Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

Saudi Journal of Biological Sciences

Volumn 21, Issue 4, 2014, Pages 311-316

  Chen, Youhua ^a   Chen, You Fang ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b HARBIN NORMAL UNIVERSITY   (China)

Author keywords

Homologous recombination; PCR contamination; Sequence analysis; Virus evolution

Indexed keywords

CLASSICAL SWINE FEVER VIRUS; PESTIVIRUS;

EID: 84906060746     PISSN: 1319562X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sjbs.2013.12.004     Document Type: Article

References (28)

1. Attoui H., Sailleau C., Jaafar F., Belhouchet M., Biagini P., Cantaloube J., Micco P., Mertens P., Zientara S. Complete nucleotide sequence of Middelburg virus, isolated from the spleen of a horse with severe clinical disease in Zimbabwe. J. Gen. Virol. 2007, 88:3078-3088.
2. Boni M., Posada D., Feldman M. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 2007, 176:1035-1047.
3. Boni M., Zhou Y., Taubenberger J., Holmes E. Homologous recombination is very rare or absent in human influenza A virus. J. Virol. 2008, 82:4807-4811.
4. Cao H., Zhang H., Cui Y. Synonymous codon usage bias of E2 genes of classical swine fever virus. Israel J. Vet. Med. 2012, 67:253-258.
5. Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
6. Gibbs M., Armstrong J., Gibbs A. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16:573-582.
7. Han G., Liu X., Li S. Cross-species recombination in the haemagglutinin gene of canine distemper virus. Virus Res. 2008, 136:198-201.
8. Han G., Worobey M. Homologous recombination in negative sense RNA viruses. Viruses 2011, 3:1358-1373.
9. He C., Ding N., Chen J., Li Y. Evidence of natural recombination in classical swine fever virus. Virus Res. 2007, 126:179-185.
10. He C., Xie Z., Han G., Dong J., Wang D., Liu J., Ma L., Tang X., Liu X., Pang Y., Li G. Homologous recombination as an evolutionary force in the avian influenza A virus. Mol. Biol. Evol. 2009, 26:177-187.
11. Leal E., Villanova F., Lin W., Hu F., Liu Q., Liu Y., Cui S. Interclade recombination in porcine parvovirus strains. J. Gen. Virol. 2012, 93:2692-2704.
12. Liu X., Wu C., Chen A. Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2. Arch. Virol. 2010, 155:685-693.
13. Lole K., Bollinger R., Paranjape R., Gadkari D., Kulkarni S., Novak N., Ingersoll R., Sheppard H., Ray S. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 1999, 73:152-160.
14. Martin D., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
15. Martin D., Posada D., Crandall K., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retroviruses 2005, 21:98-102.
16. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2010, 26:2462-2463.
17. Maynard Smith J. Analyzing the mosaic structure of genes. J. Mol. Evol. 1992, 34:126-129.
18. McCarthy A., Shaw M., Goodman S. Pathogen evolution and disease emergence in carnivores. Proc. R. Soc. B Biol. Sci. 2007, 274:3165-3174.
19. Padidam M., Sawyer S., Fauquet C. Possible emergence of new geminiviruses by frequent recombination. Virology 1999, 265:218-225.
20. Perez L., Arce H., Perera C., Rosell R., Frias M., Percedo M., Tarradas J., Doinguez P., Nuenez J., Ganges L. Positive selection pressure on the B/C domains of the E2-gene of classical swine fever virus in endemic areas under C-strain vaccination. Infect. Genet. Evol. 2012, 12:1405-1412.
21. Posada D., Crandall K. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. 2001, 98:13757-13762.
22. Shen H., Pei J., Bai J., Zhao M., Ju C., Yi L., Kang Y. Genetic diversity and positive selection analysis of classical swine fever virus isolates in south China. Virus Genes 2011, 43:234-242.
23. Shin D., Richards S., Alto B., Bettinardi D., Smartt C. Genome sequence analysis of Dengue virus 1 isolated in Key West, Florida. PLoS One 2013, 8:e74582.
24. Tang F., Pan Z., Zhang C. The selection pressure analysis of classical swine fever virus envelope protein genes Erns and E2. Virus Res. 2008, 131:132-135.
25. Tao P., Dai L., Luo M., Tang F., Tien P., Pan Z. Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 2009, 38:104-112.
26. Van der Walt E., Rybicki E., Varsani A., Polston J., Billharz R., Donaldson L., Monjane A., Martin D. Rapid host adaptation by extensive recombination. J. Gen. Virol. 2009, 90:734-746.
27. Worobey M. Extensive homologous recombination among widely divergent TT viruses. J. Virol. 2000, 74:7666-7670.
28. Wu J., Yu T., Bao Q., Zhao F. Evidence of extensive homologous recombination in the core genome of Rickettsia. Comp. Funct. Genomics 2009, 2009. 10.1155/2009/510270.