Molecular Characterization of Sweet potato feathery mottle virus (SPFMV) Isolates from Easter Island, French Polynesia, New Zealand, and Southern Africa

Characterization of virus species associated with sweetpotato virus diseases in Burkina Faso

Sweetpotato (Ipomoea batatas) production in sub-Saharan Africa is severely affected by viral diseases caused by several interacting viruses, including sweet potato feathery mottle virus (SPFMV), sweet potato chlorotic stunt virus (SPCSV), and sweet potato leaf curl virus (SPLCV). However, the aetiology of viral symptoms on sweetpotato is rarely established in most countries in Africa. Here, we aimed to investigate and characterize the incidence of sweetpotato viruses in Burkina Faso. We performed a countrywide survey in 18 districts of Burkina Faso and collected 600 plants, with and without symptoms, from 80 fields. Viral strains were identified using nitrocellulose membrane-ELISA, PCR, and reverse transcription-PCR. Three scions from each of 50 selected plants with symptoms were grafted to healthy Ipomoea setosa and then serological and molecular tests were performed on the 150 recorded samples. Three viruses were detected: 24% of samples were positive for SPFMV, 18% for SPLCV, and 2% for SPCSV. Across all diagnostic tests, 40% of all plant samples were virus-negative. Coinfections were found in 16% of samples. Partial sequences were obtained, including 13 that matched SPFMV, one that matched SPLCV, and one that matched SPCSV. All identified SPFMV isolates belonged to either phylogroup B or A-II. The SPCSV-positive isolates had 98% gene sequence homology with SPCSV-West Africa for the coat protein. Begomovirus-positive isolates clustered with SPLCV-United States. This first study of sweetpotato viral diseases in Burkina Faso indicates widespread occurrence and suggests a need for further epidemiological investigations, breeding programmes focused on virus-resistant varieties, and improved farming practices to control disease spread.

New Isolates of Sweet potato feathery mottle virus and Sweet potato virus C: Biological and Molecular Properties, and Recombination Analysis Based on Complete Genomes

Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates were obtained from sweetpotato shoot or tuberous root samples from three widely separated locations in Australia's tropical north (Cairns, Darwin, and Kununurra). The samples were planted in the glasshouse and scions obtained from the plants were graft inoculated to Ipomoea setosa plants. Virus symptoms were recorded in the field in Kununurra and in glasshouse-grown sweetpotato and I. setosa plants. RNA extracts from I. setosa leaf samples were subjected to high-throughput sequencing. New complete SPFMV (n = 17) and SPVC (n = 6) genomic sequences were obtained and compared with 47 sequences from GenBank. Phylogenetic analysis revealed that the 17 new SPFMV genomes all fitted within either major phylogroup A, minor phylogroup II, formerly O; or major phylogroup B, formerly RC. Major phylogroup A's minor phylogroup I, formerly EA, only appeared when recombinants were included. Numbers of SPVC genomes were insufficient to subdivide it into phylogroups. Within phylogroup A's minor phylogroup II, the closest genetic match between an Australian and a Southeast Asian SPFMV sequence was the 97.4% nucleotide identity with an East Timorese sequence. Recombination analysis of the 43 SPFMV and 27 SPVC sequences revealed evidence of 44 recombination events, 16 of which involved interspecies sequence transfers between SPFMV and SPVC and 28 intraspecies transfers, 17 in SPFMV and 11 in SPVC. Within SPFMV, 11 intraspecies recombination events were between different major phylogroups and 6 were between members of the same major phylogroup. Phylogenetic analysis accounting for the detected recombination events within SPFMV sequences yielded evidence of minor phylogroup II and phylogroup B but the five sequences from minor phylogroup I were distributed in two separate groups among the sequences of minor phylogroup II. For the SPVC sequences, phylogenetic analysis accounting for the detected recombination events revealed three major phylogroups (A, B, and C), with major phylogroup A being further subdivided into two minor phylogroups. Within the recombinant genomes of both viruses, their PI, NIa-Pro, NIb, and CP genes contained the highest numbers of recombination breakpoints. The high frequency of interspecies and interphylogroup recombination events reflects the widespread occurrence of mixed SPVC and SPFMV infections within sweetpotato plants. The prevalence of infection in northern Australian sweetpotato samples reinforces the need for improved virus testing in healthy sweetpotato stock programs. Furthermore, evidence of genetic connectivity between Australian and East Timorese SPFMV genomes emphasizes the need for improved biosecurity measures to protect against potentially damaging international virus movements.

Sweet potato feathery mottle virus and Sweet potato virus C from East Timorese and Australian Sweetpotato: Biological and Molecular Properties, and Biosecurity Implications

Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates from sweetpotato were studied to examine genetic connectivity between viruses from Australia and Southeast Asia. East Timorese samples from sweetpotato were sent to Australia on FTA cards. Shoot and tuberous root samples were collected in Australia and planted in the glasshouse, and scions were graft inoculated to Ipomoea setosa plants. Symptoms in infected sweetpotato and I. setosa plants were recorded. RNA extracts from FTA cards and I. setosa leaf samples were subjected to high-throughput sequencing (HTS). Complete genomic sequences (CS) of SPFMV and SPVC (11 each) were obtained by HTS, and coat protein (CP) genes from them were compared with others from GenBank. SPFMV sequences clustered into two major phylogroups (A and B = RC) and two minor phylogroups (EA[I] and O[II]) within A; East Timorese sequences were in EA(I) and O(II), whereas Australian sequences were in O(II) and B(RC). With SPVC, CP trees provided sufficient diversity to distinguish major phylogroups A and B and six minor phylogroups within A (I to VI); East Timorese sequences were in minor phylogroup I, whereas Australian sequences were in minor phylogroups II and VI and in major phylogroup B. With SPFMV, Aus13B grouped with East Timorese sequence TM64B within minor phylogroup O, giving nucleotide sequence identities of 97.4% (CS) and 98.3% (CP). However, the closest match with an Australian sequence was the 97.6% (CS) and 98.7% (CP) nucleotide identity between Aus13B and an Argentinian sequence. With SPVC, closest nucleotide identity matches between Australian and East Timorese sequences were 94.1% with Aus6a and TM68A (CS) and 96.3% with Aus55-4C and TM64A (CP); however neither pair member belonged to the same minor phylogroup. Also, the closest Australian match was 99.1% (CP) nucleotide identity between Aus4C and New Zealand isolate NZ4-4. These first complete genome sequences of SPFMV and SPVC from sweetpotato plantings in the Australian continent and neighboring Southeast Asia suggest at least two (SPFMV) and three (SPVC) separate introductions to Australia since agriculture commenced more than two centuries ago. These findings have major implications for both healthy stock programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.

Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa

Viruses infecting wild flora may have a significant negative impact on nearby crops, and vice-versa. Only limited information is available on wild species able to host economically important viruses that infect sweetpotatoes (Ipomoea batatas). In this study, Sweet potato chlorotic fleck virus (SPCFV; Carlavirus, Betaflexiviridae) and Sweet potato chlorotic stunt virus (SPCSV; Crinivirus, Closteroviridae) were surveyed in wild plants of family Convolvulaceae (genera Astripomoea, Ipomoea, Hewittia and Lepistemon) in Uganda. Plants belonging to 26 wild species, including annuals, biannuals and perennials from four agro-ecological zones, were observed for virus-like symptoms in 2004 and 2007 and sampled for virus testing. SPCFV was detected in 84 (2.9%) of 2864 plants tested from 17 species. SPCSV was detected in 66 (5.4%) of the 1224 plants from 12 species sampled in 2007. Some SPCSV-infected plants were also infected with Sweet potato feathery mottle virus (SPFMV; Potyvirus, Potyviridae; 1.3%), Sweet potato mild mottle virus (SPMMV; Ipomovirus, Potyviridae; 0.5%) or both (0.4%), but none of these three viruses were detected in SPCFV-infected plants. Co-infection of SPFMV with SPMMV was detected in 1.2% of plants sampled. Virus-like symptoms were observed in 367 wild plants (12.8%), of which 42 plants (11.4%) were negative for the viruses tested. Almost all (92.4%) the 419 sweetpotato plants sampled from fields close to the tested wild plants displayed virus-like symptoms, and 87.1% were infected with one or more of the four viruses. Phylogenetic and evolutionary analyses of the 3'-proximal genomic region of SPCFV, including the silencing suppressor (NaBP)- and coat protein (CP)-coding regions implicated strong purifying selection on the CP and NaBP, and that the SPCFV strains from East Africa are distinguishable from those from other continents. However, the strains from wild species and sweetpotato were indistinguishable, suggesting reciprocal movement of SPCFV between wild and cultivated Convolvulaceae plants in the field.

Molecular Characterization of Five Potyviruses Infecting Korean Sweet Potatoes Based on Analyses of Complete Genome Sequences

Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

The current incidence of viral disease in korean sweet potatoes and development of multiplex rt-PCR assays for simultaneous detection of eight sweet potato viruses

Sweet potato is grown extensively from tropical to temperate regions and is an important food crop worldwide. In this study, we established detection methods for 17 major sweet potato viruses using single and multiplex RT-PCR assays. To investigate the current incidence of viral diseases, we collected 154 samples of various sweet potato cultivars showing virus-like symptoms from 40 fields in 10 Korean regions, and analyzed them by RT-PCR using specific primers for each of the 17 viruses. Of the 17 possible viruses, we detected eight in our samples. Sweet potato feathery mottle virus (SPFMV) and sweet potato virus C (SPVC) were most commonly detected, infecting approximately 87% and 85% of samples, respectively. Furthermore, Sweet potato symptomless virus 1 (SPSMV-1), Sweet potato virus G (SPVG), Sweet potato leaf curl virus (SPLCV), Sweet potato virus 2 ( SPV2), Sweet potato chlorotic fleck virus (SPCFV), and Sweet potato latent virus (SPLV) were detected in 67%, 58%, 47%, 41%, 31%, and 20% of samples, respectively. This study presents the first documented occurrence of four viruses (SPVC, SPV2, SPCFV, and SPSMV-1) in Korea. Based on the results of our survey, we developed multiplex RT-PCR assays for simple and simultaneous detection of the eight sweet potato viruses we recorded.

Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs

Sweetpotato (Ipomoea batatas) plants become infected with over 30 RNA or DNA viruses in different parts of the world but little is known about viruses infecting sweetpotato crops in Central America, the center of sweetpotato domestication. Small-RNA deep-sequencing (SRDS) analysis was used to detect viruses in sweetpotato in Honduras and Guatemala, which detected Sweet potato feathery mottle virus strain RC and Sweet potato virus C (Potyvirus spp.), Sweet potato chlorotic stunt virus strain WA (SPCSV-WA; Crinivirus sp.), Sweet potato leaf curl Georgia virus (Begomovirus sp.), and Sweet potato pakakuy virus strain B (synonym: Sweet potato badnavirus B). Results were confirmed by polymerase chain reaction and sequencing of the amplicons. Four viruses were detected in a sweetpotato sample from the Galapagos Islands. Serological assays available to two of the five viruses gave results consistent with those obtained by SRDS, and were negative for six additional sweetpotato viruses tested. Plants coinfected with SPCSV-WA and one to two other viruses displayed severe foliar symptoms of epinasty and leaf malformation, purpling, vein banding, or chlorosis. The results suggest that SRDS is suitable for use as a universal, robust, and reliable method for detection of plant viruses, and especially useful for determining virus infections in crops infected with a wide range of unrelated viruses.

Effect of Host Plant, Aphid Species, and Virus Infection Status on Transmission of Sweetpotato feathery mottle virus

Sweetpotato feathery mottle virus (SPFMV) is a nonpersistently transmitted virus known to infect sweetpotato (Ipomoea batatas) and wild morning glory plants. SPFMV is vectored by various aphid species, among them the green peach aphid, Myzus persicae, and the cotton aphid, Aphis gossypii. Our objective was to determine whether differences in acquisition hosts (sweetpotato and morning glory), aphid species (M. persicae and A. gossypii), and infection status (single versus mixed infection) influenced transmission of SPFMV. SPFMV transmission from I. hederacea with a natural mixed infection by A. gossypii (39%) was significantly greater than in other host-virus combinations. Successful transmissions by A. gossypii were significantly greater compared with M. persicae in all host-virus combinations. Virus titers in source leaves were significantly greater in single- and mixed-infected I. hederacea and single-infected I. cordatotriloba compared with other host-virus combinations. There was a significant positive correlation between virus titer and transmission by both aphid species. These results suggest that, under controlled conditions, SPFMV is more readily transmitted from infected morning glory plants than from sweetpotato. Additionally, mixed-infected plants are better virus sources for transmission than single-infected, and A. gossypii is a more efficient vector than M. persicae under laboratory conditions.

Complete nucleotide sequence of an Argentinean isolate of sweet potato virus G

Sweet potato virus G belongs to the largest plant virus genus Potyvirus. This virus was detected for the first time in Argentina and then sequenced using the method of next-generation pyrosequencing. The complete genome was found to be 10,798 nucleotides excluding the poly-A tail with a predicted genome organization typical for a member of the genus Potyvirus. This is the first report of the complete genomic sequence of a SPVG isolated from South America.

Genetic identification of two sweet-potato-infecting begomoviruses in South Africa

The complete genome sequences of two monopartite begomovirus isolates (genus Begomovirus, family Geminiviridae) that occurred either alone or in mixed infection in sweet potato (Ipomoea batatas) plants collected in Waterpoort, South Africa, are presented. One of the isolates corresponds to sweet potato mosaic-associated virus (SPMaV; SPMaV-[ZA:WP:2011]), with which it shared 98.5 % nucleotide identity, whereas the second isolate corresponds to a new variant of sweet potato leaf curl Sao Paulo virus (SPLCSPV; SPLCSPV-[ZA:WP:2011]), with which it shared 91.4 % nucleotide identity. The phylogenetic and recombination relationships of these isolates to other monopartite Ipomoea-infecting begomoviruses were also investigated. SPLCSPV-[ZA:WP:2011] was found to be a natural recombinant of swepoviruses consisting of two distinct parental genomic sequences from SPLCSPV and sweet potato leaf curl Georgia virus (SPLCGV).

Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of sweet potato feathery mottle virus

Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is globally the most common pathogen of cultivated sweet potatoes (Ipomoea batatas; Convolvulaceae). Although more than 150 SPFMV isolates have been sequence-characterized from cultivated sweet potatos across the world, little is known about SPFMV isolates from wild hosts and the evolutionary forces shaping SPFMV population structures. In this study, 46 SPFMV isolates from 14 wild species of genera Ipomoea, Hewittia and Lepistemon (barcoded for the matK gene in this study) and 13 isolates from cultivated sweet potatoes were partially sequenced. Wild plants were infected with the EA, C or O strain, or co-infected with the EA and C strains of SPFMV. In East Africa, SPFMV populations in wild species and sweet potato were genetically undifferentiated, suggesting inter-host transmission of SPFMV. Globally, spatial diversification of the 178 isolates analysed was observed, strain EA being largely geographically restricted to East Africa. Recombination was frequently detected in the 6K2-VPg-NIaPro region of the EA strain, demonstrating a recombination 'hotspot'. Recombination between strains EA and C was rare, despite their frequent co-infections in wild plants, suggesting purifying selection against strain EA/C recombinants. Positive selection was predicted on 17 amino acids distributed over the entire coat protein in the globally distributed strain C, as compared to only four amino acids in the coat protein N-terminus of the EA strain. This selection implies a more recent introduction of the C strain and a higher adaptation of the EA strain to the local ecosystem. Thus, East Africa appears as a hotspot for evolution and diversification of SPFMV.