Avian paramyxovirus

Avian paramyxoviruses 1 through to 11 are multiple unique serotypes of virus in the genera Avulavirus. Newcastle disease virus is another well characterized species within the same genus and is named APMV-1. Currently, avian paramyxoviruses (APMV) consist of eleven distinct known serotypes and the numbers will increase due to isolation of new unknown serotypes. The APMVs are separated into distinct serotypes using Hemagglutination assay and Neuraminidase assay. All the APMVs hemagglutinate chicken RBCs except for APMV-5 which does not hemagglutinate any species RBC making it unique among the APMVs. APMV-6 is also unique to the presence of SH gene between F and HN genes. APMV-11 has the longest genome length among the APMVs.

Virology

APMV contain 6–10 tandemly linked genes that encode at least 7 and as many as 12 different proteins. The gene arrangement is 3'Leader-N-P-M-F-HN-L-Trailer-5'for all the serotypes except for APMV-6 which has a unique SH gene between F and HN. The 3′ and 5′ ends of the genome contain short respective extragenic ‘leader’ and ‘trailer’, regions. The following are the important proteins produced nucleoprotein (N), a phosphoprotein (P), a matrix protein (M), a fusion glycoprotein (F), an attachment glycoprotein that in the case of the APMVs is a hemagglutinin-neuraminidase (HN), and a large polymerase protein (L) The viral RNA polymerase begins transcription at the 3′ end and proceeds downstream in a sequential manner generating individual mRNAs encompass by gene-start (GS) and gene-end (GE) signals that flank each gene. The genome is transcribed sequentially from N to L with reduction in expression levels along its length. Non-coding intergenic sequences (IGS) are present between gene boundaries and are not copied into mRNAs. N encodes nucleocapsid protein that associates with the genomic RNA forming the nucleocapsid. M encodes the Matrix protein required for viral assembly. HN and F form the viral coat, and are required for viral entry into cells and also determine the antibody response. The phosphoprotein P is a cofactor for L. The atomic structure is now available for two of them, F and HN.

Revisiting the rule of 'six'

The viral genome consists of a RNA with negative polarity. The lengths of the RNA is unusually constant among the kinds and is very similar, that amount to about 13 KB (Genus Metapneumovirus) to 18 KB (Genus Henipavirus), with most paramyxoviruses usually around 15 KB. Regarding the length of individual members of the Subfamily Paramyxovirinae more exactly, then this follows a regularity unusual with viruses, the divisibility by the number of 6: e.g. Mumpsvirus 15,384 NT, Newcastle Disease virus 15,156 NT. The rule of six describes a requirement for particular viruses to have a genome length with a multiple of six. The viruses that have been proved to prescribe to this rule are the members of the Paramyxoviridae, such as: nipah virus, human parainfluenza virus 2, sendai virus and human parainfluenza virus 3. But, based on simply counting the number of nucleotides within the genome, it could extend to many more viruses within this family and outside of it, like ebola virus.

This multiples of the number of 6 are justified in a special mechanism of the RNA with these viruses. In order for this entire process to be efficient at generating full-length genomic and antigenomic molecules (and hence mRNA molecules), the genome must effectively be enclosed within its protein coat, specifically N proteins. Without this, the virus replication machinery finds it difficult to begin replication. Each N molecule associates with exactly 6 nucleotides, which gets us to the reason as to why these viruses require their genomes to be a multiple of six. If they weren't, genome synthesis would be inefficient and infection may fail and hence natural selection may favour efficient RNA synthesis. It may also have something to do with the position of the RNA bases relative to the N subunits. This being said, not all paramyxoviruses are as stringent about the rule of six as most others. Some are happy at being a bit longer/shorter.

Fusion cleavage site

APMV	F protein cleavage site
APMV-1(Virulent)	GKRQGR Ø F
APMV-1(Avirulent)	GKRQGR Ø L
APMV-2	DKRAGR Ø F
APMV-3	ARRRGR Ø L
APMV-4	ADIQPR Ø F
APMV-5	GKRKKR Ø F
APMV-6	PAREPR Ø L
APMV-7	TLPSSR Ø F
APMV-8	GYRQTR Ø L
APMV-9	RIREGR Ø I
APMV-10	DKPSQR Ø I
APMV-11	DSGTKR Ø F

GenBank accession numbers

Accession numbers for complete genome sequence submitted in GenBank are as follows.

APMV-1, AF077761. APMV-2, EU338414. APMV-3, EU403085. APMV-4KR, EU877976. APMV-4HK, FJ177514. APMV-5, GU206351. APMV-6TW, NC 003043. APMV-6HK, EU622637. APMV-6FE, EF569970. APMV-7, FJ231524. APMV-8DEL, FJ215863. APMV-8WAK, FJ215864. APMV-9, EU910942. APMV-10, HM755888. APMV-11, JQ886184

Avian Paramyxovirus - Type 1 (APMV-1)

Newcastle disease virus (NDV) strain Texas GB is a highly virulent neurotropic virus that is used as a standard vaccine challenge virus in the U.S. In this study, the complete genome sequence of strain Texas GB was determined and compared with the complete genome sequences of other NDV strains. The genome is 15,186 nucleotides (nt) long and consists of six genes in the order of 3'leader-N-P-M-F-HN-L-5'trailer. The genome contains a 55-nt leader sequence at the 3' end and a 114-nt trailer sequence at the 5' end. The intergenic sequences are 2, 1, 1, 31, and 47 nt between N/P, P/M, M/F, F/HN, and HN/L genes, respectively. The putative cleavage site of fusion protein showed amino acid sequence of R-R-Q-K-R downward arrow F in position 112 to 117, which corresponds to those of virulent NDV strains. The phylogenetic analysis showed that strain Texas GB is closely related to the neurovirulent mesogenic strain Beaudette C (BC) and to NDV viruses isolated in China and Egypt than to other strains of NDV.^[1]

Avian Paramyxovirus - Type 2 (APMV-2)

The complete RNA genome sequence of avian paramyxovirus (APMV) serotype 2, strain Yucaipa isolated from chicken has been determined. With genome size of 14,904 nucleotides (nt), strain Yucaipa is consistent with the "rule of six" and is the smallest virus reported to date among the members of subfamily Paramyxovirinae. The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 3 to 23nt. The genome contains a 55nt leader sequence at 3' end and a 154nt trailer sequence at 5' end. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Yucaipa proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-2 strain Yucaipa is more closely related to APMV-6 than APMV-1.^[2]

Avian Paramyxovirus - Type 3 (APMV-3)

The complete genome sequence was determined for prototype parakeet/Netherlands/449/75 strain of avian paramyxovirus (APMV) serotype 3. The genome is 16,272 nucleotides (nt) in length, consisting of six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5', with intergenic regions of 31-63nt. APMV-3 genome follows the "rule of six" and is the largest among the avian paramyxoviruses reported to date, with a trailer region of 707nt, the longest in the family Paramyxoviridae. The cleavage site of F protein, A-R-P-R-G-R downward arrowL, does not conform to the preferred cleavage site of the ubiquitous cellular protease furin. Therefore, exogenous protease was needed for replication in vitro. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Netherlands proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-3 strain Netherlands is more closely related to APMV-1 than APMV-6.^[3]

Avian Paramyxovirus - Type 4 (APMV-4)

Avian paramyxoviruses (APMVs) are frequently isolated from domestic and wild birds throughout the world. All APMVs, except avian metapneumovirus, are classified in the genus Avulavirus of the family Paramyxoviridae. At present, the APMVs of genus Avulavirus are divided into nine serological types (APMV 1-9). Newcastle disease virus represents APMV-1 and is the most characterized among all APMV types. Very little is known about the molecular characteristics and pathogenicity of APMV 2-9. As a first step towards understanding the molecular genetics and pathogenicity of APMV-4, we have sequenced the complete genome of APMV-4 strain duck/Hong Kong/D3/75 and determined its pathogenicity in embryonated chicken eggs. The genome of APMV-4 is 15,054 nucleotides (nt) in length, which is consistent with the "rule of six". The genome contains six non-overlapping genes in the order 3'-N-P/V-M-F-HN-L-5'. The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 9 to 42 nt. The genome contains a 55 nt leader region at 3' end. The 5' trailer region is 17 nt, which is the shortest in the family Paramyxoviridae. Analysis of mRNAs transcribed from the P gene showed that 35% of the transcripts were edited by insertion of one non-templated G residue at an editing site leading to production of V mRNAs. No message was detected that contained insertion of two non-templated G residues, indicating that the W mRNAs are inefficiently produced in APMV-4 infected cells. The cleavage site of the F protein (DIPQR downward arrowF) does not conform to the preferred cleavage site of the ubiquitous intracellular protease furin. However, exogenous proteases were not required for the growth of APMV-4 in cell culture, indicating that the cleavage does not depend on a furin site. Phylogenic analysis of the nucleotide sequences of viruses of all five genera of the family Paramyxoviridae showed that APMV-4 is more closely related to the APMVs than to other paramyxoviruses, reinforcing the classification of all APMVs in the genus Avulavirus of the family Paramyxoviridae.^[4]

Avian Paramyxovirus - Type 5 (APMV-5)

Avian paramyxoviruses (APMV) consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74. APMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt) long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3′N-P/V/W-M-F-HN-L-5′ with intergenic regions of 4–57 nt. The genome length follows the ‘rule of six’ and contains a 55-nt leader sequence at the 3′end and a 552 nt trailer sequence at the 5′ end. The phosphoprotein (P) gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R↓F) conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site.Phylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a reliable indicator of virulence among APMV serotypes 2–9. The availability of sequence information for all known APMV serotypes will facilitate studies in epidemiology and vaccinology.^[5]

Avian Paramyxovirus - Type 6 (APMV-6)

Complete genome sequences were determined for two strains of avian paramyxovirus serotype 6 (APMV-6): the prototype Hong Kong (HK) strain and a more recent isolate from Italy (IT4524-2). The genome length of strain HK is 16236 nucleotide (nt), which is the same as for the other two APMV-6 strains (FE and TW) that have been reported to date, whereas that of strain IT4524-2 is 16230 nt. The length difference in strain IT4524-2 is due to a 6-nt deletion in the downstream untranslated region of the F gene. All of these viruses follow the "rule of six". Each genome consists of seven genes in the order of 3'N-P-M-F-SH-HN-L5', which differs from other APMV serotypes in containing an additional gene encoding the small hydrophobic (SH) protein. Sequence comparisons revealed that strain IT4524-2 shares an unexpectedly low level of genome nt sequence identity (70%) and aggregate predicted amino acid (aa) sequence identity (79%) with other three strains, which in contrast are more closely related to each other with nt sequence 94-98% nt identity and 90-100% aggregate aa identity. Sequence analysis of the F-SH-HN genome region of two other recent Italian isolates showed that they fall in the HK/FE/TW group. The predicted signal peptide of IT4524-2 F protein lacks the N-terminal first 10 aa that are present in the other five strains. Also, the F protein cleavage site of strain IT4524-2, REPR downward arrow L, has two dibasic aa (arginine, R) compared to the monobasic F protein cleavage site of PEPR downward arrow L in the other strains. Reciprocal cross-hemagglutination inhibition (HI) assays using post-infection chicken sera indicated that strain IT4524-2 is antigenically related to the other APMV-6 strains, but with 4- to 8-fold lower HI tiers for the test sera between strain IT4524-2 and the other APMV-6 strains. Taken together, our results indicated that the APMV-6 strains represents a single serotype with two subgroups that differ substantially based on nt and aa sequences and can be distinguished by HI assay.^[6]

Avian Paramyxovirus - Type 7 (APMV-7)

The complete genome sequence of avian paramyxovirus serotype 7 (APMV-7) prototype strain dove/Tennessee/4/75 was determined. The genome size is 15,480 nucleotides (nt) long and follows the "rule of six". The genome contains six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5'. The 3'-leader and 5'-trailer sequences of the genome are 55 and 127nt long, respectively. The first 12nt of the leader and trailer sequences are complementary to each other. The viral genes are flanked by highly conserved gene-start (GS) and gene-end (GE) transcription signals, and in addition the 3'-leader sequence contains a sequence ((35)AAUUAUUUUUU(45)) that is identical to the GE signal present at two of the genes. The genes are separated by intergenic sequences (IGS) ranging between 11 and 70nt. The phosphoprotein (P) gene contains a conserved RNA editing site (3'-UUUUUCCC-5') presumed to be involved in the production of V and W proteins. The viral fusion (F) protein has a single basic amino acid at the putative cleavage site ((101)TLPSSR [see formula in text] F(107)); however, the virus did not require exogenous protease for in vitro replication. The virus grew in only a few established cell lines, indicating a restricted host range. Sequence alignment and phylogenetic analysis of the predicted amino acid sequence of APMV-7 proteins with the cognate proteins of the viruses of all five genera of the family Paramyxoviridae showed that APMV-7 is more closely related to APMV-2, -6, -8 than to APMV-1, -3, -4 and -9. The mean death time in embryonated chicken eggs was found to be more than 144h, indicating APMV-7 to be avirulent for chickens.^[7]

Avian Paramyxovirus - Type 8 (APMV-8)

Complete consensus genome sequences were determined for avian paramyxovirus type 8 (APMV-8) strains goose/Delaware/1053/76 (prototype strain) and pintail/Wakuya/20/78. The genome of each strain is 15,342 nucleotides (nt) long, which follows the "rule of six". The genome consists of six genes in the order of 3'-N-P/V/W-M-F-HN-L-5'. The genes are flanked on either side by conserved transcription start and stop signals, and have intergenic regions ranging from 1 to 30nt. The genome contains a 55nt leader region at the 3'-end and a 171nt trailer region at the 5'-end. Comparison of sequences of strains Delaware and Wakuya showed nucleotide identity of 96.8% at the genome level and amino acid identities of 99.3%, 96.5%, 98.6%, 99.4%, 98.6% and 99.1% for the predicted N, P, M, F, HN and L proteins, respectively. Both strains grew in embryonated chicken eggs and in primary chicken embryo kidney cells, and 293T cells. Both strains contained only a single basic residue at the cleavage activation site of the F protein and their efficiency of replication in vitro depended on and was augmented by, the presence of exogenous protease in most cell lines. Sequence alignment and phylogenic analysis of the predicted amino acid sequence of APMV-8 strain Delaware proteins with the cognate proteins of other available APMV serotypes showed that APMV-8 is more closely related to APMV-2 and -6 than to APMV-1, -3 and -4.^[8]

Avian Paramyxovirus - Type 9 (APMV-9)

The complete genome consensus sequence was determined for avian paramyxovirus (APMV) serotype 9 prototype strain PMV-9/domestic Duck/New York/22/78. The genome is 15,438 nucleotides (nt) long and encodes six non-overlapping genes in the order of 3'-N-P/V/W-M-F-HN-L-5' with intergenic regions of 0-30 nt. The genome length follows the "rule of six" and contains a 55-nt leader sequence at the 3' end and a 47-nt trailer sequence at the 5' end. The cleavage site of the F protein is I-R-E-G-R-I downward arrowF, which does not conform to the conventional cleavage site of the ubiquitous cellular protease furin. The virus required exogenous protease for in vitro replication and grew only in a few established cell lines, indicating a restricted host range. Alignment and phylogenetic analysis of the predicted amino acid sequences of APMV-9 proteins with the cognate proteins of viruses of all five genera of family Paramyxoviridae showed that APMV-9 is more closely related to APMV-1 than to other APMVs. The mean death time in embryonated chicken eggs was found to be more than 120h, indicating APMV-9 to be avirulent for chickens.^[9]

Avian Paramyxovirus - Type 10 (APMV-10)

The biological, serological, and genomic characterization of a paramyxovirus recently isolated from rockhopper penguins (Eudyptes chrysocome) suggested that this virus represented a new avian paramyxovirus (APMV) group, APMV10. This penguin virus resembled other APMVs by electron microscopy; however, its viral hemagglutination (HA) activity was not inhibited by antisera against any of the nine defined APMV serotypes. In addition, antiserum generated against this penguin virus did not inhibit the HA of representative viruses of the other APMV serotypes. Sequence data produced using random priming methods revealed a genomic structure typical of APMV. Phylogenetic evaluation of coding regions revealed that amino acid sequences of all six proteins were most closely related to APMV2 and APMV8. The calculation of evolutionary distances among proteins and distances at the nucleotide level confirmed that APMV2, APMV8, and the penguin virus all were sufficiently divergent from each other to be considered different serotypes. We propose that this isolate, named APMV10/penguin/Falkland Islands/324/2007, be the prototype virus for APMV10. Because of the known problems associated with serology, such as antiserum cross-reactivity and one-way immunogenicity, in addition to the reliance on the immune response to a single protein, the hemagglutinin-neuraminidase, as the sole base for viral classification, we suggest the need for new classification guidelines that incorporate genome sequence comparisons (J Virol. 2010 Nov;84(21):11496-504. Epub 2010 Aug 11)(^[10]).

Avian Paramyxovirus - Type 11 (APMV-11)

We report here the complete genome of a new avian paramyxovirus (APMV-11) isolated from common snipes. Sequence data from this virus showed that it has the largest genome of APMV and unusual P gene mRNA editing.Paramyxoviruses are enveloped viruses with a negative single-stranded RNA genome of 13 to 19 kb. This family is subdivided into two subfamilies, Paramyxovirinae and Pneumovirinae. The Paramyxovirinae subfamily comprises five genera: Rubulavirus, Respirovirus, Morbillivirus, Henipavirus, and Avulavirus (5). The genus Avulavirus comprises avian paramyxoviruses (APMV) isolated from avian species. To date, only 10 different APMV serotypes (APMV-1 to -10) have been described (7) based on hemagglutination inhibition assays (3) and confirmed by phylogenetic analysis (1). APMV-2, APMV-3, APMV-6, and APMV-7 may induce respiratory disease and/or a drop in egg production in turkeys; APMV-3 may cause encephalitis in several psittacine species; and APMV-5 is associated with diarrhea and high mortality in budgerigars (1). Finally, Newcastle disease induced by APMV-1 is one of the most serious diseases in poultry, and virulent APMV-1 outbreaks must be reported to the World Organisation for Animal Health (8). During avian influenza (AI) active surveillance in 2010, a viral hemagglutinant agent was isolated in 9-day-old embryonated specific-pathogen-free chicken eggs from cloacal swabs collected from live common snipe (Gallinago gallinago) but was not an AI virus. The virus was negative by a hemagglutination inhibition assay using reference antisera against APMV-1 to APMV-10 (except APMV-5, which was not available). Viral RNA was extracted from allantoic fluid and reverse transcribed to cDNA by the use of Superscript II (Invitrogen) and random hexamers. The complete genome sequence corresponding to a new APMV was obtained using overlapping PCR and Platinum Taq DNA Polymerase (high fidelity; Invitrogen). PCR products were sequenced with an Applied Biosystems 3130 Sanger-based genetic analyzer. A contig containing high-quality trace files was assembled using vNTI (Invitrogen). Genome extremities were acquired using rapid amplification of cDNA ends (RACE) and recircularization strategies (6, 9). The genome was 17,412 nucleotides (nt) long with a GC content of 39%, complying with the rule-of-six of Paramyxovirus (4). To date, this is the largest APMV genome reported. Genome organization was typical of APMV (with the exception of APMV-6), with six genes (3′-NP-P/V/W-M-F-HN-L-5′) encoding 8 different proteins. Theoretical amino acid lengths of the eight putative proteins are as follows: NP, 455 amino acids (aa); V, W, and P, 277 aa, 181 aa, and 447 aa, respectively; M, 371 aa; F, 562 aa; HN, 583 aa, and L, 2,251 aa. The highest genomic nucleotide identity (48.9%) was obtained with APMV2/Chicken/California/Yucaipa/56. P gene mRNAs of paramyxovirus are cotranscriptionally edited in response to a cis-acting signal (4). The various editing groups are arranged according to the pattern of G insertion into P gene mRNA editing signals to produce proteins P, V, and W (2). All APMV already described require a +1 or +2 frameshift from P mRNA to obtain the V or W protein, respectively. In contrast, sequence data from this new APMV suggested that editing in the P gene is the same as is seen with mumps virus or simian virus 5. For these viruses, the P gene encodes V mRNA, and the addition of one or two nontemplated G residues in the editing site produces W or P mRNA, respectively. Based on the phylogenetic analysis, we have proposed the Common_snipe/France/100212/2010 isolate as the prototype for a new APMV type, APMV-11. (^[11]).

References