Arch Virol DOI 10.1007/s00705-014-2083-6

ANNOTATED SEQUENCE RECORD

Complete genome sequence of a novel calicivirus from a goose Qinfeng Liao • Xiaoyan Wang • Dan Wang Dabing Zhang



Received: 23 February 2014 / Accepted: 6 April 2014 Ó Springer-Verlag Wien 2014

Abstract A novel goose calicivirus (GoCV) was sequenced. The 8013-nt-long genome was organized into two open reading frames that were in the same frame and separated by 3 nucleotides. This feature is similar to what has been observed in turkey calicivirus (TuCV). Comparison of GoCV with other caliciviruses showed that it shared the highest amino acid sequence identities of 62, 38, and 52 % in the nonstructural protein, VP1, and VP2, respectively, with TuCV. Phylogenetic analysis based on the amino acid sequences of nonstructural protein and VP1 demonstrated that GoCV was most closely related to but distinct from TuCV. Thus, GoCV was identified as a novel member in the proposed genus Nacovirus.

Introduction To date, the family Caliciviridae consists of five official genera (Lagovirus, Nebovirus, Norovirus, Sapovirus, and The GenBank accession number for the study sequence is KJ473715.

Electronic supplementary material The online version of this article (doi:10.1007/s00705-014-2083-6) contains supplementary material, which is available to authorized users. Q. Liao  X. Wang  D. Wang  D. Zhang (&) Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian district, Beijing 100193, People’s Republic of China e-mail: [email protected] Q. Liao Department of Animal Science and technology, Chongqing Three Gorges Vocational College, Chongqing, People’s Republic of China

Vesivirus) and four proposed genera (Bavovirus, Nacovirus, Recovirus, and Valovirus) [2, 3, 7, 15, 16, http://www. caliciviridae.com/]. In addition, a novel calicivirus, ‘‘secalivirus’’, has recently been partially sequenced [9]. Caliciviruses possess single-stranded, positive-stranded, polyadenylated RNA genomes that are organized into either two or three major open reading frames (ORFs) [2]. ORF1, located close to the 50 terminus of the genome, encodes nonstructural (NS) proteins that are present in all caliciviruses in the same order: N-terminal protein (Nterm), NTPase, 3A-like protein, VPg, protease (Pro), and RNA polymerase (Pol) [2]. In noro-, reco-, and vesiviruses, additional ORFs, ORF2 and ORF3, encode the major capsid protein VP1 and the minor structural protein VP2, respectively [2, 3]. In the case of bavo-, lago-, naco-, nebo-, sapo-, and valoviruses, the VP1 is encoded within the ORF1, and the ORF encoding VP2 is ORF2 [2, 7, 15, 16]. Caliciviruses are known to infect a variety of hosts. They have been detected in various birds, including chickens [16], goldfinches [13], guinea fowl [5], pheasants [4], turkeys [15], and white terns [11]. To date, no caliciviruses have been reported in geese. In this study, we report the complete sequence of a novel calicivirus detected from a goose.

Provenance of the virus material A fecal sample (designated N) was collected from a 60-day-old healthy Landes goose in October 2012 in China. The sample was treated using the method described by Sauvage et al. [12]. RNA was extracted using an RNeasy Mini Kit (QIAGEN), and randomly amplified as described previously [1]. Random PCR products were separated on a 1 % agarose gel, yielding a DNA smear.

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Fig. 1 Predicted genome organization of GoCV. Nucleotide positions of the ORFs (including stop codons) in the genome and predicted cleavage sites of the ORF1 polyprotein are shown above the

boxes representing genes. The predicted proteins and their amino acid lengths are indicated in each box. Dotted lines indicate the location of the initial sequences obtained by random amplification

DNA ranging in size from 200 to 1000 bp was excised from the gel, purified using a QIAquick Gel Extraction Kit (QIAGEN), and cloned for sequencing. Sequences were analyzed and assembled into contigs as described previously [6]. Following BLAST searches (http://blast.ncbi. nlm.nih.gov/Blast.cgi), we obtained 10 calicivirus-like sequences that were assembled into five fragments (Fig. 1). Gaps between sequenced viral fragments were closed by reverse transcription (RT)-PCR with primers designed based on the sequences of the fragments, while the 50 and 30 ends of the genome were amplified using a SMARTerTM RACE cDNA Amplification Kit (Clontech). The primers used to complete the genome sequence are shown in Supplementary Table S1. The initial genome sequence was confirmed using seven overlapping DNA fragments amplified by RT-PCR with additional primers (Supplementary Table S2). In all cases, sequencing was performed after cloning of the PCR products. For each PCR product, at least three positive clones were sequenced. The complete genomic sequence of the goose calicivirus (GoCV) N strain has been deposited in GenBank under accession number KJ473715. DNAMAN 5.2.2 (Lynnon) was used for ORF prediction and translation of ORFs into amino acid sequences. Amino acid sequence comparisons were performed using ClustalW 1.83 (http://www.genome.jp/tools/clustalw/). Based on the aligned sequences, phylogenetic trees were constructed by the neighbor-joining method, using the Poisson model and 1000 bootstrap replicates in MEGA 5.0 [14].

separated by 3 nt (UAAAACAUG; the stop codon of ORF1 and the start codon of ORF2 are underlined), similar to what has been observed in Turkey calicivirus (TuCV) [15]. The 50 and 30 untranslated regions (UTRs) of GoCV were 10 and 215 nt long, respectively. The 6960-nt ORF1 was predicted to encode a large polyprotein of 2319 aa, with a calculated molecular mass

(a)

(b)

Sequence properties The predicted genomic organization of the GoCV N isolate is shown in Fig. 1. The complete genome comprised 8013 nt, excluding the poly(A) tail, making it a relatively large calicivirus genome (Supplementary Table S3). The G?C content (54.6 %) was most similar to that of St-Vale´rien virus (54.5 %) (Supplementary Table S3). The polyadenylated genome was organized into two ORFs, extending from nt 11 to 6970 and from nt 6974 and 7798, respectively. The two ORFs were in the same frame and

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Fig. 2 Phylogenetic relationship between GoCV and other caliciviruses. The analyses were based on full-length amino acid sequences of the NS protein (a) and VP1 (b). The bar indicates genetic distance. The abbreviation of caliciviruses and accession numbers of the sequences used in phylogenetic analysis are shown in Supplementary Table S3

Novel calicivirus in goose

(Mr) of 255 kDa. Based on alignment with amino acid sequences from rabbit hemorrhagic disease virus, Sapporo virus, and TuCV [8, 10, 15], the ORF1 polyprotein of GoCV was predicted to be cleaved at five sites, which would generate Nterm (41.5 kDa), NTPase (37.9 kDa), p29 protein (28.8 kDa), VPg (8.7 kDa), Pro-Pol (73.7 kDa), and VP1 (64.4 kDa) (Fig. 1). The 825-nt-long ORF2 was predicted to encode a small protein of 274 aa, with a calculated Mr of 28.4 kDa and predicted isoelectric point of 10.2. The sizes of the deduced NS proteins of GoCV were almost identical to those of TuCV, whereas the sizes of VP1 and VP2 of GoCV were greater than those of TuCV [15]. Examination of the 1721-aa NS protein sequence of GoCV revealed that it contained characteristic motifs that are conserved in picornaviruses and other caliciviruses, including motifs typical for helicase at positions 528 (GPPGIGKT) and 606 (KGRVWASRVVAMTTN), VPg at position 1002 (EEYNTW), protease at 1174 (GDCG), and RNA polymerase at positions 1382 (KDELL), 1457 (DYKKWD), 1512 (GLPSG), 1560 (YGDD) and 1607 (FLKR). Within the VP1 sequence, the amino acids PPD at position 146 and FCLMREP at position 233 conformed with the conserved PPG motif and the FxxLxxP hinge segment between the shell and protruding domains described previously for other caliciviruses. To investigate the relationship of GoCV to other caliciviruses, phylogenetic analyses were undertaken based on amino acid sequences of the NS protein and VP1 of GoCV and the representative members of the five official and four proposed genera (Supplementary Table S3; Fig. 2). GoCV was shown to be most closely related to but distinct from TuCV. In terms of identity, GoCV shared the highest amino acid sequence identities of 62, 38, and 52 % with TuCV in the NS protein, VP1, and VP2, respectively. Identity was less than 24 % (NS protein), 35 % (VP1) and 26 % (VP2) with other caliciviruses (Supplementary Table S3). A detailed domain comparison of the NS proteins between GoCV and TuCV revealed that the NTPase showed the greatest identity (72 %). In VPg and Pro-Pol, there were also high levels of identity (64 and 67 %). As expected, lower aa identity values were observed in Nterm (49 %) and the 3A-like p29 protein (57 %). Our data on the complete sequence of GoCV demonstrate that this virus represents a novel member in the proposed genus Nacovirus. Acknowledgments This work was supported by the China Agriculture Research System (CARS-43) and the Special Fund for AgroScientific Research in the Public Interest (201003012).

References 1. Allander T, Tammi MT, Eriksson M, Bjerkner A, TiveljungLindell A, Andersson B (2005) Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci 102:12891–12896 2. Clarke IN, Estes MK, Green KY, Hansman GS, Knowles NJ, Koopmans MK, Matson DO, Meyers G, Neill JD, Radford A, Smith AW, Studdert MJ, Thiel H-J, Vinje´ J (2012) Caliciviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (ed) Virus taxonomy. Classification and nomenclature of viruses. Ninth report of the International Committee on Taxonomy of Viruses. Elsevier, London, pp 977–986 3. Farkas T, Sestak K, Wei C, Jiang X (2008) Characterization of a rhesus monkey calicivirus representing a new genus of Caliciviridae. J Virol 82:5408–5416 4. Gough RE, Drury SE, Bygrave AC, Mechie SC (1992) Detection of caliciviruses from pheasants with enteritis. Vet Rec 131:290–291 5. Gough RE, Spackman D (1981) Virus-like particles associated with disease in guinea fowl. Vet Rec 109:497 6. Kapoor A, Victoria J, Simmonds P, Wang C, Shafer RW, Nims R, Nielsen O, Delwart E (2008) A highly divergent picornavirus in a marine mammal. J Virol 82:311–320 7. L’Homme Y, Sansregret R, Plante-Fortier E, Lamontagne AM, Ouardani M, Lacroix G, Simard C (2009) Genomic characterization of swine caliciviruses representing a new genus of Caliciviridae. Virus Genes 39:66–75 8. Meyers G, Wirblich C, Thiel HJ, Thumfart JO (2000) Rabbit hemorrhagic disease virus: genome organization and polyprotein processing of a calicivirus studied after transient expression of cDNA constructs. Virology 276:349–363 9. Ng TFF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (2012) High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol 86:12161–12175 10. Oka T, Yamamoto M, Katayama K, Hansman GS, Ogawa S, Miyamura T, Takeda N (2006) Identification of the cleavage sites of sapovirus open reading frame 1 polyprotein. J Gen Virol 87(Pt 11):3329–3338 11. Poet SE, Skilling DE, Megyesl JL, Gilmartin WG, Smith AW (1996) Detection of a non-cultivatable calicivirus from the white tern (Gygis alba rothschildi). J Wildl Dis 32:461–467 12. Sauvage V, Ar Gouilh M, Cheval J, Muth E, Pariente K, Burguiere A, Caro V, Manuguerra JC, Eloit M (2012) A member of a new Picornaviridae genus is shed in pig feces. J Virol 86:10036–10046 13. Sironi G (1994) Concurrent calicivirus and Isospora lacazei infections in goldfinches (Carduelis carduelis). Vet Rec 134:196 14. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 15. Wolf S, Reetz J, Hoffmann K, Gru¨ndel A, Schwarz BA, Ha¨nel I, Otto PH (2012) Discovery and genetic characterization of novel caliciviruses in German and Dutch poultry. Arch Virol 157:1499–1507 16. Wolf S, Reetz J, Otto P (2011) Genetic characterization of a novel calicivirus from a chicken. Arch Virol 156:1143–1150

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Complete genome sequence of a novel calicivirus from a goose.

A novel goose calicivirus (GoCV) was sequenced. The 8013-nt-long genome was organized into two open reading frames that were in the same frame and sep...
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