Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

Computer Science and Information Technology at the University of Prince Edward Island

 

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ISAV/PRV Analyses

Infectious salmon anaemia virus (ISAV) is an economically important pathogen of marine-farmed Atlantic salmon. The disease caused by ISAV, infectious salmon anaemia (ISA), is the most feared viral disease of the marine-farmed Atlantic salmon industry. For the past 30 years, ISA continues to cause severe economic losses to the salmon-farming industry in an increasing number of countries.

 

Heart and skeletal muscle inflammation (HSMI) is an emerging disease of marine-farmed Atlantic salmon, first recognized in 1999, and recently associated with piscine reovirus (PRV) infection.

 

I am a member of a research group led by Dr. Fred Kibenge in the Atlantic Veterinary College at UPEI since 2006. This group consists of researchers from Chile, Brazil, British Columbia, and UPEI. The papers published by this group were highly accessed and had great influences. I have only obtained access statistics for three papers, they are:

[6]: accessed 16054 times.

[7]: accessed 10397 times.

[8]: accessed 1985 times.

These statistics numbers include accesses on the journal website. They do not include accesses from PubMed Central or other archive sites. The total access statistics are therefore likely to be significantly higher.

 

My work in this group is to perform data analysis and phylogenetic analysis. I have been deeply involved in the ISAV/PRV research and I have already got familiar with the background of the research.

 

Performing data analysis and phylogenetic analysis to real-world data is a challenging task. The features of this research can be described as team work and creative work. I tried to fully use my computer knowledge and bioinformatics knowledge, and to creatively use bioinformatics methods and tools. I also used manual adjustments and developed new tools when necessary. Because of these efforts, we were able to generate high-quality alignments, to predict divergence time in the past, and to generate reliable phylogenetic trees. Our research results provided deeper understanding related to the mutation and migration of ISAVs. Such results were vital in ISAV prevention and policy making. Dr. Kibenge described my role in the research group in an interview. He highly rated my work.

 

Paper [7] has been referred in Wikipedia as one source of definition for family

Reoviridae.

 

Bloomberg.com is one of the most-tracked financial sites on the Web. It is regarded as a premier site for news and financial information. On July 20, 2009, this media published an article "Chilean Salmon Disease May Date Back to 1996, Researchers Say", and this article was referenced by many media sites.

·         Bloomberg.com, "Chilean Salmon Disease May Date Back to 1996, Researchers Say"

·         Searead, "Chilean Salmon Disease May Date Back to 1996, Researchers Say"

This article describes a conclusion of a research paper published in Virology Journal which I co-authored with Dr. Fred Kibenge and others [6]. This conclusion suggested that the salmon virus decimating fish farms in Chile may have been introduced from Norway in 1996, circulating undetected for more than a decade before changing into a deadly outbreak in 2005. This research had obtained international attention and might have influenced policies of related countries, although the spokeswoman of Norway's Ministry of Fisheries and Coastal Affairs refused to comment immediately when asked about this article.

 

This conclusion was proposed by me through bioinformatics analysis based on much work accomplished by other co-authors. I was listed at the third position in the list of 12 co-authors. The paper has a note to indicate that the first three co-authors are equal contributors.

 

My work in this area not only generated academic progress and papers, but also contributed to aquatic farms. In Oct. 2008, a Chile aquatic farm, Camanchaca, requested that we perform phylogenetic analysis to the virus samples discovered in different locations of their farm. They were especially interested in the relationship of the viruses found in their farm with other major virus strains. They were willing to pay fees to Kibenge’s Lab for the service. Since then, another two aquatic farms, Multiexport and Los Fiordosthey, also requested similar services. I was very glad that my research was useful in real life.

Related Publications

[11] Molly J.T. Kibenge, Yingwei Wang, Alexandra Morton, Richard Routledge, Frederick S.B. Kibenge, Discovery of variant infectious salmon anaemia virus (ISAV) of European genotype, Journal of General Virology, 2015, submitted.

[8] Marcos G Godoy, Rudy Suarez, Eduardo S Lazo, Katerina O Llegues, Molly JT Kibenge, Yingwei Wang, and Frederick SB Kibenge, Genetic analysis and comparative virulence of Infectious Salmon Anemia Virus (ISAV) types HPR7a and HPR7b from recent field outbreaks in Chile, Virology Journal 11/2014; 11(1):204. DOI:10.1186/s12985-014-0204-1, 2.09 Impact Factor (Highly Accessed)

[7] Molly J.T Kibenge, Tokinori Iwamoto, Yingwei Wang, Alexandra Morton, Marcos G Godoy and Frederick S.B Kibenge, Whole-genome analysis of piscine reovirus (PRV) shows PRV represents a new genus in family Reoviridae and its genome segment S1 sequences group it into two separate sub-genotypes, Virology Journal, 2013,10:230 doi:10.1186/1743-422X-10-230?2.09 Impact Factor (Highly Accessed)

[6] Frederick SB Kibenge, Marcos G Godoy, Yingwei Wang, Molly JT Kibenge, Valentina Gherardelli, Soledad Mansilla, Angelica Lisperger, Miguel Jarpa, Geraldine Larroquete, Fernando Avendano, Marcela Lara, and Alicia Gallardo. Infectious salmon anaemia virus (ISAV) isolated from the ISA disease outbreaks in Chile diverged from ISAV isolates from Norway around 1996 and was disseminated around 2005, based on surface glycoprotein gene sequences. Virology Journal, 6:88, 2009. The first three co-authors are equal contributors. 2.09 Impact Factor (Highly Accessed)

[5] Frederick S.B. Kibenge, Molly J.T. Kibenge, Yingwei Wang, Biao Qian, Shebel Hariharan and Sandi McGeachy. Mapping of putative virulence motifs on infectious salmon anaemia virus surface glycoprotein genes, Journal of General Virology, 88:3100-3111, 2007. 3.53 Impact Factor

[4] Frederick S.B. Kibenge, Molly J.T. Kibenge, Yingwei Wang, Biao Qian, Shebel Hariharan, and Sandi McGeachy, Correlates of virulence of infectious salmon anaemia virus. OIE Global Conference on Aquatic Animal Health, Bergen, Norway, October 2006.

[3] Molly T. Kibenge, Yingwei Wang, Biao Qian, Sandi McGeachy, Frederick Kibenge, Virulence Phenotypes of Infectious Salmon Anaemia Virus (ISAV), 5th International Symposium on Aquatic Animal Health B ISAAH, San Francisco Marriott, San Francisco, California, USA, September 2006

 

 

 

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