homologous arms of orf135 was generated by PCR with the plasmid pKD3 which contains CmR as the template. By transforming the linear fragment into the E. coli containing the bacterial artificial chromosome of HaSNPV and with the help of a plasmid expressing l recombinase, the recombinants on which the homologue replacement had taken place were selected by chloramphenicol resistance. This method greatly shortens the process of constructing recombinant baculovirus.since the process was performed in E. coli and does not need to construct transfer vectors. It can be further used for gene replacement and gene deletion of other large viral genomes.

关键词： phage λ red system, baculovirus Bacmid, gene replacement, gene deletion, HaSNPV, recombinant virus.

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Comparative study of haemagglutination inhibition, Agar gel precipitation test, Serum neutralization and Enzyme linked immunosorbent assay for detection to avian influenza virus.s

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Health 2010年第2期2卷 97-100页

作者： Shahid Faraz Muhammad Abubakar Mohammad Farooque Sarfaraz Ali Fazlani Ghluam Hussain Jaffar 不详

The sensitivity, specificity and reproducibility of the serological tests for detection of avian in-fluenza virus.s were carried-out by using Ham- agglutination inhibition (HI), Agar gel precipita-tion test (AGPT), and Enzyme linked immu-nosorbent assay (ELISA) and Serum neutraliza-tion test. The geometric mean titre (GMT) of hae- magglutination inhibition antibodies recor- ded as log2 indicated that the post vaccination titres in the field were on higher side i.e., 7.9 for H7 and 5.9 for H9. The correlation between HI titre and AGPT affirmed that for the AGPT test need high antibody titre for positive reaction. The pooled sera were also used to correlate the se-rum neutralization test and enzyme linked im- muno-sorbent assay. The serial two fold dilute- ons were tested for the serum neutralization ac- tivity and concluded that the HI titre log2 4 pro-vided 100% protection, than 52% and 45% pro-tection in 1:2 and 1:4 dilution was recorded, respectively. Similarly, the ELISA test showed positive results up to 1:16 HI titre, i.e. log2 4 and confirmed the linear relation between these two serological tests. In HI test, the concentration of antigen can influence the result. It also needs careful preparation of concentration of eryth-rocyte suspension. Agar Gel immuno-diffusion is basically a qualitative test as it can not de-termine the quantity of antigen or antibody with the help of this test. It lacks the level of sensi-tivity as offered by other test. If serum neutrali-zation test is performed on a pooled serum sam- ples, then it could lead to a false conclusion on antibodies status. ELISA is most sensitive, spe-cific and accurate as compare to all other sero-logical tests.

关键词： Serology HI ELISA and Avian Influenza virus.

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