Cesar E. Fribourg

Maximum likelihood (ML) phylogenies of 109 tymoviruses, including 3 obtained directly from metagenomes, were calculated from all three open reading frames separately, but the concatenated sequences of their replicase and coat protein genes gave the most representative trees. ML phylogenies were also calculated from all recorded tymovirus coat protein genes, and from datasets of the turnip yellow mosaic virus cluster, and separately of tomato blistering mosaic, Andean potato latent, and Andean potato mild mosaic viruses. These phylogenies showed that the basal divergence of tymoviruses occurred in a population infecting Eurasian brassicas (rosids), and more recently, one of the basal lineages diversified and adapted to infect some solanaceous (asterid) plants and crops of Central and South America. Heterochronous dating of the phylogenies failed, but heuristic comparisons based on patristic distances, branching patterns, and external events suggested that the “most recent common ancestor” of all known tymoviruses existed before the last Ice Age. Some lineages reached the Americas about 15,000 years ago. However, most of the spread of the few tymoviruses now found on more than one continent occurred during the past 2 centuries. The only recombinants were two sequences of chiltepin yellow mosaic virus, both with Nemesia ring necrosis virus as the minor parent. Population genetic analysis found significant evidence of population contraction in the tymovirus populations infecting asterid hosts in the Americas. It also found the replicase and coat protein genes were significantly negatively selected. By contrast, the overlapping movement protein genes were positively selected, which may help them adapt to new host species, including infecting economically significant crops. This knowledge about tymoviruses is important to plant biosecurity authorities.

Potato virus X (PVX) occurs worldwide and causes an important potato disease. Complete PVX genomes were obtained from 326 new isolates from Peru, which is within the potato crop′s main domestication center, 10 from historical PVX isolates from the Andes (Bolivia, Peru) or Europe (UK), and three from Africa (Burundi). Concatenated open reading frames (ORFs) from these genomes plus 49 published genomic sequences were analyzed. Only 18 of them were recombinants, 17 of them Peruvian. A phylogeny of the non-recombinant sequences found two major (I, II) and five minor (I-1, I-2, II-1, II-2, II-3) phylogroups, which included 12 statistically supported clusters. Analysis of 488 coat protein (CP) gene sequences, including 128 published previously, gave a completely congruent phylogeny. Among the minor phylogroups, I-2 and II-3 only contained Andean isolates, I-1 and II-2 were of both Andean and other isolates, but all of the three II-1 isolates were European. I-1, I-2, II-1 and II-2 all contained biologically typed isolates. Population genetic and dating analyses indicated that PVX emerged after potato’s domestication 9000 years ago and was transported to Europe after the 15th century. Major clusters A–D probably resulted from expansions that occurred soon after the potato late-blight pandemic of the mid-19th century. Genetic comparisons of the PVX populations of different Peruvian Departments found similarities between those linked by local transport of seed potato tubers for summer rain-watered highland crops, and those linked to winter-irrigated crops in nearby coastal Departments. Comparisons also showed that, although the Andean PVX population was diverse and evolving neutrally, its spread to Europe and then elsewhere involved population expansion. PVX forms a basal Potexvirus genus lineage but its immediate progenitor is unknown. Establishing whether PVX′s entirely Andean phylogroups I-2 and II-3 and its Andean recombinants threaten potato production elsewhere requires future biological studies.

Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVS^A and PVS^O, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVS^O and two PVS^A isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVS^A and PVS^O elicited similar foliage symptoms. Following graft inoculation, all except two PVS^O isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVS^A and PVS^O. Myzus persicae transmitted all nine PVS^A isolates but none of the three PVS^O isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVS^A isolates but less than 21 days for the three PVS^O isolates. Dilution end points were 10⁻³ for two PVS^O isolates but 10⁻⁴ to 10⁻⁶ with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.

Two virus isolates, T1 and T2, causing necrotic spots on leaves and stems of pepper and tomato, respectively, were isolated in the La Joya valley, Arequipa, Peru, in 2010. These two isolates were inoculated to differential hosts for tospoviruses and showed differential fitness: T1 induced necrotic local lesions in Vigna unguiculata, whereas T2 produced only chlorotic spots. The complete nucleotide sequence of the small (S) RNA from T2 and 1863 bp of the S RNA from T1 were determined. The deduced N protein sequence showed high amino acid identity (97%) between the isolates, indicating that the T1 and T2 are isolates of the same virus. Sequence comparisons indicated that the amino acid sequence of the N protein shared 53.49-87.98% identity with known American tospoviruses. Phylogenetic analysis of both the NSs and N proteins revealed that this new tospovirus belongs to the American group. We conclude that this tospovirus should be considered a member of a new species. The name Pepper necrotic spot virus (PNSV) is proposed.

Viruses of the species Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) were simultaneously detected by the different size of PCR amplicons in lima bean plants (Phaseolus lunatus) displaying deforming mosaic symptoms in Peru. Phylogenetic analysis of partial deduced CP amino acid sequences indicated that the Peruvian BCMV isolates belong to new strains. One isolate differed from the other Peruvian isolates, and also from the ten previously described BCMV strains recognized by responses on differential bean varieties. The sequence of the 3′-proximal part (2547 nucleotides) of the genome confirmed that this isolate also belongs to BCMV.

Two isolates (SL1 and SL6) of Peru tomato virus (PTV, genus Potyvirus) were obtained from cocona plants (Solanum sessiliflorum) growing in Tingo María, the jungle of the Amazon basin in Peru. One PTV isolate (TM) was isolated from a tomato plant (Lycopersicon esculentum) growing in Huaral at the Peruvian coast. The three PTV isolates were readily transmissible by Myzus persicae. Isolate SL1, but not SL6, caused chlorotic lesions in inoculated leaves of Chenopodium amaranticolor and C. quinoa. Isolate TM differed from SL1 and SL6 in causing more severe mosaic symptoms in tomato, and vein necrosis in the leaves of cocona. Pepper cv. Avelar (Capsicum annuum) showed resistance to the PTV isolates SL1 and SL6 but not TM. The 5′- and 3′-proximal sequences of the three PTV isolates were cloned, sequenced and compared to the corresponding sequences of four PTV isolates from pepper, the only host from which PTV isolates have been previously characterised at the molecular level. Phylogenetic analyses on the P1 protein and coat protein amino acid sequences indicated, in accordance with the phenotypic data from indicator hosts, that the PTV isolates from cocona represented a distinguishable strain. In contrast, the PTV isolates from tomato and pepper were not grouped according to the host. Inclusion of the sequence data from the three PTV isolates of this study in a phylogenetic analysis with other PTV isolates and other potyviruses strengthen the membership of PTV in the so-called “PVY subgroup” of Potyvirus. This subgroup of closely related potyvirus species was also distinguishable from other potyviruses by their more uniform sizes of the protein-encoding regions within the polyprotein.

SUMMARY: During indexing of a potato germplasm collection from Bolivia, a strain of potato virus X (PVX), X_HB, which failed to cause local lesions in inoculated leaves of Gomphrena globosa was found in 7% of the clones. X_HB was transmitted by inoculation of sap to 56 species from 11 families out of 64 species from 12 families tested. It was best propagated in Nicotiana glutinosa or N. debneyi; Montia perfolia and Petunia hybrida were useful as local lesion hosts. Inoculated leaves of G. globosa plants kept at 10°, 14°, 18°, 22°, or 26 °C after inoculation were always infected symptomlessly. X_HB caused a mild mosaic, systemic chlorotic blotching or symptomless infection in 16 wild potato species and eight Andean potato cultivars, systemic necrotic symptoms in clone A6 and cultivar Mi Peru, and bright yellow leaf markings in cultivar Renacimiento. It caused necrotic local lesions in inoculated leaves of British potato cultivars with the PVX hypersensitivity gene Nb but then invaded the plants systemically without causing further necrosis; with gene Nx systemic invasion occurred but no necrotic symptoms developed. These reactions resemble those of PVX strain group four. X_HB differed from other known strains of PVX in readily infecting PVX‐immune clones 44/1016/10, G. 4298.69 and USDA 41956, cultivars Saphir and Saco, and Solanum acaule PI 230554.X_HB had slightly flexuous filamentous particles with a normal length of 516 nm. It was transmitted readily by plant contact and it partially protected G. globosa leaves from infection with X_CP, a group two strain of PVX. Sap from infected N. glutinosa was infective after dilution to 10^‐‐⁶ but not 10^‐‐⁷ after 10 min at 75° but not 80 °C and after 1 yr at 20 °C. X_HB was readily purified from infected N. debneyi leaves by precipitation with polyethylene glycol followed by differential centrifugation. Microprecipitin tests showed that X_HB and X_CP are closely related serologically.