Abstract
Introduction The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa. Recently, outbreaks have been reported in tropical and sub-tropical areas of countries that were previously unaffected (e.g., Brazil, Colombia). Currently, the following geographical genotypes have been identified through phylogenetic analysis of CHIKV E1 gene sequences: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes. Outbreaks in a geographical area can happen with the same or different genotypes. Determining which genotypes are circulating in an outbreak is important for public health management. Objectives To create a computer-based system available online that is suitable for detecting changes in CHIKV nucleotide and amino acid sequences and identifying their corresponding geographical genotype. Methods We used several computer frameworks, tools, programming languages, algorithms, and infrastructure systems to build a software tool that analyzes changes in nucleotide and amino acid sequences and identifies different geographical genotypes through phylogenetic analysis. Results We have built an online software tool called Pathogen Sequence Signature Analysis (PSSA) that allows researchers to analyze nucleotide and amino acid sequence variations between sample CHIKV sequences taken from infected patients and obtained through conventional Sanger sequencing, to identify their corresponding geographical genotype. Conclusion PSSA is able to analyze sequences in a simple and effective manner, and includes proper documentation (i.e., UML diagrams) and also basic examples that serve to test the algorithm. Furthermore, PSSA provides various ways to visualize the data in order to aid understanding and interpretation of results. Results provided by PSSA will be useful for the identification of circulating CHIKV genotypes and public health surveillance. PSSA is available at: http://pssa.itiud.org.
Highlights
The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa
Results provided by Pathogen Sequence Signature Analysis (PSSA) will be useful for the identification of circulating CHIKV genotypes and public health surveillance
The following geographical genotypes have been identified through phylogenetic analysis of CHIKV E1 gene sequences: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes[3,4,5]
Summary
The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa. Chikungunya virus (CHIKV) is an arbovirus (arthropod-borne virus), which is part of the Alphavirus genus and belongs to the Togaviridae family It is vectored by Aedes mosquitoes and infects humans in tropical and sub-tropical areas of Asia and Africa[1]. 2. Reviewer feels that since the reference data included in the software is only suitable for Chikungunya virus, the authors should refrain from making a broad claim in the title of the manuscript that it can be used for other microorganisms. The user interface prompts ‘incorrect sequence length’, without giving any clue that the input sequence should be of equal length (which I ‘guessed’ from the test data set). What happens for the mutation analysis if a user gives out of frame sequences? Will it again prompt that ‘incorrect sequence length’?
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