The Preliminary Study On Unnatural Origin Of SARS CoV By Molecular Evolution Method

Background：The end of2002, the outbreak of SARS emerged infectious diseases on aglobal scale,it tests for infectious diseases of national public health emergency responsecapacity, Also inspired us to explore new ideas for new virus researches. In the April16,2003, The World Health Organization officially declared pathogens led to the outbreak ofSARS is a novel coronavirus. Ten years later, Many experts explore the origin andevolution of the virus began extensive and in-depth research, Many previous studiesconfirmed that the SARS coronavirus is an independent branch of the coronavirus, Fortwice outbreak of SARS epidemic in early2003and the end of2003, the researchers alsohold different views about the origin of the epidemic and virus sub-type. Objective：In this bioinformatics study, The author calculate the neutral mutation rate ofthe SARS coronavirus; using neighbor-joining method to build SARS coronavirusphylogenetic tree, and compare two period SARS coronavirus genetic distance andphylogenetic relationships; Through the calculation of the most recent common ancestorof the SARS coronavirus Date and build a phylogenetic tree root systems, To get furtherresearch of the origin and evolution of the SARS coronavirus mode, we propose a newdirection of research and viewing.The author provide a scientific basis for the future findthe host of the SARS coronavirus, and respond to other major infectious diseases andresearch ideas.Methods：1. Build SARS CoV Data set: won nine of SARS CoV genome sequencesin the NCBI, from inland China and Hong Kong, where5is a human host, the host fromcivet cats,11February2003The date collected GZ02outgroup to build data sets A.Download the beginning of2004the22strains previously uploaded complete genomesequences in the NCBI,22sequences do not come from Guangzhou, Shenzhen, HongKong, Singapore, Taiwan, the same GZ02as outgroup, build dataset B.2. In ClustalX1.81, respectively, the sequence of the data sets A, B for comparison; inMEGA4.1, virus using Pamilo-Bianchi-Li calculated Ks value results in Excel (2010), Ksvalue create a scatter plot with the date of acquisition and fitting a straight line for theneutral mutation rate and R~2..3. In software MEGA4.1in, respectively, for A, B dataset Application NJ phylogenetictree.4. According to the formula, calculate the two sets of SARS COV time of the most recentcommon ancestor (TMRCA).5. NJ tree and the calculation results of the TMRCA were plotted data sets A and B of thephylogenetic tree.Results：1. The dataset A neutral mutation rate to7.6x10-6/bit days R~2=0.98; thedataset B neutral mutation rate of7.1x10-6/points Day R~2=0.92.2. The calculated PC04dataset A group TMRCA early November2003; the PC03groupTMRCA late January2003; the HP04group TMRCA early November2003; the HP03 group TMRCA is In early March2003. The dataset B PC04group TMRCA early October2003; the PC03group TMRCA is mid-January2003; the HP04group TMRCA earlyNovember2003; HP03group TMRCA February2003early; the GD01group TMRCA ismid-April2003.3. CUHK-Ag01、 CUHK-Ag02, GZ50of sampling date and the measurement groupTMRCA time there is a contradiction.4. Phylogenetic analysis showed that the evolutionary sequence of the different stages ofSARS CoV should be:02-03popular late strains→02-03years popular mid-strain→02-03years popular popular early strain→03-04years strains.Conclusions：1. Different stage of the epidemic viral sequences phylogenetic studies03-04years of epidemic strains02-03kinship popular early strain compared to02-03latein the popular closer, and contrary to the normal direction of evolution SARS CoVevolution "reverse evolution".2. CUHK-Ag01,CUHK-Ag02, a GZ50of sampling date and the measurement groupTMRCA time there is a contradiction between the description of the evolution of theSARS CoV does not fully comply with the theory of evolution.3. In summary, the origin of the SARS CoV may be non-natural, non-full of animalorigin.