Arracacha Virus Research Articles

Genomic sequence and host range studies reveal considerable variation within the species Arracacha virus B.

Arracacha virus B type (AVB-T) and oca (AVB-O) strains from arracacha (Arracacia xanthorrhiza) and oca (Oxalis tuberosa) samples collected in 1975 and two additional isolates obtained from arracacha (AVB-PX) and potato (AVB-6A) in Peru in 1976 and 1978, respectively, were studied. In its host responses and serological properties, AVB-PX most resembled AVB-T, whereas AVB-6A most resembled AVB-O. Complete genomic sequences of the RNA-1 and RNA-2 of each isolate were obtained following high-throughput sequencing of RNA extracts from isolates preserved for 38 (AVB-PX) or 32 (the other 3 isolates) years, and compared with a genomic sequence of AVB-O obtained previously (PV-0082). RNA-2 was unexpectedly divergent compared to RNA-1, with the nucleotide (nt) sequence identity of different AVB isolates varying by up to 76% (RNA-2) and 89% (RNA-1). The coat protein amino acid sequences were the most divergent, with AVB-O and AVB-6A having only 68% identity to AVB-T and AVB-PX. Since the RNA2 sequence differences between the two isolate groupings also coincided with host range, symptom, and serological differences, AVB demonstrates considerable intraspecific divergence.

Full-Genome Sequencing of a Virus from a 33-Year-Old Sample Demonstrates that Arracacha Mottle Virus Is Synonymous with Arracacha Virus Y.

We describe here the first genome sequence of Arracacha virus Y (ArVY) derived from an arracacha (Arracacia xanthorrhiza) sample originally collected in 1976 in Peru and compare it with other potyvirus genome sequences. It had a 79% nucleotide identity with a 2013 Brazilian Arracacha mottle virus (AMoV) sequence, suggesting that AMoV is ArVY.

High-throughput sequencing reveals a novel closterovirus in arracacha (Arracacia xanthorrhiza).

High-throughput sequencing analysis detected a clostero-like virus from arracacha plants (Arracacia xanthorrhiza) in Brazil. The complete genome sequence, confirmed by RACE and Sanger sequencing, consists of 15,763 nucleotides with nine predicted open reading frames (ORFs) in a typical closterovirus genome organisation. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70 homologue (Hsp70h), and coat protein showed 55-65, 38-44, and 20-36% amino acid sequence identity, respectively, to the homologous proteins of known closteroviruses. Phylogenetic analysis of Hsp70h showed that this putative novel arracacha plant virus was related to members of the genus Closterovirus in the family Closteroviridae. These results suggest that this virus, tentatively named "arracacha virus 1" (AV-1), is a novel member of the genus Closterovirus. This is the first closterovirus identified in arracacha plants.

First Complete Genome Sequence of Arracacha virus A Isolated from a 38-Year-Old Sample from Peru.

ABSTRACTWe present here the first complete genomic sequence of Arracacha virus A from a Peruvian arracacha sample collected in 1975 and compare it with the genomes of other nepoviruses. Its RNA1 and RNA2 both had greatest amino acid identities with those of the subgroup A nepovirus Melon mild mottle virus.

A novel vitivirus-like sequence found in Arracacia xanthorrhiza plants by high throughput sequencing.

High throughput sequencing (HTS) is a very powerful tool for detecting and discovering novel viral-like sequences without prior knowledge of the sequence. Here we describe the complete genome of a new vitivirus-like sequence that was found in arracacha (Arracacia xanthorrhiza) plants using HTS technology. The complete genome sequence was validated by Sanger sequencing. The genomic organization of the new putative vitivirus resembles that of grapevine virus B (GVB) and grapevine virus D (GVD). The putative coat protein showed 41 to 49% identity with similar proteins of known vitiviruses, while the RNA-dependent RNA polymerase shared 52 to 55% identity with those encoded by grapevine vitiviruses. Based on the demarcation criteria for the genus Vitivirus, the virus described in this work, provisionally named as "Arracacha virus V", represents a novel species in this taxon.

Complete genome sequence of arracacha virus B: a novel cheravirus

The complete genome sequences of RNA1 and RNA2 of the oca strain of the potato virus arracacha virus B were determined using next-generation sequencing. The RNA1 molecule is predicted to encode a 259-kDa polyprotein with homology to proteins of the cheraviruses apple latent spherical virus (ALSV) and cherry rasp leaf virus (CRLV). The RNA2 molecule is predicted to encode a 102-kDa polyprotein which also has homology to the corresponding protein of ALSV and, to a lesser degree, CRLV (30% for RNA1, 24% for RNA2). Detailed analysis of the genome sequence confirms that AVB is a distinct member of the genus Cheravirus.

Detection and Differentiation of Comoviridae Species using a Semi‐nested RT‐PCR and a Phylogenetic Analysis based on the Polymerase Protein

AbstractA nested reverse transcription polymerase chain reaction (RT‐PCR) method is described that allows detection and identification of Comoviridae species and possibly other bipartite plant picorna‐like viruses. It involves an RT‐PCR, in which a combination of degenerate deoxyinosine (dI)‐substituted primers amplified part of the RNA‐dependent RNA polymerase (RdRp) domain, followed by a semi‐nested PCR amplification that increased detection sensitivity. The PCR amplicons can be easily cloned and sequenced to obtain initial sequence information of Comoviridae genomes for virus species differentiation and characterization. The method can be used on total RNA extracts from infected plants, when viral genomic double‐stranded RNA (dsRNA) or the viral RNA is unavailable. Previously uncharacterized RdRp domains of Potato black ringspot virus (PBRSV), Cherry leafroll virus (CLRV) and Arracacha virus B (AVB) were amplified and sequenced. Neighbour‐joining trees calculated from the homologous partial RdRp amino acid sequences were used to establish the taxonomic relationships between members of plant picorna‐like viruses, revealing lineages that classified all species within their respective genera and clearly distinguished each genus from the other genera. Phylogenetic analysis confirmed the classification of PBRSV and CLRV within the genus, Nepovirus whereas AVB was placed into a cluster different from the Nepovirus, Comovirus and Fabavirus lineages.

In vitro virus elimination in three Andean root crops: Oca (Oxalis tuberosa), ulluco (Ullucus tuberosus), and arracacha (Arracacia xanthorrhiza)

Accessions of three Andean root crops— oca (Oxalis tuberosa Molina), ulluco (Ullucus tuberosus Caldas), and arracacha (Arracacia xanthorrhiza Bancr.) were imported into quarantine in New Zealand. Using nitrocellulose membrane‐ELISA, herbaceous hosts, and electron microscopy, the accessions were found to be infected with the following viruses. In oca: Arracacha virus B (AVB), Papaya mosaic virus (PapMV), and Ullucus mild mottle virus (UMMV); in ulluco: Ullucus virus C (UVC), Ullucus mosaic virus (UMV), PapMV, and UMMV; and in arracacha: Arracacha A virus (AVA). To comply with quarantine requirements the viruses had to be eliminated. Except with one accession of oca that was infected with TMV/U, this was successfully achieved using a protocol of in vitro virus elimination that combined heat and chemical therapy. Stem nodal sections of oca and ulluco and shoot tips of arracacha were established in tissue culture on a growth medium containing 50 mg/litre ribavirin. These explants underwent 10 days of continuous heat therapy of alternating 4 h light at 35°C: 4 h dark at 31°C, after which time the resultant shoots were 1 cm long and ready to be excised and grown up on growth medium without ribavirin. They were grown under normal tissue culture conditions of 24°C under fluorescent lights with a photoperiod of 16 h. The plantlets were then introduced to glasshouse conditions in preparation for field trials, analyses, and evaluations.

Detection of quarantine viruses of potato by ELISA

According to EC regulations, imported material of tuber‐forming Solarium spp. has to be tested for the absence of defined quarantine viruses. In order to allow an efficient and timesaving application of the quarantine inspection procedure, antisera have been developed and scrutinized for their use by the ELISA technique. The viruses concerned were Andean potato latent virus (APLV), Andean potato mottle virus (APMV), arracacha virus B oca strain (AVB‐O), potato virus T (PVT) and tobacco ringspot virus Andean potato calico strain (TRSV‐Ca). The results show that all viruses can be reliably detected by double‐antibody sandwich (DAS) ELISA. The detection limits were in the range ≤ 1–32 ng ml−1. The strain specificity by DAS‐ELISA of the antisera for APLV and APMV was overcome by mixing antisera from the different strains and strain groups, respectively. Strains C and Lm of APMV seemed to be serologically identical. A comparison of the suceptibility of several wild species of tuber‐forming Solanum with that of several cultivars of Solanum tuberosum showed a higher frequency of infection in the wild species.

Tests for transmission of four potato viruses through potato true seed

SUMMARYThe Andean potato calico strain of tobacco ringspot virus (TRSV‐Ca) was detected in 2–9% of potato seedlings grown from true seed from plants of cv. Cara and clone G5998(6) infected with TRSV‐Ca. Similarly, a potato isolate of the oca strain of arracacha virus B (AVB‐O) was detected in 4–12% of progeny seedlings of cv. Cara and clone D42/8 infected with AVB‐O. Potato virus T (PVT) passed through 33–59% of seed from PVT‐infected cv. Cara, but only 0–2% infection was detected in seedlings from seed of PVT‐infected clone D42/8. By contrast, no infection was detected in seedlings grown from seed from plants of G5998(6), D42/8 or cv. Cara infected with Andean potato latent virus strains Hu (APLV‐Hu) or Caj (APLV‐Caj), although both strains passed through seed of Nicotiana clevelandii.AVB‐O, PVT and TRSV‐Ca were detected in all tests of pollen from flowers of infected potato plants, but APLV‐Hu and APLV‐Caj were detected less frequently. AVB‐O and PVT were transmitted through 2% and 8% respectively, of seed from healthy potato plants pollinated with pollen from infected plants. However, no transmission through seed was detected when pollen from TRSV‐Ca infected plants was used. None of the four viruses were transmitted to healthy potato plants pollinated with pollen from infected plants.APLV‐Hu caused exceptionally severe symptoms in the cv. Cara plants used for seed production, but the Bolivian strain of PVT induced only mild symptoms rather than the severe systemic necrosis previously reported for the type of strain of PVT in this cultivar. No symptoms developed in potato seedlings infected with TRSV‐Ca, AVB‐O or PVT through the seed.

Oca Strain of Arracacha Virus B from Potato in Peru

Oca Strain of Arracacha Virus B from Potato in Peru

Arracacha virus B, a second isometric virus infecting arracacha (Arracacia xanthorrhiza; Umbelliferae) in the Peruvian Andes

SUMMARYArracacha virus B (AVB), a previously undescribed virus, was found together with arracacha virus A or with a 750 nm flexous filamentous virus in arracacha (Arracacia Xanthorrhiza; Umbelliferae) growing in the Huanuco region of the Peruvian Andes. AVB was transmitted by inoculation of sap to 30 species from eight families out of 45 species from 10 families tested. It was transmitted through seed of Chenopodium quinoa but not by Myzus persicae. AVB was best propagated in C. Quinoa or Tetragonia expansa and assayed in C. quinoa, C. murale or C. amaranticolor. Sap from infeted <C. Quinoa was occasionally infective after dilution to 10‐4 but not 10‐5, after 10 min at 65 d̀ C but not 70 d̀ C, and after 12 but not 14 days at 20 d̀ C.In neutral phosphotungstate, AVB has isometric partilces c. 26 nm in diameter with a hexagonal profile. About 50‐ 150 A1 cm260 units of purified virus were obtained from 1 kg infected C. quinoa leaf by extraction in 0.5 M phosphate buffer at pH 7.5, containing 0.05 M ethylene‐daiminetetra‐acetate (EDTA) and 0.2% mercaptoethanol, and clarificatin with chloroform, followed by two precipitations with polyethylene glycol and three cylces of differential centrifugation. Purified virus coefficent (Sd̀20 w,) of 126 S and A260/A280 ratio of 1.80, bnut formed two isopycnic bands in CsC1 of buoyant density 1.481 and 1.492 g/cm3 with estimated nucleic acid contents of 40 and 41% respectively. AVB particles contained two proteins of mol.wt 26 000 (major component) and 20 000. AVB was not serologically related to any of 20 other morphologically similar viruses. Its properties suggest that it does not fall into any recognised group of viruses.the cryptogram of AVB is */*:*/40–41:S/S:S/*