PHYLOGENETIC ANALYSIS OF CORONA VIRUS


A phylogenetic tree, also known as a phylogeny, is a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor. Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing insight into events that occurred during evolution. Furthermore, because these trees show descent from a common ancestor, and because much of the strongest evidence for evolution comes in the form of common ancestry, one must understand phylogenies in order to fully appreciate the overwhelming evidence supporting the theory of evolution. Tree diagrams have been used in evolutionary biology since the time of Charles Darwin. Therefore, one might assume that, by now, most scientists would be exceedingly comfortable with "tree thinking"--reading and interpreting phylogenies. However, it turns out that the tree model of evolution is somewhat counterintuitive and easily misunderstood. This may be the reason why biologists have only in the last few decades come to develop a rigorous understanding of phylogenetic trees. This understanding allows present-day researchers to use phylogenies to visualize evolution, organize their knowledge of biodiversity, and structure and guide ongoing evolutionary research.

China released the genetic sequence of a new coronavirus believed to be responsible for a cluster 0f unusual pneumonia cases in Wuhan. Phylogenetic analysis shows the coronavirus to be closely related to SARS CoV, the virus responsible for the SARS pandemic which began in China in 2003.


Phylogenetic ananlysis copares the cluster of genetic codes to other various clusters in many organisms and BLAST is the tool used here to analyse the similarty and difference with other members of it's family to produce a tree to see it's genetic evolution an to find possiblity of gene that are responsible for various functionality and factors responsible for factors like : toxicity , Angio tensin convertase enzyme 2 ( ACE 2 ) which is also identified potential docking site for various drugs like LIPONAVIR which in out previous research showed best docking energy results and thus showed promising results and can be used ass potential drug for treatment from coronavirus infection , so below we would first analyze the genetic code for corona virus for that the we took FASTA FORMAT .




This is a NCBI site which is encyclopedia for genetic codes and phylogenetic trees , now below is the code , we have included full code if anybody want to read it and download it or copy it feel free to do it and code is very long so we have reduced it and click on see more to see all full code for it , just for now we are displaying snippet of code that are important in virus and present important information

5'UTR 1..265 gene 266..21555 /gene="orf1ab" CDS join(266..13468,13468..21555) /gene="orf1ab" /ribosomal_slippage /note="pp1ab; translated by -1 ribosomal frameshift" /codon_start=1 /product="orf1ab polyprotein" /protein_id="QHD43415.1" /translation="MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQ HLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGE TLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN WNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQ LDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFP LNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTG DFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESG LKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNL LEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN FKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAA ITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKL KPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLV NKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEK YCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK

Below is the explanation of each gene segment and function by specificity and particular every section to each gene section :






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