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1 Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou city, Hainan province 571737, PR China
2 State Key Laboratory for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
Correspondence
Shaozhong Ji
szji002{at}yahoo.com.cn
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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The GenBank/EMBL/DDBJ accession numbers for the full genomic sequences and their deduced protein sequence data of the novel adult diarrhoea rotavirus strain J19 are: VP1 gene DQ113897, protein AAZ03485.1; VP2 gene DQ113898, protein AAZ03486.1; VP3 gene DQ113900, protein AAZ03488.1; VP4 gene DQ113899, protein AAZ03487.1; VP6 gene DQ113902, protein AAZ03490.1; VP7 gene DQ113905, protein AAZ03493.1; NSP1 gene DQ113901, protein AAZ03489.1; NSP2 gene DQ113903, protein AAZ03491.1; NSP3 gene DQ113904, protein AAZ03492.1; NSP4 gene DQ113906, protein AAZ03494.1; NSP5 gene DQ113907, protein AAZ03495.1.
Supplementary material is available with the online version of this paper.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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; Estes et al., 1984; Mitchell & Both, 1990). Its RNA segments encode six structural proteins (VP1, VP2, VP3, VP4, VP6 and VP7) and five non-structural proteins (NSP1, NSP2, NSP3, NSP4 and NSP5) (Estes, 2001). VP6 is the group antigen determinant, making up approximately 50 % of the viral protein (Estes et al., 1984; Estes & Cohen, 1989). The antigenic properties of VP6 are used to define seven antigenically different rotavirus groups, named groups A–G. Groups A, B and C rotaviruses infect humans, while other groups have been found only in animal species (Saif & Jiang, 1994). Group A rotaviruses cause severe diarrhoea in infants and young children, but they can also infect adults. Group C rotavirus infection occurs both in children and in adults, usually in sporadic cases or clustered outbreaks (Rodger et al., 1982; Caul et al., 1990; Jiang et al.,1995; Kuzuya et al., 1996; Nilsson et al., 2000; Adah et al., 2002; Chen et al., 2002; Ji et al., 2002; Schnagl et al., 2004).
In China, large waterborne epidemics caused by the human group B rotavirus strain adult diarrhoea rotavirus (ADRV) infected thousands of people aged between 10 and 40 years of age in the 1980s (Hung et al., 1983, 1984; Chen et al., 1985, 1990). Since then, only sporadic ADRV waterborne epidemics have been detected in China. However, two human group B rotavirus strains identified in 1998 in India (CAL-1) and 2000 in Bangladesh (Bang373), showed high sequence identity with the Chinese ADRV (Krishnan et al., 1999; Sanekata et al., 2003).
The Chinese novel ADRV (NADRV) was first identified in sporadic cases in Huaihua city in 1987 and in Fuzhou city in 1988, identification was based on a specific electrophoresis migration pattern (Wang et al., 1987). The same rotavirus was implicated in gastroenteritis outbreaks in Beijing city in 1994 and in Shijiazhuang city in 1997. Partial genes of NADRV were cloned and sequenced from stool samples of patients and primary results showed that the novel rotavirus did not belong to known groups A, B or C rotaviruses (Yang et al., 1998, 2004a). Later, an unusual human rotavirus strain, B219, was detected in a stool specimen from a 65-year-old patient with diarrhoea in Bangladesh during April 2002, which is genetically closely related to the NADRV strain (Alam et al., 2007). Recently, the novel rotavirus causing adult diarrhoea in a large scale in Shijiazhuang city in China in 1997 was isolated from stool samples and was found to be similar to NADRV. It was propagated successfully in human embryonic kidney cells in vitro and was designated a novel ADRV strain, J19 (Ji et al., 2002). Here, we further characterized strain J19 by cloning and analysing its genome segments. The information will provide direction toward understanding the origin and evolution of this novel rotavirus.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). The rotavirus dsRNA was extracted from infected tissue cultures (Gouvea et al., 1990) and treated with RNase T1 (Promega) to degrade the single-stranded RNA (for details see Supplementary material available in JGV Online).
cDNA preparation, PCR amplification and coding assignment.
The complete J19 genome was amplified and cloned using an improved single-primer sequence-independent method (Lambden et al., 1992; Jiang et al., 2006). The cloning method involved ligation of a single-amino-linked modified oligonucleotide to the 3' termini of each dsRNA segment by using T4 RNA ligase. The tailed RNA was converted to cDNA by using a complementary primer and reverse transcriptase. The resultant cDNA was annealed and repaired and amplified by PCR by using a single complementary oligonucleotide primer. The PCR products were ligated into pMD-18T-vector (TaKaRa) and transformed into JM109 cells. In order to amplify and clone genome segments of J19 larger than 2 kb, pairs of inhibitory primers, which were blocked with NH2 at the 3' termini designed from the 5' and 3' termini of seven known J19 genes by a single-primer sequence-independent method, were used to prevent amplification of short gene sequences and improve amplification of genome segments larger than 2 kb (Lambden et al., 1992; Jiang et al., 2006). Conditions for these PCR reactions were the same as described above, with the addition of inhibition primers. Inhibition primers would anneal to their corresponding genes during the PCR amplification and prevent their PCR amplification as their 3' termini was blocked by NH2. Dig-labelled cDNA probes for gene assignment studies were generated as described previously (Ando et al., 1995) and the coding assignments were determined by Northern blot analysis (for details see Supplementary material available in JGV Online).
Sequence analysis and phylogenetic analysis.
The nucleotide sequences were analysed using the ORF Finder and BLAST software program (NCBI). Using the known structural and non-structural protein sequences representing the three known rotavirus groups and J19, B219 and NADRV rotaviruses, the phylogenetic trees were generated using the MEGALIGN part of the DNASTAR software package (DNA Star). All viral protein accession numbers were previously published in GenBank.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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, seven small genes of J19 were amplified, cloned and sequenced. Although four large genes more than 2 kb could be amplified with the single primer, they failed to clone with the T-vector. This meant that the quantity of DNA from the PCR products of large genes was not enough to clone them. In order to increase the yields of PCR products of these large genes, seven pairs of inhibitory primers designed from the small genes were used to amplify the reverse transcribed cDNA. To determine the right combination of inhibitory primers, one pair, two pairs and three pairs of inhibitory primers were tested in the PCR. Results showed that one pair of inhibitory primers from genes 8, 9 or 11 could effectively improve amplification of the four genes that are larger than 2 kb. This means that every pair of inhibitory primers would have different inhibitory effects to improve yields of large genome segments. When two pairs of inhibitory primers were added to one PCR, all combinations significantly improved the amplification of the large genome segments. This means that two pairs of inhibitory primers have synergistic effects to improve yields of the large genome segments. When three pairs of inhibitory primers were added in one PCR, results were no better than those of two pairs of inhibitory primers. Therefore, we chose to use two pairs of inhibitory primers to improve yields of the PCR products of the large genome segments of rotaviruses. Although PCR yields of large genome segments were improved by adding inhibitory primers, PCR yields of small genome segments were still significant. This implied that amplification of small genome segments was only partially inhibited. Although PCR yields of the four large genome segments of J19 were increased significantly with the addition of inhibition primers, we still failed to clone the full-length cDNA of gene 1 of J19. However, a shorter fragment of gene 1 was cloned and the full-length sequencing of gene 1 was completed by genome walking. Finally, the complete genome of J19 was obtained, and the 5' and 3' terminal nucleotides of 11 genes of NADRV-J19 (Table 1) illustrated that they have the same conserved terminal sequence (5'-GGXA......ACCC-3') as rotaviruses and proved that genomic data of these 11 genes of NADRV-J19 should contain the full-length terminal nucleotide sequences of their corresponding dsRNA genes.
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) corresponding to the equivalents of VP1–VP4, VP6, VP7 and NSP1–NSP5 of group A rotavirus strain SA11. The genome of J19 is AU-rich (66.49 %), with a base composition of A (36.45 %), G (17.83 %), T (30.04 %) and C (15.68 %), and 66.1 % sequence identity with SA11. The complete genome of J19 is 17 961 bp in length, which is 51 nt longer than the genome of human group C rotavirus Bristol (17 910 bp), but 594 and 884 nt shorter than group A rotavirus strains SA11 (18 555 bp) and PO-13 (18 845 bp), respectively.
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shows non-protein-coding features of these 11 gene segments of NADRV J19. From these data, a terminal GG-sequence, common to all rotaviruses, was located at the 5'-end of all the cloned genes, while at the 3'-end of the genes -ATACCC sequence was found in 10 cloned genes (1–7 and 9–11), -ACACCC sequence was found only in the NSP3 gene, which is similar to that of NADRV and B219, but different from those of groups A, B and C rotaviruses (Yang et al., 2004a; Alam et al., 2007). Analysis of the 11 messenger sense RNA fragments with an RNA secondary structure prediction program (GeneBee) demonstrated that all of them could base-pair with themselves for nearly the entire length of the RNA and their 5' and 3' termini could form panhandle structures (Brodsky et al., 1992, 1995). Nucleotide sequence comparison (data not shown) indicated that three J19 genes have almost the same nucleotide sequences as NADRV, which further proved that J19 was isolated from similar stool samples of NADRV. Results showed that these 11 genes of J19 showed higher nucleotide sequence identities with B219 (more than 90 % at nucleotide acid level), but nucleotide sequence of 10 genes of J19 from the VP1 gene showed less than 60 % identity to groups A, B and C representative strains.
Deduced protein sequence comparisons between J19 and NADRV, B219 and groups A, B and C
Protein alignments with the corresponding proteins of NADRV and J19 showed that J19 and NADRV have the same protein sequences in NS1, VP6 and NSP3, which further proved that J19 was isolated from the novel rotavirus that caused an outbreak of gastroenteritis in China. Protein alignments with the corresponding proteins of J19 with B219, and groups A, B and C rotaviruses, produced higher per cent sequence identities to B219 (generally more than 90 % at the amino acid level) (Table 3). Among groups A, B and C rotaviruses, 10 proteins from group B rotaviruses exhibited slightly higher amino acid sequence identities to the J19 proteins (13.1–55.7 %), but proteins of J19 showed low amino acid sequence identities (less than 30 % at the amino acid level) with groups A and C rotaviruses.
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). However, analysis with the available VP6 proteins in GenBank showed 69.8–99.2, 84.4–99.0 and 39.8–100.0 % identities, respectively, among groups A, B and C rotaviruses. Combining with the previous results of serological analysis with groups A, B and C rotaviruses, this implies that J19 would be a representative strain of a new group.
Phylogenetic analysis
Unrooted phylogenetic trees were constructed using a set of known proteins and representatives of NADRV, B219 and three known rotavirus groups A, B and C. It was revealed that six of the structural proteins encoded by J19 (VP1–VP4, VP6 and VP7) were positioned close to B219 and the basal nodes of groups A, B and C lineages, although with a preferred association with group B lineages (Fig. 1). The VP6 tree comprises four distinct lineages: two lineages including only J19, B219 and group B rotaviruses, and the other two lineages including groups A and C rotaviruses. The group B rotavirus lineage is further divided into infectious diarrhoea of infant rats (IDIR) and two sister groups: the Chinese lineage containing human group B rotavirus strains ADRV and WH1 and the Indian–Bangladeshi lineage containing human group B rotavirus strains CAL-1 and Bang373. Rooted with NSP1–NSP5, the trees for NSP1–NSP5 (Fig. 2) are topologically consistent with trees constructed by using six structural proteins. From these results and consulting the demarcation criteria used for rotavirus species assignment (Ramig et al., 2005), J19 would be genetically related to NADRV, B219 and group B rotaviruses, which would be proposed as the prototype of a new species with great significance for the evolution and origin of group B rotaviruses.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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; Cashdollar et al., 1984), or directly cloned into the TA vector pCR2.1 (Zhang & Rowhani, 2000), which is considered technically complicated, inefficient and also limited by the starting material (Potgieter et al., 2002). Other methods have been improved on the basis of a single-primer dsRNA cloning sequence-independent method (Lambden et al., 1992). The method was initially used to clone small fragments and was improved further by extending the primer that ligates to dsRNA with a poly(A) tail to facilitate oligo(dT) priming of poly(dA)-oligonucleotide-ligated dsRNA (Vreede et al., 1998). However, the effectiveness of the improved method is also limited by the amount of starting material. Recently, it was shown that the use of methylmercuric hydroxide for denaturing dsRNA instead of the commonly used combination of heat and DMSO also improved the method. The improved method was used to amplify complete genomes of six dsRNA viruses using a series of one-tube reactions with a small amount of starting material (Potgieter et al., 2002; Maan et al., 2007). However, results did not report obtaining the complete genome sequences of those viruses.
Here, is the first study to put forward the concept of inhibitor priming. Because pairs of inhibitory primers originate from small gene fragments, small gene fragments could be amplified and cloned by the single-primer amplification sequence-independent dsRNA technique described by Lambden et al. (1992). PCR amplification of genome segments larger than 2 kb was improved by the use of two pairs of inhibitory primers and the product could then be cloned and sequenced. Based on the efficiency of amplifying and cloning large genome segments of J19, it is proposed that the improved method would be effective in amplifying and cloning large genome segments of other rotaviruses.
The largest reported rotavirus epidemic affected over one million people in China in 1980s and was caused by ADRV. As a result of the outbreak, significant effort has been directed towards discovering ADVR's origin. The percentage of amino acid identity between the VP6 equivalent proteins of various groups A, B and C rotaviruses and different group A subgroups suggested that the group B (ADRV) VP6 protein has diverged from groups A and C proteins in the distant past, most probably from a common ancestral VP6 precursor protein (Chen et al., 1991). It was presumed that there must be an ancestral strain for group B rotaviruses in China or other areas. This novel ADRV has since caused several outbreaks of adult diarrhoea in China (Hung et al., 1983, 1984; Chen et al., 1985), while sporadic cases caused by two group B rotavirus strains, CAL-1 and Bang373, were detected in India and Bangladesh (Kobayashi et al., 2001; Ahmed et al., 2004), respectively. CAL-1 and Bang373 were found to be genetically related and showed high nucleotide sequence identities (91–92 %) to ADRV, suggesting that these two human group B rotaviruses may have the same origin (Kobayashi et al., 2001; Ahmed et al., 2004). Protein sequence analyses and phylogenetic analyses of NSP2 from group B rotavirus strain CAL-1 showed that the strain may be the progenitor of ADRV (Sen et al., 2001). However, repeated sequencing of the ADRV NSP2 and NSP3 genes combined with phylogenetic analyses indicated that the ADRV and CAL strains evolved from a common ancestor (Jiang et al., 2005). Another human group B rotavirus strain WH1 was detected in an adult sporadic case of diarrhoea in Wuhan city, China, 20 years after the identification of ADRV. Although WH1 was found to be genetically close to ADRV, some WH1 protein genes had notable characteristics that are not found in ADRV, but are commonly observed in CAL-1 and Bang373 (Yang et al., 2004b).
Analyses of the mutation rate of human group B rotaviruses indicated that the Indian–Bangladeshi lineage must have diverged from the Chinese lineage several decades ago (Yang et al., 2004b). In this study, phylogenetic analyses of four structural proteins (VP2, VP4, VP6 and VP7) and five non-structural proteins (NSP1–NSP5) also suggest that the Indian–Bangladeshi lineage and the Chinese lineage diverged from the same progenitor during the evolution of group B rotaviruses. We examined 11 rotavirus proteins and showed that the strain J19 could be one prototype of group B rotaviruses, including ADRV, CAL-1 and Bang373, as well as others. Therefore, we offer a plausible explanation that China may be an epicentre for human group B rotaviruses, in contrast with earlier research (Sen et al., 2001). Our hypothesis could explain the sudden appearance of ADRV or NADRV that caused outbreaks of adult diarrhoea in China.
Phylogenetic analyses suggested that human group B rotaviruses in Asia originated from NADRV J19 and B219; however, we also found that these two strains cluster close to IDIR, a group B rotavirus causing diarrhoea in infant rats and later discovered in humans in the USA (Eiden et al., 1985). IDIR differs significantly from any other human group B rotaviruses found in China and India, such as ADRV and CAL-1. Therefore, group B adult diarrhoea rotavirus strains, such as ADRV, WH1, CAL-1 and Bang373 may have evolved from other ancestral strains in Asia that have not yet been isolated or identified. Recently, an unusual human rotavirus strain B219 was detected in Bangladesh. Cloning and sequence analysis of B219 strain indicated that this virus is genetically closely related to the NADRV strain (J19), which suggests that the NADRV (J19)-like novel human rotaviruses would be distributed to a geographically wider area (Alam et al., 2007). Further extensive surveillance of rotaviruses of humans and animals in China will help to understand better the origin and evolution of human group B rotavirus. Now, the availability of the full genome sequence of J19, in conjunction with the fact that the J19 strain can apparently be propagated in cell culture (Ji et al., 2002), will allow a more detailed functional analysis of the viral replication cycle.
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ACKNOWLEDGEMENTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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Received 8 March 2008;
accepted 20 May 2008.
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