Page 99 - Avian Virology: Current Research and Future Trends

92 | Paldurai and Samal

Genome structure genetic classification guideline should be developed for APMV
The genome of APMV is a non-segmented, negative-sense, serotypes.
single-stranded RNA. The viral genomes of APMV serotypes
for which complete genome sequences are available to date,
vary in length from 14,904 nucleotides (nt) for APMV-2 to Viral proteins
17,412 nt for APMV-11 and contain 6–7 genes in a linear All members of the subfamily Avulavirinae encode a nucleocapsid
array (Lamb and Parks, 2013). Comparison of full genome protein (N), a phosphoprotein (P), a matrix protein (M), a fusion
sequences are shown in Fig. 3.3. The nt length of the genome protein (F), a haemagglutinin-neuraminidase protein (HN), and
of all paramyxoviruses is an even multiple of six, known as “rule a large polymerase protein (L) (Lamb and Parks, 2013). How-
of six”, a requirement for precise packaging of the genome in ever, APMV-6 encodes an extra envelope protein, known as small
the nucleocapsid (Kolakofsky et al., 1998). Consistent with the hydrophobic protein (SH), the function of which is not known.
rule, the complete genome lengths of APMV serotypes are a The N proteins bind to the entire length of the viral genomic and
multiple of six. The 3′ and 5′ ends of the genome contain short antigenomic RNAs to form a functional nucleocapsid that is only
extragenic sequences known as the leader and trailer regions, recognized by the viral RNA polymerase. The P and L proteins
respectively. These are the control regions for transcription and associate with the nucleocapsid and serve as the RNA polymer-
replication of the viral genome. The leader region of all APMVs ase. The M protein forms the inner layer of the envelope and plays
is 55 nt (Fig. 3.4) and the trailer region varies between 17 nt for a major role in the assembly of the virus. The F protein mediates
APMV-4 to 707 nt for APMV-3. The first 12 nt of the 3′-leader viral entry and cell-to-cell fusion. The HN protein initiates infec-
and 5′-trailer regions are highly conserved among APMV sero- tion by attaching to sialic acid-containing receptor on cell surface
types. The viral RNA polymerase enters the genome at the and also possess neuraminidase activity that releases progeny
3′ end and proceeds in a sequential manner transcribing indi- virus from cell surface. The structures of F and HN proteins of
vidual mRNAs by a start-stop mechanism guided by gene-start APMV-2 are shown in Fig. 3.9. The features of F and HN pro-
(GS) and gene-end (GE) signals that flank each gene (Fig. 3.5). teins are shown in Tables 3.5 and 3.6, respectively. The L protein
Non-coding intergenic sequences (IGS) are present between is the viral RdRp. The P protein is essential for RNA synthesis.
genes and are not copied into mRNAs. During RNA replication All members of the subfamily Avulavirinae encode additional pro-
the GS and GE signals are ignored and a complementary copy teins from the P gene by RNA editing (Fig. 3.10). This involves
of the genome (antigenome) is synthesized, which is used as insertion of one or more G residues into the P mRNA by the viral
the template for synthesis of progeny genome. polymerase at a conserved RNA editing sequence. This results in
Comparisons of nucleotide sequences of individual genes or translational frameshifts that access alternate open reading frames
the full genome show great genetic variation among APMV sero- at the site of G insertion, generating the V and W proteins. Thus,
types. A phylogenetic tree generated using the complete amino the P, V, and W proteins share a common N-terminal region
acid sequences of RdRp or L protein and using the complete but differ in their C-terminal regions. The V protein is involved
coding sequences of the F gene are shown in Figs. 3.6 and 3.7, in regulating RNA synthesis and in counteracting host antiviral
respectively. Comparisons of the deduced aa sequence identi- responses (Goodbourn et al., 2000). The function of the W
ties of the ORFs of F and HN proteins are shown in Table 3.3. protein is not known. The sequences of the putative RNA edit-
Comparison of the genetic distance based on complete coding ing sites of all APMV serotypes are similar, but the nucleotide
sequences of the F gene between two APMV serotypes were in positions in the genome varies among different APMV serotypes.
the range from 0.439 to 1.207 (Table 3.3). A phylogenetic tree All viruses of the subfamily Avulavirinae (with the exception of
generated using the complete genome sequences of the APMV APMV-11) encode the P protein as the translation product from
serotypes is shown in Fig. 3.8. the unedited mRNA (+ 0G; see Fig. 3.10). The V protein is pro-
The lowest nt sequence identity between complete genomes duced from a transcript containing an additional G residue at the
of two different APMV serotypes is found between APMV-4 insertion site (+ 1G). The W protein is produced from a transcript
and APMV-6 (41.6%) and between APMV-3 and APMV-5 containing two G residues at the insertion site (+ 2G). As shown
(41.7%). The highest nt identity between complete genomes in Fig. 3.10, APMV-11 differs from other APMV serotypes in that
of two APMV serotypes is found between APMV-1 and the the V protein is produced from the unedited mRNA and the P
APMV-16 (65.8%) and between serotypes APMV-17 and protein is produced from a two-G insertion transcript, which is
APMV-18 (65.2%). The pairwise genome sequence identity and found in rubulaviruses.
the evolutionary divergence estimate between APMVs is shown The F protein of paramyxoviruses is synthesized as an inactive
in Table 3.4. The genome sequences of subgroups within APMV precursor (F0) that is cleaved by host cell protease into two bio-
serotypes also show great genetic diversity. For example, between logically active F1 and F2 subunits that are linked by a disulfide
APMV-3 strains Netherlands and Wisconsin (67.1%), between bond. Cleavage of the F protein is a prerequisite for virus entry
APMV-2 strains Yucaipa and Bangor (68.8%), and between and cell-to-cell fusion. The sequence of the F protein cleavage
APMV-6 strains Hong Kong and Italy/4524-2 (70.6%), sug- site is a well-characterized determinant of APMV-1 pathogenic-
gesting evidence for existence of greater genetic diversity within ity in chickens (Nagai et al., 1976; Peeters et al., 1999; Panda et
APMV serotypes (Kumar et al., 2010b; Subbiah et al., 2010a; al., 2004). The F protein of virulent APMV-1 strains typically
Xiao et al., 2010). These results also suggest that a consistent contains a multibasic cleavage site ([R/K]RQ[R/K]RF) that