Abstract
Members of the family Rhabdoviridae have been assigned to eight genera but many remain unassigned. Rhabdoviruses have a remarkably diverse host range that includes terrestrial and marine animals, invertebrates and plants. Transmission of some rhabdoviruses often requires an arthropod vector, such as mosquitoes, midges, sandflies, ticks, aphids and leafhoppers, in which they replicate. Herein we characterize Niakha virus (NIAV), a previously uncharacterized rhabdovirus isolated from phebotomine sandflies in Senegal. Analysis of the 11,124 nt genome sequence indicates that it encodes the five common rhabdovirus proteins with alternative ORFs in the M, G and L genes. Phylogenetic analysis of the L protein indicate that NIAV’s closest relative is Oak Vale rhabdovirus, although in this analysis NIAV is still so phylogenetically distinct that it might be classified as distinct from the eight currently recognized Rhabdoviridae genera. This observation highlights the vast, and yet not fully recognized diversity, of this family.
Keywords: Niakha virus (NIAV), Rhabdoviridae, phlebotomine sandflies, complement fixation, West Africa
INTRODUCTION
Phlebotomine sandflies are small hematophagous insects that serve as vectors of protozoa, bacteria, and a diverse group of vertebrate viruses, including members of the families Rhabdoviridae, Bunyaviridae, Flaviviridae and Reoviridae (Karabatsos, 1985; Shope and Tesh, 1987; Tesh, 1988). Of the rhabdoviruses associated with sandflies, most are members of the genus Vesiculovirus, including such human and veterinary pathogens as Chandipura (CHPV), Vesicular stomatitis Indiana (VSIV) and Vesicular stomatitis New Jersey (VSNJV) viruses (Karabatsos, 1985; Shope and Tesh, 1987)
In this communication we report the characterization of a novel virus (DakArD 88909), which we designate as Niakha virus (NIAV) after the site where it was first isolated in Senegal. NIAV was isolated from a pool of 200 sandflies collected in front of a termite hill located near a seasonal ground pool in Niakha in March 1992. This location is situated 4 km west of the village of Barkedji, within the Sahelian shrubby savannah ecotype, Senegal (Fontenille et al., 1994). This virus was sensitive to chloroform treatment and was isolated after 2 passages in newborn mice, which were paralyzed by day 2 post infection (p.i.). According to Fontenille et al., complement fixation (CF) suggested that this isolate was different from 80 other African arboviruses registered at the time at the World Health Organization Collaborating Center for Reference and Research on Arboviruses (CRORA) located at the Institut Pasteur de Dakar, as well as a couple of Phleboviruses isolated in Africa at the time (Fontenille et al., 1994). To date, there is no evidence that NIAV infection leads to human disease. Here we show that NIAV is a new rhabdovirus species with a distinctive morphology and genome organization that it is distantly related to Oak Vale virus isolated in Australia.
RESULTS AND DISCUSSION
Growth in cell culture
NIAV produced marked cytopathic effect (CPE) in BHK (baby hamster kidney), Vero E6 (African green monkey kidney) and C6/36 (Aedes albopictus) cells, 4, 8 and 7 days after inoculation, respectively, but it did not produce CPE in PP-9 (Phlebotomus papatasi) cells. Ultrathin-section electron micrographs of the virus in infected BHK and PP-9 cells are shown in Figures 1 A-D and E-F, respectively.
Figure 1. Ultrastructure of NIAV strain DakArD 88909 in baby hamster kidney (BHK) (A-D) and sandfly (Phlebotomus papatasi) PP-9 (E-F) cells.
(A) Stacks of virus particles in an expansion of perinuclear space (arrows) of an infected BHK cell. Ribosomes are decorating the outer surface of its membrane. N = cell nucleus; (B) A stack of virus particles in a cistern of granular endoplasmic reticulum of BHK cell; (C) Cross section of a stack of virus particles in a cistern of granular endoplasmic reticulum; (D) Virions budding from the surface of an infected BHK cells; (E) Virus particles in space between infected PP-9 cells. They are ~50 nm in diameter, virion at the top is 350 nm long. Arrow indicates a virus budding from the host cell membrane; (F) Aggregate of virus particles in an extracellular space of infected PP-9 cells. Bars = 1 μm.
Virus morphology
Virus particles were regularly found packed in stacks in expansions of perinuclear space and in cisterns of granular endoplasmic reticulum of BHK cells (Figure 1, A-C). They were ~45 nm in diameter and 180-200 nm in length. The accumulation of NIAV particles in intracellular vesicles is not unusual for rhabdoviruses. In fact, particles stacked in intracellular vesicles were reported in the first description of VSV morphogenesis in 1968 (Hackett et al., 1968). While mature virions of animal rhabdoviruses exit the cell by a budding process through the cell membrane, it is possible that the observed stacks of NIAV will be transported through these membrane bound vesicles (e.g endoplasmic reticulum) to the cell surface for budding. Virions observed budding from the BHK cell surfaces (Figure 1, D), exhibited a two-rounded end bullet-like particle morphology of ~40 nm in diameter, rather than the classic one-rounded end bullet-like rhabdovirus morphology. A similar particle morphology was observed with Oak Vale virus (OVRV)(Gubala, 2009), and Tupaia virus (Kurz et al., 1986). In ultrathin sections of PP-9 cells, virus particles ~50 nm in diameter and up to 350 nm long were observed mostly at the cell surface, where they could be seen budding (Figure 1, E). Aggregates of tightly packed virions were also observed in the extracellular space of the sandfly cells (Figure 1, F).
Antigenic relationships
Complement fixation (CF) tests were conducted using NIAV mouse brain antigen and hyperimmune ascitic fluid (MIAF) and antisera against 23 other rhabdoviruses, including 19 viruses isolated previously in Africa (Table 1). NIAV MIAF reacted only with the homologous (NIAV) antigen at a dilution of 1:512. No CF cross-reactions were detected with any of the other 23 rhabdoviruses.
Table 1.
Antigenic relationship by complement fixation (CF) test of NIAV with other representative members of the family Rhabdoviridae
| Rhabdoviridae | Antigen Virus (strain) | NIAV antibody * |
Homologous antibody |
|---|---|---|---|
|
Vesiculovirus genus
| |||
| Species in the genus | Chandipura (DakArD 1125) | 0 | 512 |
| Isfahan (91026-167) | 0 | 64 | |
| VSV Indiana (VP98F) | 0 | 512 | |
| VSV New Jersey (PA AN 3566) | 0 | 64 | |
|
|
|||
| Related viruses not yet approved as vesiculovirus |
Boteke (DakArB 1077) | 0 | ≥256 |
| species | Perinet (DakArMg 802) | 0 | 512 |
|
| |||
|
| |||
| Other animal rhabdoviruses not yet approved as species |
Bangoran (DakArB 2053) | 0 | 256 |
| Bimbo(DakAnB 1054) | 0 | ≥256 | |
| Durham (CC 228-05) | 0 | 512 | |
| Garba (DakAnB 439) | 0 | 1024 | |
| Gossas (DakAnD 401) | 0 | 512 | |
| Kamese (MP 6186) | 0 | ≥256 | |
| Keuraliba (DakAnD 5314) | 0 | 1024 | |
| Kolente (DakArK7292) | 0 | 1024 | |
| Kolongo (DakArB 1094d) | 0 | 8 | |
| Le Dantec (Dak SH 763) | 0 | ≥1024 | |
| Mossuril (SA Ar 1995) | 0 | 32 | |
| Nasoule (DakAnB 4289) | 0 | ≥256 | |
| Nkolbisson (YM 31-65) | 0 | ≥256 | |
| Ouango (DakArB 2053) | 0 | 64 | |
| Yata (DakArB 2181) | 0 | 256 | |
| Niakha (DakArD 88909) | 512 | - | |
CF titer expressed as reciprocal of highest positive antibody dilution, 0 = <8
Phylogenetic analysis
The ML tree of 45 rhabdovirus L protein sequences is shown in Figure 2. Members of the Cytorhabdovirus, Novirhabdovirus and Nucleorhabdovirus genera are highly divergent from all other rhabdoviruses including NIAV and hence were excluded from this analysis to maximize phylogenetic resolution with respect to NIAV. Notably, in this analysis NIAV falls as a distinct lineage within the major group of animal rhabdoviruses, which includes a number of recognized and proposed viral genera. While NIAV is most closely related to Oak Vale rhabdovirus (OVRV) in this phylogeny, and with relatively good bootstrap support (75%), these viruses are still relatively divergent, indicative of a long evolutionary separation. Although a lack of bootstrap support at the base of this part of the tree prevents fine-scale resolution of the evolutionary history of NIAV, its divergent phylogenetic position, combined with its lack of cross-reaction to other rhabdoviruses in CF tests (see above), strongly suggests that it represents a novel virus species. Indeed, NIAV is clearly more phylogenetically distinct than a number of recognized species within the Rhabdoviridae.
Figure 2. ML phylogenetic tree of 45 rhabdovirus L protein sequences.
The position of NIAV is shaded and bootstrap support values (>70%) are shown for key nodes. All horizontal branch lengths are drawn to a scale of amino acid substitutions per site, and the tree is rooted in the position observed in a broader analysis of the Rhabdoviridae (i.e. including members of the Cytorhabdovirus, Novirhabdovirus and Nucleorhabdovirus; not shown). (*) Genera proposed but not yet formally approved by the International Committee on Taxonomy of Viruses (ICTV).
Genome organization and assembly
A sequencing library was prepared from the sample RNA extracted from BHK infected cells, using an Illumina TruSeq RNA v2 kit following the manufacturer’s protocol. The sample was sequenced on a HiSeq 1000 using the 2×50 paired-end protocol. Reads in fastq format were quality-filtered, and any adapter sequences were removed, using Trimmomatic (Lohse et al., 2012) software. The de novo assembly program ABySS (Simpson et al., 2009) was used to assemble the reads into contigs, using several different sets of reads, and k values from 20 to 40. A nearly full-length contig was obtained from a 250,000 read random subset of the total reads that included non-viral and viral reads and a k value of 25. Reads were mapped back to the contig using bowtie 2 (Langmead and Salzberg, 2012), and visualized with the Integrated Genomics Viewer (Robinson et al., 2011) to verify that the assembled contig was correct. About 5% of the reads in the sample mapped to the viral contig, resulting in about 350,000 reads mapped out of about 7.6 million total.
The 11,124 nt NIAV genome comprises partially complementary 3′- and 5′-terminal non-coding regions (approximately 57 nt and 54 nt, respectively) and five coding regions (genes), each bounded by putative transcriptional regulatory sequences (Figure 3A-C). The transcription termination/polyadenylation (TTP) signals ([G/U]UAC[U]7) are relatively conserved and similar to those of most other animal rhabdoviruses (Figure 3B). However, transcription initiation (TI) sequences, although also similar to those of many other rhabdoviruses, are more cryptic and apparently quite variable, with only the first three nucleotides (UUG) fully conserved and alternative initiation sites appear to be available in the first three coding regions. Uniquely among those rhabdoviruses sequenced to date, the gene 2 TI sequence appears to be located upstream of the gene 1 TTP sequence to create an overlap that is more commonly associated with rhabdovirus L genes. Gene 1 contains a single ORF encoding a 426 amino acid (aa) polypeptide (47.4 kDa) with identifiable sequence identity to the N proteins of other rhabdoviruses. Gene 2 also contains a single ORF encoding a 297-aa acidic polypeptide (33.6 kDa; pI 4.78) that exhibits the highest sequence similarity to the TUPV P protein and a similar size and charge distribution to the P proteins of other animal rhabdoviruses. Gene 3 contains two consecutive ORFs: the first ORF encodes a 187-aa polypeptide (20 kDa) that aligns with the M proteins of other animal rhabdoviruses; and the second ORF (U1) encodes an 81-aa polypeptide (9.4 kDa) that shows no significant sequence identity with any other known protein and is of unknown function. The termination codon of the M ORF and the initiation codon of the U1 ORF overlap by a single nucleotide, resulting in a -1 shift in reading frames. Gene 4 encodes the 511-aa NIAV G protein. It displays the common features of rhabdovirus G proteins which are class I transmembrane glycoproteins containing an N-terminal signal peptide, a C-terminal transmembrane domain, multiple N-glycosylation sites and a set of highly conserved cysteine residues (Figure 4). Multiple sequence alignments indicated that the NIAV G protein is most similar to those of TUPV and DURV with which it shares ten of the twelve cysteine residues (C1 to CXII) that are highly conserved amongst animal rhabdoviruses (Walker and Kongsuwan, 1999) (Figure 4A). Unlike those rhabdoviruses analyzed to date, the NIAV contains an alternative ORF in the N-terminal region of the G gene. ORF U2 encodes a small 97-aa hydrophobic protein (10.8 kDa) with two predicted transmembrane domains and the predicted topology of a class IVb transmembrane protein with a C-terminal ectodomain and no predicted N-glycosylation sites (Figure 4B). The function of the NIAV putative U2 is presently unknown.
Figure 3. Organisation of NIAV single-strand negative-sense RNA genome.
(A). Schematic representation of the genome organisation of NIAV and several distantly related rhabdoviruses (Oak Vale virus, OVRV Genbank JF705877; Durham virus, DURV, Genbank FJ952155; Tupaia virus, TUPV, Genbank NC007020; and Moussa virus, MOUV, Genbank FJ985749). Block arrows indicate the location of long ORFs, including consecutive and overlapping ORFs (light shading). The DURV genome organisation is based on the available partial sequence. Several alternative long ORFs in the OVRV genome have not been reported previously. (B). NIAV coding regions, designated ORFs and putative transcription regulatory sequences. (C). Sequences of NIAV gene junctions illustrating potential transcription initiation sequences (shaded), transcription termination/polyadenylation sequences (solid underlined) and initiation and termination codons of the flanking ORFs (dotted underline). Alternative initiation codons at the G-L gene junction are for the U3 and L ORFs in different reading frames.
Figure 4. Deduced amino sequences of polypeptides encoded in NIAV G gene.
(A). Sequence alignment of the DURV (GenBank ADB88756), TUPV (GenBank YP238533), VSINV (GenBank) and NIAV G proteins showing predicted signal peptides (broken line), transmembrane domains (light shading) and N-glycosylation sites (bold and underlined). Cysteine residues in the ectodomains (dark shading) are numbered according to the conserved patterns observed in all animal rhabdovirus G proteins [25]. Fully conserved (*), strongly conserved (:) or weakly conserved (.) amino acids are indicated below the alignment. (B). Deduced amino acid sequence and predicted membrane topology of the NIAV U2 protein. Predicted transmembrane domains are shaded.
Significantly, NIAV shared with DURV and TUPV (but not OVRV) 10 of the 12 cysteine residues that are highly conserved among animal rhabdoviruses. Each of these viruses lacks the CVIII-CX disulphide bridge which, in the VSIV G protein, links the second segment of pleckstrin homology domain (domain III) to helix C which sits just before the junction with the fusion domain (domain IV)(Roche et al., 2006; Roche et al., 2007). The NIAV G protein does have an additional pair of cysteine residues downstream of CXII in the lateral domain (domain I). These cysteine residues, which are likely to form a disulphide bridge, are absent from the tupavirus G proteins. They are in a region that appears to correspond to the [s’t] loop of VSINV which is exposed on the G protein surface and is the location of an antigenic site (Vandepol et al., 1986). NAIV gene 5 encodes the L protein (RNA-dependent RNA polymerase). Also unique among known rhabdoviruses is that an alternative ORF (U3) overlaps the N-terminal region of the L ORF by 142 nucleotides. ORF U3 encodes a highly basic 51-aa polypeptide (6.4 kDa; pI 11.65) of unknown function. U3 is the first ORF that would be detected by ribosomal scanning on the L mRNA suggesting that it may attenuate L ORF expression as appears to have been achieved in some other rhabdoviruses by an overlap with the gene upstream (Tordo et al., 1986) (reviewed in (Walker et al., 2011)).
Immunodetection of NIAV proteins
Western immunoblotting was conducted using NIAV MIAF and control pre-immune serum on NIAV- and mock-infected Vero cells. At 4 days post infection (dpi), infected whole-cell extracts contained seven proteins that were not present in mock-infected cell extracts (Figure 5). Identification of the putative viral proteins encoded by the genomic nucleotide sequence was based on their predicted sizes. Since the bands are not individually identified (e.g. against protein specific antisera), they are referred to below as putative proteins. The largest of these proteins is presumed to be the L protein, which was predicted to have mass of 243.2 kDa. The second largest is the G protein with a calculated size of 59.9 kDa (55.9 with the signal peptide removed and unglycosylated). This protein contains two predicted N-glycosylation sites each adding approximately 3.5 kDa, which corresponds to the observed size of approximately 63 kDa (Figure 5). The third largest protein is the N protein with a calculated size of 47.4 kDa. The P protein, with a calculated size of 33.6 kDa is the fourth largest protein. This protein is usually very immunogenic and reacts strongly with MIAF. However, its strong charge characteristics and alternating acidic and basic domains and high proportion of proline residues render its electrophoretic characteristics in SDS-gels very inaccurate. Thus, conclusive identification of the P band is difficult using MIAF in the absence of other information, as either of the two strong bands migrating at approximately 35 kDa and 45 kDa could be P (Figure 5). The other may be a digested fragment of a larger protein (probably G). The M protein with a calculated size of 18kDa is the fifth largest protein. Resolution of the length of the M protein may be unreliable to determine by SDS-PAGE alone for which size estimations can be influenced by structural features. Furthermore, in this MIAF-probed immunoblot there is no evidence for expression of the putative U1, U2, or U3 ORFS (Figure 3A, B), and such evidence will require additional work. Lastly, the absence of any identifiable bands in the mock-infected cell lysates probed with NIAV-raised MIAF or the mock- and NIAV-infected cell lysates probed with a control pre-immune mouse serum, suggests that the additional bands beyond the 5 that match the predicted sizes of the canonical ORFs (N-P-N-G-L) in the NIAV genome sequence are due to non-specific reactivity of the NIAV-MIAF.
Figure 5. Immunoblotting of NIAV- and mock-infected BHK cells at four days post infection using pre-immune mouse serum and mouse ascitic fluid made to NIAV.
Proteins unique to NIAV-infected cells are highlighted by arrows. The molecular mass landmarks of the Rainbow Molecular Weight Marker® (GE Healthcare Life Sciences) are also indicated.
NIAV pathology in mice
Three litters of newborn (1-2 day old) ICR mice with an average size of 10 pups were inoculated intracerebrally (i.c.)(15-20μL each), intraperitoneally (i.p.)(100μL each) or subcutaneously (s.c.)(100μL each) with a stock of Vero-grown NIAV (DakArD 88909) virus containing ~106.5 TCID50/mL. The animals were observed daily for illness and were euthanized when they became severely ill. By day 3 post-inoculation, all members of the i.c.-inoculated group were dead or dying. The groups inoculated i.p.- or s.c. developed signs of illness (lethargy, loss of balance, spastic movements) more slowly, but all were dead or very sick by day 7. In contrast, adult ICR mice injected i.p. with a 10% brain suspension from infected newborn mice survived and did show signs of illness They subsequently developed high levels of CF antibody. Collectively, these observations suggest that the susceptibility of mice to NIAV disease is age related.
Sequentially cut thin sections of tissues (brain, lung, liver, spleen and kidney), collected from three sick i.p.-infected mice, were stained with hematoxylin and eosin (H&E) for histopathology and for immunohistochemistry, using a NIAV-specific polyclonal antibody (mouse immune ascitic fluid). Sections of the brain showed numerous apoptotic bodies in the granular layer of the cerebellum (Figure 6A, black arrow). Purkinje cells in many sections were degenerating with eosinophilic nuclei and vacuolated cytoplasm (Figure 6A, blue arrow). There was perivascular cuffing (Figure 6B) and meningitis (Figure 6C). Purkinje cells demonstrated lightly esosinophilic areas in the cytoplasm most consistent with viral inclusions (Figure 6D). Immunohistochemistry showed NIAV antigen - positive neurons in the cerebrum (Figure 6E) and in the cerebellum including Purkinje cells (Figure 6F-G).
Figure 6. Representative histopathology in brain of newborn mice infected with NIAV.
(A) Apoptotic bodies in the granular layer of the cerebellum (black arrow) and degenerating Purkinje cells with eosinophilic nuclei and vacuolated cytoplasm (blue arrow). (B) Perivascular cuffing. (C) Meningitis. (D) Purkinje cells with lightly easinophilic areas in the cytoplasm most consistent with viral inclusions. (E) NIAV-positive neurons in the cerebrum. (F-G) NIAV-positive neurons including Purkinje cells in the cerebellum (Figure 6F-G).
Sections of the heart, lung and kidney showed no significant histopathologic changes. Extramedullary hematopoiesis was present in the liver and spleen, but this was likely due to the young age of the animals. No abnormalities were identified in the liver or spleen.
CONCLUSIONS
NIAV is a novel rhabdovirus isolated from phlebotomine sandflies in Senegal. Despite the 20 years that have elapsed since its isolation, little is known about its host range and epidemiology. The fact that NIAV has been isolated only once suggests either that NIAV is rare (in particular, it is unlikely to be associated with serious disease in humans or livestock, where it would likely have been tested and found repeatedly), or that the limited epidemiological information and paucity of serosurvey data from that sparsely populated region of West Africa prevents a comprehensive and accurate assessment of its full geographic range, prevalence, and host range. Since the natural host(s) of NAIV beyond the insect source are unknown, acquisition of human and animal sera from the same geographic area would offer insights to the extent of human and veterinary exposure to NIAV infection.
Although the rhabovirus genomes are similar in size, the NIAV genome organization varies greatly from those of the other rhabdoviruses with respect to the location of alternative ORFs potentially encoding accessory proteins. Furthermore, the L protein phylogeny indicates that NIAV is relatively distantly related to all other known rhabdoviruses. Analysis of the NIAV genome indicates several unique aspects among those rhabdoviruses characterized to date. Specifically, the M gene contains two consecutive ORFs whose mechanism of expression is unclear but similar to the alpha genes (α1 and α2) observed in ephemeroviruses (reviewed in (Walker et al., 2011)). The G gene contains an alternative ORF in the N-terminal domain, which was previously been observed as an overlapping ORF in the C-terminal domain of Wongabel virus (Gubala et al., 2008). The U2 encoded in the G gene is a small hydrophobic protein but appears to have a different structure to those described in other rhabdoviruses. Lastly, the L gene also uniquely contains an alternative ORF, which overlaps the N-terminal region of the L ORF and is the first ORF that would be detected by ribosomal scanning on the L mRNA.
Immunodetection of NIAV-infected cells indicates that some of the predicted novel proteins may be expressed in infected cells; additional studies are currently underway which hopefully will elucidate their role and function in the NIAV replication cycle.
The uniqueness of NIAV underscores the diversity of the Rhabdoviridae and highlights the necessity of further studies to decipher this diverse and complex family of viruses. The recent sudden emergence of Bas Congo rhabdovirus from an unknown source in West Africa and its association with acute hemorrhagic fever and death (Grard et al., 2012) illustrates the importance of more comprehensive investigation of uncharacterized viruses.
MATERIALS AND METHODS
Virus source
Niakha virus (DakArD 88909) was isolated from a single pool of 200 mixed sandfly species (Phlebotomus duboscqi and Sergentomyia sp.) collected in light traps near a ground pool at Niakha in the district of Barkedji in the Ferlo region (15°17′ N; 14°53′ W) of Senegal in March 1992 (Fontenille et al., 1994). The original isolation was made at the Institut Pasteur de Dakar by intracerebral inoculation of newborn mice with a homogenate of the sandfly pool. Initial serological studies at the Institut Pasteur de Dakar failed to demonstrate an antigenic relationship of DakArD88909 with 80 other African arboviruses (Fontenille et al., 1994); a sample of the virus of unknown passage history was subsequently sent by Dr. Jean Pierre Digoutte to the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) for further study. Stocks were prepared after 3 passages in Vero cells. Because NIAV plaques poorly in Vero or BHK cells, quantification was based on its cytopathic effect (CPE) in serial 10-fold dilutions of Vero cells (TCID50).
Cells
Four different cell lines [BHK-21 (baby hamster kidney), Vero E6 (African green monkey kidney), C6/36 (Aedes albopictus) and PP-9 (Phlebotomus papatasi)] were used in this study. Each was originally obtained from the American Type Culture Collection (ATCC) (Manassas, VA). The PP-9 cell line was initiated by Robert Tesh and Govind Modi from embryonated eggs of Phlebotomus papatasi, using techniques described previously (Tesh and Modi, 1983). Monolayer cultures of vertebrate (BHK, Vero E6) or insect (PP-9) cells in T-25 flasks were inoculated with 100 μl of ~105.5 TCID50 of a Vero stock. After 2 hours of incubation at 37°C (vertebrate cells) or 28°C (insect cells), maintenance medium (Vasilakis et al., 2013) was added and the culture was maintained at either 37°C or 28°C, respectively, and examined daily for evidence of viral cytopathic effect (CPE).
Transmission electron microscopy
For ultrastructural analysis, ultrathin sections of infected cells were fixed for at least 1 h in a mixture of 2.5% formaldehyde prepared from paraformaldehyde powder, and 0.1% glutaraldehyde in 0.05 M cacodylate buffer pH 7.3 to which 0.03% picric acid and 0.03% CaCl2 were added. The monolayers were washed in 0.1 M cacodylate buffer, cells were scraped off and processed further as a pellet. The pellets were post-fixed in 1% OsO4 in 0.1 M cacodylate buffer pH 7.3 for 1 h, washed with distilled water and en bloc stained with 2% aqueous uranyl acetate for 20 min at 60° C. The pellets were dehydrated in ethanol, processed through propylene oxide and embedded in Poly/Bed 812 (Polysciences, Warrington, PA). Ultrathin sections were cut on a Leica EM UC7 ultramicrotome (Leica Microsystems, Buffalo Grove, IL), stained with lead citrate and examined in a Philips 201 transmission electron microscope at 60 kV.
Preparation for vRNA extraction
BHK cell monolayers, grown to 90% confluence in a T150 flask, were inoculated with approximately 4 ml of DakArD 88909 virus harvested from a T25 flask of BHK cells (as described above). Infected cells were incubated for 1 h with periodic gentle rocking to facilitate virus adsorption at 37°C. Following incubation, the viral inocula were removed, cell monolayers were washed thrice with PBS to remove unadsorbed virus, 12 ml of culture medium (DMEM-high glucose supplemented with 10% FBS, and 50mg/ml penicillin/streptomycin) (Invitrogen, Grand Island, NY) was then added, and the cells were incubated at 37°C. Supernatants were harvested approximately 4 days later when marked CPE was developed and clarified by low speed centrifugation (2,000 X g, 10 min at 4°C). To remove remaining cellular debris, the supernatant was filtered through a 0.45 μM filter (EMD Millipore, Billerica, MA). The clarified supernatant was transferred to a 50 ml tube and treated with a cocktail of DNases [14 U Turbo DNase (Ambion, Austin, TX), 20 U Benzonase (EMD Millipore, Billerica, MA) and 20 U RNase One (Promega, Madison, WI)] for 1 h at 37°C. To further reduce the volume, 24 ml of supernatant was loaded on top of 8 ml of 30% sucrose (in TEN, pH 7.4) located on the bottom of a SW28 Beckman UltraClear tube, and centrifuged at 150,000 x g for 4 h at 4°C. The pellet was resuspended in 250 μl RNase/DNase and protease-free water (Ambion, Austin, TX). vRNA was then extracted through the Trizol method and resuspended in 50 μl RNase/DNase and protease-free water (Ambion, Austin, TX).
Next generation sequencing
Library construction
Viral RNA (0.1-0.2 μg) quantified by Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA), was fragmented by incubation at 94°C for 8 min in 19.5 μl of fragmentation buffer (Illumina 15016648). First and second strand synthesis, adapter ligation and amplification of the library were performed using the TruSeq RNA Samplec Preparation kit under conditions prescribed by the manufacturer (Illumina, San Diego, CA). Samples were tracked using the “index tags” incorporated into the adapters as defined by the manufacturer.
Sequence analysis
Cluster formation of the library DNA templates was performed with the Illumina TruSeq PE Cluster Kit v3 and the Illumina cBot workstation using conditions recommended by the manufacturer. Paired end 50 base sequencing by synthesis was performed using Illumina TruSeq SBS kit v3 on an Illumina HiSeq 1000 using protocols defined by the manufacturer. Cluster density per lane was 645-980 k/mm2 and post filter reads ranged from 148-178 million per lane. Base call conversion to sequence reads was performed using CASAVA-1.8.2. Virus assembly was performed using SeqMan Lasergene software (DNASTAR, Madison, WI). In certain cases, pre-filtering of reads to remove host sequence enhanced the assembly process. Assembly was carried out using a fasta file of Aedes albopictus sequences to remove host DNA from the assembly thus reducing the number of contigs present.
Genomic analysis
BLASTX was used to identify sequence homologies with other viruses. Open reading frames were identified using MacVector® version 12.0 (Accelrys, Cary, NC). The presence of conserved protein domains was determined using the SMART webserver (Letunic et al., 2012; Schultz et al., 1998)
Nucleotide sequence accession numbers
The complete genome sequence of NIAV was determined in this study and assigned GenBank accession number KC585008. The GenBank accession numbers for the genome sequences of other rhabdoviruses used in the phylogenetic analyses are as follows: ARV, Adelaide River virus (AFR23540); ABLV, Australian bat lyssavirus (NP478343); ARAV, Aravan virus (ABV03822); BEFV, bovine ephemeral fever virus (NP065409); CHPV, Chandipura virus (AED98393); COCV, Cocal virus (ACB47438); CPV, coastal plains virus (ADG86364); DMelSV, Drosophila megalomaster sigmavirus (YP003126913); DObSV, Drosophila obscura sigmavirus (ACU65444); DURV, Durham virus (ADB88761); DUVV, Duvenhage virus (AFK93192); EVEX, Eel virus European X (AFX58972); EBLV1, European bat lyssavirus 1 (YP001285392); FLAV, Flanders virus (AAN73288); HIRV, Hirame rhabdovirus (NP919035); IKOV, Ikoma lyssavirus (AFQ26098); IHNV, infectious hematopoietic necrosis virus (NP042681); IRKV, Irkut virus (ABV03823); ISFV, Isfahan virus (CAH17548); JURV, Jurona virus (AEG25349); KHUV, Khujand virus (ABV03824); KIMV, Kimberley virus (AFR67096); KOTV, Kotonkan virus (YP006202628); LBV, Lagos bat virus (AFW16650); MARAV, Maraba virus (AEI52253); MOKV, Mokola virus (YP142354); MOUV, Moussa virus (ACZ81407); NGAV, Ngaingan virus (YP003518294); OVRV, Oak Vale virus (AEJ07650); OBOV, Obodhiang virus (YP0062000965); OZEV, Ozernoe virus (ACS70797); PRV, Perinet virus (AEG25355); PFRV, Pike fry rhabdovirus (ACP28002); RABV, rabies virus (ABN11300); SBV, Shimoni bat virus (ADD84511); SCRV, Siniperca chuatsi rhabdovirus (YP802942); SHRV, snakehead virus (NP050585); SVCV, spring viraemia of carp virus (NP116748); TIBV, Tibrogargan virus (ADG86355); TUPV, Tupaia virus (YP238534); VSAV, Vesicular stomatitis Alagoas virus (ACB47443); VHSV, viral hemorrhagic septicemia virus (BAM29126); VSIV, Vesicular Stomatitis virus, Indiana (NP041716); VSNJV, Vesicular stomatitis New Jersey virus (AAA48442); WCBV, West Caucasian bat virus (ABV03821); and WONV, Wongabel virus (YP002333280). The ICTV has not yet recognized NIAV as a member species in the family Rhabdoviridae. As a consequence, its abbreviation should be considered tentative and subject to approval.
Phylogenetic analysis
The L protein sequence of NIAV was compared with those of 44 other rhabdoviruses downloaded from GenBank. Because of their excessive sequence divergence to the other rhabdoviruses including NIAV, members of the Cytorhabdovirus, Novirhabdovirus and Nucleorhabdovirus genera were excluded from this analysis; their inclusion resulted in reduced phylogenetic resolution at internal nodes of the tree, including those relating to NIAV (not shown). All protein sequences were aligned using MUSCLE (Edgar, 2004) under default settings. Ambiguously aligned regions, which may negatively effect phylogenetic analysis, were removed using the Gblocks program (Talavera and Castresana, 2007); this resulted in a final sequence alignment of 1110 amino acid residues. The phylogenetic relationships among these sequences were determined using the maximum likelihood (ML) method available in the PhyML 3.0 program (Guindon et al., 2010), employing the WAG+Γ model of amino acid substitution and subtree pruning and regrafting (SPR) branch-swapping. The support for each node was determined using 1,000 bootstrap replicates.
Antigens and immune reagents
Antigens used in complement fixation (CF) tests and for immunizing animals were prepared from infected newborn mouse brains. CF antigens were prepared by the sucrose/acetone extraction method (Clarke and Casals, 1958). Specific hyperimmune mouse ascitic fluids were prepared against each of the 24 rhabdoviruses listed in Table 1. The immunization schedule consisted of four intraperitoneal injections given at weekly intervals. Immunogens consisted of 10% suspensions of homogenized infected mouse brain in PBS mixed with Freund’s adjuvant just prior to inoculation. Sarcoma 180 cells were also given intraperitoneally after the final immunization to induce ascites formation. All animal experiments were carried out under an animal protocol approved by the University of Texas Medical Branch IACUC committee.
Serologic testing
Complement fixation tests were conducted using a microassay described previously (Tesh et al., 1983), using 2 full units of guinea-pig complement. Titers were recorded as the highest antibody dilutions giving 3+ or 4+ fixation of complement on a scale of 0–4+.
Immunoblotting
BHK monolayers were grown to 90% confluency in 25 cm2 tissue culture flasks and were infected with NIAV or were mock infected as described above. After 2 h, the virus inoculum was aspirated from the cells, unabsorbed virus was removed by thrice washing, and fresh media (DMEM) (Invitrogen) supplemented with 5% fetal bovine serum (FBS) (Atlanta Biologicals, GA) and 1% penicillin/streptomycin (Invitrogen, Grand Island, NY) was added. Four days after infeciton (p.i.) and incubation at 37°C, when marked CPE had developed, the cells were harvested into cell lysis buffer (50mM Tris-HCl, pH 8.0, 150 mM NaCl, 1% Triton X-100). The cell preparations were then treated according to the Biorad instructions for MiniPROTEAN TGX gel analysis of proteins. Briefly, 20 μl sample loading buffer containing β-mercaptoethanol were added to 20 l aliquots of the cell preparations. Samples were heated at 95°C for 10 min, and centrifuged for 1 min at 500 x g at 4°C. Proteins were separated under reducing conditions on MiniPROTEAN TGX 10-20% Tris-Glycine SDS-PAGE gels, and were transferred onto Hybond-P PVDF membrane (GE Healthcare Biosciences, Pittsburgh, PA)) with Transfer Buffer (Biorad, San Diego, CA) according to the Biorad western blotting transfer protocol. Membranes were processed by the WesternBreeze© Chromogenic Immunodetection system (Invitrogen, Grand Island, NY) following the manufacturer’s protocol. The control pre-immune mouse serum and polyclonal MIAF raised to NIAV were used at 1:5,000 dilution, whereas the secondary, goat anti-mouse alkaline phosphatase-conjugated antibody was used as was pre-diluted by the manufacturer’s WesternBreeze© Chromogenic Immunodetection system (Invitrogen, Grand Island, NY).
Animal studies
All animal studies were carried out under a protocol approved by the UTMB Institutional Animal Care and Use Committee. Approximately 10 pups from each of three litters of newborn (1-2 day old) ICR mice were inoculated intracerebrally (i.c.), intraperitoneally (i.p.) or subcutaneously (s.c.) with a Vero stock of NIAV containing ~106.5 TCID50/mL. Each of the i.c.-inoculated pups received 15-20μl of virus, whereas 100μl of virus was injected in each of the i.p. and s.c.-inoculated pups. The animals were observed daily for illness and were euthanized when they became seriously ill. Tissues (brain, lung, liver, spleen and kidney) were collected from three of the sick i.p.-infected mice for histopathology.
Tissues were fixed in 10% neutral buffered formalin (RICCA Chemical Company, Arlington, TX) for 24 hours and transferred to 70% ethanol for storage and subsequent embedding in paraffin. Sections (5μm) were cut and stained by the hematoxylin and eosin method.
Immunohistochemistry
Slides were deparaffinized in Xylene for 15 min, followed by rehydration in ethanol and ethanol/water mixtures as follows: 100% ethanol for 9 min, 95% ethanol/5% deionized water for 3 min, 80% ethanol/20% deionized water for 5 min. Antigen retrieval was facilitated by Protease XXIV (BioGenex, Fremont, CA) incubation for 5 min at RT, followed by three Tris-buffered saline containing 0.1% Tween 20 (TBST) washes. Further processing of the slides was according to the VECTASTAIN® ABC AP Kit (Burlingame, CA) protocol. Incubation with a NIAV-specific hyperimmune mouse ascitic fluid was performed overnight at 4°C. Developed slides were counterstained by the hematoxylin and eosin method and mounted with DePex (EMS, Hatfield, PA).
Highlights.
Niakha virus (NIAV) is a new rhabdovirus species isolated from phlebotomine sandflies
NIAV genome exhibits typical rhabdovirus organization
NIAV has a distinctive morphology, genome organization and expression strategy
Alternative ORFs in the NIAV M, G and L genes are a unique feature amongst rhabdovirus genomes
Phylogeny indicates that NIAV is distantly related to Tupaia virus, Durham virus and Oak Vale viruses
Acknowledgements
The authors are grateful to the late Jean Pierre Digoutte for providing Niakha virus strain DakArD 88909, to Gerald Campbell for his assistance in the histological evaluation of stained brain sections, and to Frederick A. Murphy for help in interpreting the electron micrographs of the virus. This work was supported in part by the Department of Pathology start up funds and a grant from the Institute for Human Infection and Immunity to NV and NIH contract HHSN272201000040I/HHSN27200004/D04 to RBT. ECH is supported by an NHMRC Australia Fellowship.
Footnotes
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