Detection of positive selection in the major capsid protein VP60 of the rabbit haemorrhagic disease virus (RHDV)

Abstract

a b s t r a c tMutations were analysed in the major capsid protein VP60 of the rabbit haemorrhagic disease virus (RHDV), a calicivirus responsible for high mortality rates in both wild and domestic European rabbits (Oryctolagus cuniculus). Likelihood of positive selection was estimated using the PAML software applied to 43 non-identical complete sequences of the major capsid protein. Three codons showed signs of positive selection (with posterior probabilities over 95%), one of them is located in the region containing the major antigenic determinants (region E). The presence of positively selected codons (PSCs) in other regions may suggest the existence of other antigenic regions on the major capsid protein that stimulate protective immune responses. At all the 3 PSCs, variation contributes to putative N-glycosylation sites of the protein.An N-glycosylation site is deleted in the non-pathogenic strain RCV. Some of the substitutions at PSCs may alter the polarity and the charge of the protein with possible implications in the protein structure and host interaction. The detection of PSCs should allow a better understanding of the interaction between RHDV and the rabbit immune system.

Diversity of RHD virus: epidemiological, diagnostic and immunological importance

“…432) zawierających główne determinanty antygenowe odpowiedzialne za specyficzność szczepu RHDV, w obrębie subdomeny P2 kodującej zewnętrzną powierzchnię kapsydu, a trzeci we fragmencie F (poz. 476) (24). Ważną rolę w interakcjach z receptorami komórek gospodarza może odgrywać najbardziej wyeksponowany powierzchniowo region C. Relacje pomiędzy pozytywną selekcją i antygenowością sugerują udział w ewolucji RHDV mechanizmu zależnego od układu odpornościowego.…”

“…Procesy rekombinacji genetycznej stwierdzono już u RHDV i RHDVa, ale skala zjawisk była ograniczona i nie miała decydującego wpływu na szeroką pojętą zmienność wirusa RHD (1,24,28). Znacznie większy udział mechanizmów rekombinacji lagowirusów wykazano, badając sekwencje kilkudziesięciu portugalskich szczepów RHDV z lat 1994-2014 (7,49).…”

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

“…Identifying genes subject to positive natural selection since two closely related pathogens diverged may identify antigenic compounds (Esteves et al 2008). The low median d S value of 0.023 calculated from the 6763 orthologs conserved between C. posadasii and C. immitis indicates that the taxa diverged recently enough to identify the signature of positive selection via comparisons of d N and d S .…”

Comparative analysis of rabbit hemorrhagic disease virus strains originating from outbreaks in the Russian Federation

“…All rabbits infected with strains Belgorodskiy-03, Solnechnogorskiy-2003, Mihailov-09, Manihino-09, Perm-2010, Ramenskiy-10, Balashiha-2011, Nizhny Novgorod-11, Nizhny Novgorod-12, and Tambov-2010 developed fever ([40°C) by 36-96 hours postinfection (pi) and died 2-7 days pi. Typical RHD lesions were observed in the liver, including [24]. A one-letter amino acid abbreviation in a column indicates evidence of positive selection at the PSC for each RHDV isolate Rabbit hemorrhagic disease virus strains in Russia peripheral multifocal necrosis with a granular surface and pale yellow and dark reddish spots.…”

“…The RHDV VP60 protein (largely E and F regions) appears to be informative for study of virus evolution [24].…”