Phylogenetic analysis of Heliothis armigera cytoplasmic polyhedrosis virus type 14 and a series of dwarf segments found in the genome

Abstract

Full-length nucleotide sequences for the genome segments (S1-S6) of Heliothis armigera cytoplasmic polyhedrosis virus type 14 (HaCPV-14) have been characterized. Each segment consists of a single open reading frame with conserved motifs AGAA and AGCU at the 59 and 39 ends, respectively. Comparison of the proteins of HaCPV-14 with those of other members of the family Reoviridae suggests that S1 encodes an RNA-dependent RNA polymerase (RdRp), whilst S2 encodes a major capsid protein of the virus. Phylogenetic analysis of RdRps from 16 viruses in the family Reoviridae reveals that the genera Cypovirus and Oryzavirus may have originated from a common insect virus ancestor. A series of viable dwarf segments originating from S5 of HaCPV-14 has been identified. Analysis of the predicted secondary structures for these dwarf segments suggests that the signals essential for replication and packaging are located within the terminal sequences of these segments.

Molecular characterization of genome segments 1 and 3 encoding two capsid proteins of Antheraea mylittacytoplasmic polyhedrosis virus

“…Secondary structure was predicted using PHD and GOR4 programs [36]. To understand the evolutionary relationship between AmCPV and other members of Reoviridae , the amino acid sequences of AmCPVS1 and S3 were compared with those of other reoviruses and cypoviruses, and Phylogenetic trees were generated by neighbor-joining method with the program MEGA (http://www.megasoftware.net/index.html) [37]. Tree drawing was performed with the aid of TREEVIEW program [38].…”

Molecular characterization of genome segment 2 encoding RNA dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus

“…BLAST analysis showed that nucleotide sequence of AmCPV S2 was 29% identical with RdRp of CoCPV, LdCPV and BmCPV encoded by their genome segment 2 and allows to conclude that AmCPV S2 could also encode viral RdRp. This is supported by the MotifScan result which showed the presence of characteristic signature motifs for the RdRp of members of the Reoviridae: the conserved GDD motif at positions 681-683 and GKQXGXXXD motif at positions 526-534 (Li et al, 2007). In addition, comparison of the sequences of AmCPV S2 encoded RdRp with those of poliovirus, rabbit hemorrhagic disease virus (RHDV), reovirus, and hepatitis C virus (HCV) showed the presence of catalytic motif A (with conserved aspartates separated by four residues), motif B (with conserved "XSG" sequence), motif C (with conserved 'XDD" sequence), motif D (with conserved hydrophilic E and K residue) in the palm sub domain, as well as motif F (with submotifs, F1, F2 and F3 containing conserved positively charged, basic residues K or R) in the finger sub domain ( Fig.…”

“…AmCPV S2 amino acid sequences were then aligned with the amino acid sequence of RdRp from polio virus, rabbit hemorrhagic disease virus (RHDV), reovirus, hepatitis C virus and using the ESPript 2.2 program (http://espript.fr/ ESPript/ESPript/) to obtain and compare different conserved functional motifs. Finally to evaluate the evolutionary relationship between AmCPV and other members in the family Reoviridae, the amino acid sequences of AmCPV RdRp were compared with that of twenty seven viruses in the family Reoviridae and phylogenetic tree was generated by the neighbour-joining method with the program MEGA (http://www.megasoftware.net/index.html) (Li et al, 2007;Saitou and Nei, 1987;Tamura et al, 2007). Tree drawing was performed with the help of TREEVIEW program (Kumar et al, 2004).…”

Genomic and Biological Characterization of a New Cypovirus Isolated from Dendrolimus punctatus

“…The genome of HaCPV-14 is composed of 10 dsRNA segments. Four deletion mutants of S5, with differently deleted internal regions, have been identified in HaCPV-14 [45]. The genome of AmCPV-4 is composed of 11 dsRNA segments, and two defective variant forms of S10 were identified in AmCPV-4 [15].…”