Mining the Alkhumra Hemorrhagic Fever Virus Genomes in 2015

Ruiz-Ayma, Gabriel; Tovar-Herrera, Omar E.; González-Álvarez, Rafael; Villanueva-Segura, Olga Karina; Gómez-Govea, Mayra A.; Fajardo-Ramírez, Óscar R; Zamudio-Osuna, Michelle; Martínez-de-Villarreal, Laura Elia; Córdova, Carlos Andrés Urbina; Garza‐Guajardo, Raquel; Ponce‐García, Gustavo; Barboza-Quintana, Oralia; Flores, Adriana E.; Rodríguez‐Sánchez, Iram P.

doi:10.3958/059.041.0110

Cited by 2 publications

(2 citation statements)

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“…Dodd et al have predicted the absence of positive selection in AHFV, which is in support of our results [45]. On the contrary, Ruiz-Aymá et al have predicted that the complete protein and the NS3 protein in AHFV have undergone positive selection [47]. Ruiz-Aymá et al used Kimura 2-parameters instead of the Jukes-Cantor model (used in the present study) to predict the substitution rates [47].…”

Section: Homology Modeling Of Protease and Polymerasesupporting

confidence: 89%

“…On the contrary, Ruiz-Aymá et al have predicted that the complete protein and the NS3 protein in AHFV have undergone positive selection [47]. Ruiz-Aymá et al used Kimura 2-parameters instead of the Jukes-Cantor model (used in the present study) to predict the substitution rates [47]. Kimura 2-parameters model has few assumptions; all the four nucleotides have the same frequency and all the sites have the same substitution rates [48].…”

Section: Homology Modeling Of Protease and Polymerasementioning

confidence: 86%

See 1 more Smart Citation

Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the in silico approach

Palanisamy

Akaberi

Lennerstrand

et al. 2018

Pathogens and Global Health

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Alkhumra hemorrhagic fever virus (AHFV), a relatively new member of the Flaviviruses, was discovered in Saudi Arabia 23 years ago. AHFV is classified in the tick-borne encephalitis virus serocomplex, along with the Kyasanur forest disease virus (KFDV) and tick-borne encephalitis virus (TBEV). Currently, very little is known about the pathologies of AHFV. In this study, using the available genome information of AHFV, KFDV and TBEV, we have predicted and compared the following aspects of these viruses: evolution, nucleotide and protein compositions, recombination, codon frequency, substitution rate, N- and O-glycosylation sites, signal peptide and cleavage site, transmembrane region, secondary structure of 5' and 3' UTRs and RNA-RNA interactions. Additionally, we have modeled the 3D protease and RNA-dependent RNA polymerase structures for AHFV, KFDV and TBEV. Recombination analysis showed no evidence of recombination in the AHFV genome with that of either KFDV or TBEV, although single break point analysis showed that nucleotide position 7399 (in the NS4B) is a breakpoint location. AHFV, KFDV and TBEV are very similar in terms of codon frequency, the number of transmembrane regions, properties of the polyprotein, RNA-RNA interaction sequences, NS3 protease and NS5 polymerase structures and 5' UTR structure. Using genome sequences, we showed the similarities between these closely- related viruses on several different areas.

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Section: Homology Modeling Of Protease and Polymerasesupporting

confidence: 89%