Genome Variability and Gene Content in Chordopoxviruses: Dependence on Microsatellites

Eneida Hatcher,Elliot Lefkowitz,Chunlin Wang

doi:10.3390/v7042126

Eneida Hatcher, Elliot Lefkowitz + Show 1 more

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Journal: Viruses	Publication Date: Apr 22, 2015
Citations: 22	License type: CC BY 4.0

Affiliation: University of Alabama at Birmingham, Stanford University

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To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution.

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The Poxviridae family consists of viruses with a wide host range and potential for causing disease.The family is divided into subfamilies based on host range, consisting of the Entomopoxvirinae which infect insects, and the Chordopoxvirinae (ChPV) which infect vertebrates [1]
We annotated the genes of representative viruses from each chordopoxvirus genus, and characterized those genes as intact, truncated, or fragmented (Table 1)
When identifying non-intact genes, we define truncated genes as less than 80% the length of intact genes but with the 5' end intact, as opposed to fragmented genes which maintain nucleotide sequence homology to intact genes but either do not have an intact 5' end of the gene, or the remaining orthologous open reading frames (ORFs) is less than 30 amino acids long

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The Poxviridae family consists of viruses with a wide host range and potential for causing disease. The family is divided into subfamilies based on host range, consisting of the Entomopoxvirinae which infect insects, and the Chordopoxvirinae (ChPV) which infect vertebrates [1]. The chordopoxviruses are Viruses 2015, 7 further divided into several genera, including the Orthopoxvirus genus, which includes the most well-known and the best characterized poxviruses, variola virus and vaccinia virus. Smallpox disease is caused by the viruses belonging to the Variola virus (VARV) species, and is well known both for its severity and its eradication through a worldwide vaccination effort. The vaccine used was based on viruses belonging to the species Vaccinia virus (VACV), which at some point replaced cowpox virus that was originally used in Jenner’s smallpox vaccine, the natural host of vaccinia viruses is unknown [2]. In addition to the Orthopoxvirus genus, chordopoxviruses are categorized into nine other genera, namely Avipoxvirus, Capripoxvirus, Cervidpoxvirus, Crocodylidpoxvirus, Leporipoxvirus, Molluscipoxvirus, Parapoxvirus, Suipoxvirus, and Yatapoxvirus, as well as the unassigned species

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