Construction of phylogenetic tree using neighbor joining algorithms to identify the host and the spreading of SARS epidemic

Mohammad Isa Irawan*, Siti Amiroch

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


The epidemic of SARS is a dramatic example of how quickly the virus spread throughout the world. The pattern of spread of the SARS virus can be likened to a tree called a phylogenetic tree. All of SARS virus related to one another are connected to a network that is transmitted from one individual to another. The results of this branching process to determine the beginning of the epidemic as well as the host of the corona virus. To construct a phylogenetic tree takes inputs in the form of a distance matrix. In this study the distance matrix is derived from the alignments between sequence by using Super Pairwise Alignment (SPA). The output of the alignment is in the form of number of differences of sequences that determine in genetic distance. From the distance matrix, the genetic distance is converted to evolutionary distances using the Jukes Cantor model of which was established by phylogenetic tree by using the neighbor joining algorithm. From the results of the phylogenetic tree formation are known as host SARS Co-V is a palm civet with evolutionary distance of 0.1314. The epidemic began on December 16, 2002 in Guangzhou of South China and then spread to Zhongshan. Rallying point of the epidemic in Guangzhou Hospital and the Metropole hotel subsequently spread to Hanoi, Toronto, Singapore, Taiwan, and Hong Kong so that SARS to be international case. Furthermore, from the result of alignments of hosts and human SARS Co-V with SPA is known that the mutation is a mutation that occurs with type I protein replacement at position 77, 139, 147, 244, 344, 360, 472, 480, 487, 577, 609, 613, 665, 765, 778, and 1163.

Original languageEnglish
Pages (from-to)424-429
Number of pages6
JournalJournal of Theoretical and Applied Information Technology
Issue number3
Publication statusPublished - 31 Jan 2015


  • Neighbor joining algorithm
  • Phylogenetic tree
  • SARS coronavirus
  • Super pairwise alignment


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