Molecular epidemiology of cassava mosaic disease in Madagascar

Cassava is the staple food for hundreds of millions of people in Africa but its cultivation is seriously constrained by cassava mosaic disease (CMD) in Madagascar, and in Africa in general. This study identified the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their associated epidemiological characteristics from countrywide surveys. Molecular characterization of CMGs in Madagascar revealed an unprecedented diversity and co‐occurrence of six viruses: African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Kenya virus (EACMKV), East African cassava mosaic virus (EACMV), South African cassava mosaic virus (SACMV) and the recently described Cassava mosaic Madagascar virus (CMMGV). Distinct geographical distributions were observed for the six viruses. While ACMV was more prevalent in the central highlands, EACMV and EACMKV were prevalent in lowlands and coastal regions. Both EACMCV and SACMV occurred in almost all the localities visited. PCR diagnosis revealed that mixed infection (up to four co‐infected viruses) occurred in 21% of the samples and were associated with higher symptom severity scores. Pairwise comparisons of virus associations showed that EACMCV was found in mixed infections more often than expected while ACMV and SACMV were mostly found in single infections. A greater abundance of whiteflies was observed in lowland and coastal areas. Nevertheless, infected cuttings remain the primary source of CMD propagation (95%) in Madagascar.     

Identification of a defective molecule derived from DNA-A of the bipartite begomovirus of East African cassava mosaic virus

Geminivirus defective interfering DNAs arise spontaneously in mechanically inoculated test plants, and have previously been found with DNA-B of the bipartite cassava mosaic geminiviruses, but not DNA-A. Reported here for the first time is the cloning and characterization of a naturally occurring truncated form of cassava mosaic geminivirus DNA-A, which at 1525 nt is around half the expected full size. Sequence analysis has shown it to be a defective (df) form of East African cassava mosaic virus (EACMV) DNA-A that has retained its cis elements essential for replication by the helper virus, and it has been termed df DNA-A 15. Phylogenetic comparisons placed the df DNA-A 15 molecule close to mild and severe isolates of EACMV-UG2. Biolistic inoculation of Nicotiana benthamiana with infectious df DNA-A 15 clone and East African cassava mosaic Cameroon virus (EACMCV) resulted in symptom amelioration as compared with EACMCV singly inoculated plants, and there was an accumulation of df DNA-A 15 in systemically infected leaves. In addition, the level of EACMV DNA-B accumulation was reduced in the coinoculated plants compared with those inoculated with EACMCV alone. PCR and sequence analysis confirmed the helper virus as EACMV.     

Epidemiological assessment of cassava mosaic disease in Burkina Faso

Surveys were conducted in 2016 and 2017 across the main cassava-growing regions of Burkina Faso to assess the status of cassava mosaic disease (CMD) and to determine the virus strains causing the disease, using field observation and phylogenetic analysis. CMD incidence varied between regions and across years but was lowest in Hauts-Bassins (6.0%, 2016 and 5.4%, 2017) and highest in Centre-Sud (18.5%, 2016) and in Boucle du Mouhoun (51.7%, 2017). The lowest CMD severity was found in Est region (2.0) for both years and the highest in Sud-Ouest region (3.3, 2016) and Centre-Sud region (2.8, 2017). The CMD infection was primarily associated with contaminated cuttings in all regions except in Hauts-Bassins, where whitefly-borne infection was higher than cuttings-borne infection in 2016. PCR screening of 687 samples coupled with sequence analysis revealed the presence of African cassava mosaic-like (ACMV-like) viruses and East African cassava mosaic-like (EACMV-like) viruses as single infections at 79.5% and 1.1%, respectively. Co-infections of ACMV-like and EACMV-like viruses were detected in 19.4% of the tested samples. In addition, 86.7% of the samples positive for EACMV-like virus were found to be positive for East African cassava mosaic Cameroon virus (EACMCMV). Phylogenetic analysis revealed the segregation of cassava mosaic geminiviruses (CMGs) from Burkina Faso into three clades specific to ACMV, African cassava mosaic Burkina Faso virus (ACMBFV), and EACMCMV, confirming the presence of these viruses. The results of this study show that EACMCMV occurrence may be more prevalent in Burkina Faso than previously thought.     

Dual begomovirus infections and high Bemisia tabaci populations: two factors driving the spread of a cassava mosaic disease pandemic

A cassava mosaic disease (CMD) pandemic currently affects much of East and Central Africa. To understand the factors driving the pandemic's continued spread, complementary data sets were collected from cassava plots, planted with healthy cuttings, at eight sites along a north–south transect in southern Uganda, through the pandemic's leading edge. Data were collected on virus incidence, symptom severity, populations of the whitefly vector, Bemisia tabaci , their infectivity and ability to transmit different viruses. In 1996, 6 months after planting, CMD incidences were highest at sites 1 and 2, then decreased progressively until site 6, and remained low at sites 7 and 8. The largest B. tabaci populations also occurred at northernmost sites, 1–3. In 1997, CMD incidence increased significantly at sites 5–8 and this was associated with significant increases in the B. tabaci populations. The pandemic's spread was also associated with significant increases in the percentage of dual infections of East African cassava mosaic virus -Uganda and African cassava mosaic virus , which caused the severest symptoms and the greatest reduction in leaf area. Whitefly adults collected from within the pandemic area were infective, whereas those collected ahead of the pandemic were not. The transmission rate of African cassava mosaic virus from plants with dual infections was significantly less than that of East African cassava mosaic virus -Uganda, which may explain the latter's predominance within the pandemic. These results show that the arrival of East African cassava mosaic virus -Uganda into areas affected previously only by African cassava mosaic virus , has resulted in novel virus/vector/host–plant interactions that drive the pandemic's continued spread.     

High throughput real‐time RT‐PCR assays for specific detection of cassava brown streak disease causal viruses,and their application to testing of planting material

Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) is causing severe losses in cassava production in Kenya, Tanzania and Uganda. Two real‐time RT‐PCR assays based on TaqMan chemistry capable of detecting and distinguishing these two viruses are described. These assays were used to screen 493 cassava samples collected from western and coastal Kenya, the main cassava regions of Uganda and inland Tanzania. Both viruses were found in all three countries and across regions therein. Association of CBSD leaf symptom status with CBSV and UCBSV assay results was weak, confirming the need for a diagnostic assay. For leaf samples that were observed with CBSD‐like leaf symptoms but shown as CBSV and UCBSV negative by the RT‐PCR assay, deep sequencing using a Roche 454 GS‐FLX was used to provide additional evidence for the absence of the viruses. The probability of the CBSD associated diagnostics detecting a single CBSV or UCBSV positive sample amongst other non‐CBSD samples was modelled. The results of this study are discussed in the context of the application of diagnostics of CBSD‐associated viruses under the Great Lakes Cassava Initiative and the need to minimize the risk of further spread of the viruses with cassava multiplication material. It is shown that high throughput testing undertaken at Fera of 300 cassava leaves taken from fields for seed multiplication, when analysed in pools of 10, has given a 95% probability of detecting 1% infected plants in the field.     

Characterization of a begomovirus causing horsegram yellow mosaic disease in India

The virus causing horsegram (Macrotyloma uniflorum) yellow mosaic disease has been shown to be a typical Old World bipartite begomovirus. The viral origin of the disease has been established through agroinoculation of horsegram using partial tandem repeat clones of both DNA-A and DNA-B. The DNA-A genome shows less than 89% identity with the corresponding sequences of all the begomoviruses in the databases earlier to this sequence submission (AJ627904). Therefore Horsegram yellow mosaic virus (HgYMV-[IN:Coi]) can be considered to be a new species of the genus Begomovirus (family Geminiviridae). Phylogenetic analysis shows that this virus is part of the cluster of mungbean yellow mosaic viruses of legumes from South and South East Asia.     

Components of resistance of cassava to African cassava mosaic virus

Components of resistance of cassava (Manihot esculenta) to African cassava mosaic virus (ACMV) and their interrelationships were confirmed and quantified in a series of experiments at Adiopodoumé (Ivory Coast, West-Africa). The response to virus infection and toBemisia tabaci infestation of a large collection of cassava, including local cultivars and others derived from inter-specificM. glaziovii hybrids was assessed. A consistent correlation was found between virus titre, symptom intensity, disease incidence and non-systemicity (recovery) which suggests that they are different expressions of the same genetic resistance. By contrast, there was no correlation between whitefly infestation and incidence of ACMV, suggesting that resistance to virus and vector are determined by two distinct genetic mechanisms. Several improved cultivars derived from inter-crossing cassava withM. glaziovii as well as some local cultivars were highly resistant and combined low susceptibility, low symptom intensity, low virus content and high level of recovery. Although yield losses ranged from 10% to 30% in such resistant cultivars, the combined effect of high field resistance and high rate of recovery lead to low disease incidence and limited yield losses, even in areas of high infection pressure such as Adiopodoumé.     

Distribution and accumulation of cassava brown streak viruses within infected cassava (Manihot esculenta) plants

Cassava brown streak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), ranks among the top seven biological threats to global food security. The disease poses a significant threat to cassava production in East and Central Africa (ECA). In Uganda, overall CBSD incidence increased by c. 20% since it re‐emerged in 2004, and the disease persistently reduces cassava yields and storage root qualities. The spread of CBSD has been studied spatially in fields in different agroecologies. However, within‐host distribution and accumulation of CBSV and UCBSV in naturally infected cassava plants is unknown. Therefore, within‐host CBSV and UCBSV distribution was studied to correlate CBSD symptoms with virus titre in organs of infected cassava. Leaf, stem and storage root samples, with and without symptoms, were collected from 10 genotypes of field‐grown cassava. Presence of CBSV and UCBSV was detected by RT‐PCR and virus levels determined by qRT‐PCR. CBSV was present in 100% of CBSD samples with symptoms, with 45·3% positive for presence of both CBSV and UCBSV. Tolerant cassava genotypes were infected with CBSV alone and accumulated higher titre in roots than in aerial organs. Susceptible genotypes were co‐infected with CBSV and UCBSV and exhibited variation in virus titre in each organ. Across genotypes, virus titre was lowest in the youngest leaves and highest in mature non‐senescing leaves. This information provides insight into the relationship between CBSV, UCBSV and their cassava host, and is valuable for CBSD resistance breeding, epidemiology studies and CBSD control.     

Molecular identification of an Ageratum enation virus isolate associated with mosaic disease of pointed gourd (Trichosanthes dioica) in India

A severe mosaic disease of pointed gourd (Trichosanthes dioica Roxb.) was observed with significant disease incidence in Gopalganj, India, during 2008. Begomovirus was detected from symptomatic leaf samples by polymerase chain reaction (PCR) using coat protein gene-specific primers of a well characterized begomovirus which revealed positive amplification of expected size ~800 bp DNA band. To confirm begomovirus association, the complete DNA-A was amplified using three sets of begomovirus DNA-A primers. The amplicons were cloned, sequenced, and sequence of the complete DNA-A (2757 nt) was determined by combining the sequence data of all amplicons (Accession no. GQ268327). The sequence data showed 99–93% sequence identities and close phylogenetic relationships with isolates of Ageratum enation virus (AgEV). The begomovirus associated with mosaic disease of T. dioica was identified as an isolate of Ageratum enation virus, which is a new record from India.     

Occurrence of Honeysuckle Yellow Vein Virus (HYVV) containing a monopartite DNA-A genome in Korea

Two newly emerged begomoviruses were isolated from naturally infected tomato (Solanum lycopersicum) plants grown in greenhouses at Jeju Island and Dangjin in Korea and their genomes were characterized. These viruses-infected plants had very small leaves that curled upward, yellow margins and a leathery appearance, and a bushy and stunted appearance with short internodes. Nucleotide (nt) sequence analysis of their genomes showed that they have a DNA-A component of a monopartite begomovirus. Their genomes comprised 2763 and 2764 nucleotides with six open reading frames. The results of nt sequence similarity analysis of DNA-A genome between the two Korean isolates and isolates of Tobacco leaf curl Japan virus (TbLCJV), Honeysuckle yellow vein virus (HYVV), Honeysuckle yellow vein mosaic virus (HYVMV), and Eupatorium yellow vein virus in Japan (EpYVV) showed that they are likely similar to HYVV-[Masuda] (89.4–92.8% nt identity). Consequently, we tentatively propose the two isolates’ names as HYVV-Jeju and -DJ according to the ICTV geminivirus rules. Phylogenetic relationship analysis of 33 DNA-A genome sequences using PAUP* 4.0b10 and MrBayes revealed that HYVV-Jeju and -DJ belong to the Far East Asian begomovirus species complex. Within the Far East Asian begomovirus species complex, HYVV-Jeju and -DJ are distantly related to EpYVV, HYVMV, and TbLCJV groups. Based on the presence of a recombination fragment spanning the C3 ORF, a recombinant origin was suggested for both HYVV-Jeju and –DJ, with parents close to Japanese isolates HYVMV-[SP1:00] and Eupatorium yellow vein virus (EpYVV)-[Suya]. In addition, the presence of a further recombination fragment spanning the IR suggested the parents of HYVV-DJ were close to HYVV-Jeju and EpYVV-[Suya].     

First natural co-occurrence of tomato leaf curl New Delhi virus DNA-A and chili leaf curl betasatellite on tomato plants (<Emphasis Type="Italic">Solanum lycopersicum</Emphasis> L.) in India

Tomato leaf curl disease (ToLCD) affected 25% of the tomato crop in Chitrakoot, India and symptomatic leaves were collected for molecular assay. The complete sequences of bipartite begomovirus DNA-A and a betasatellite DNA were amplified. In a sequence analysis, begomovirus DNA-A and betasatellite shared highest sequence identity (91–99%) with Tomato leaf curl New Delhi virus (ToLCNDV) DNA-A and chili leaf curl betasatellite (ChLCB), respectively. The virus was transmitted by whitefly to tomato plants and caused ToLCD symptoms with 70% transmission rate. To our knowledge, this is the first report of the natural occurrence of ToLCNDV and ChLCB in India.     

First occurrence of <Emphasis Type="Italic">Sugarcane streak mosaic virus</Emphasis> infecting sugarcane in Indonesia

On plants at 59 sugarcane plantations in Central and East Java, Indonesia, we found virus-like symptoms such as streak mosaic. The virus was transmitted mechanically and was sett-borne. The nucleotide sequence of the coat protein gene had the highest identity with that of Sugarcane streak mosaic virus (SCSMV) isolate Pakistani. We tentatively designate this isolate as SCSMV-Idn (Indonesia).     

Occurrence of viruses in field-grown pepper crops and some of their reservoir weed hosts in Samsun, Turkey

Pepper production is affected by several viral diseases in Samsun, Turkey. To determine the identity of these viruses, a total of 313 samples from field-grown peppers were collected during surveys in 1998 and 1999, and tested by enzyme linked immunosorbent assay (ELISA). Six viruses,Alfalfa mosaic virus (AMV),Cucumber mosaic virus (CMV),Potato virus Y (PVY),Tomato mosaic virus (ToMV),Tobacco mosaic virus (TMV) andTomato spotted wilt virus (TSWV) were detected in the samples. Of 313 plants tested, 42 were doubly infected, and TMV+PVY (15.4%) was the most common double infection. This is also the first report of AMV in pepper fields in Turkey. The effect of some weed species that may act as reservoir of these viruses was also investigated in the region and of 24 weed species belonging to 15 families tested, 16 were found to be infected with at least one virus.Amaranthus retroflexus (Redroot pigweed) appeared to be a common host of CMV, PVY, ToMV, TMV and TSWV, whereasHibiscus trionum (Venice mallow) was recorded as a new weed host of PVY and TSWV. The majority of weed species found to be virus infected were very common in the pepper growing areas of the region. This indicates that pepper fields contaminated with these weeds are under risk of viral infections. http://www.phytoparasitica.org posting July 21, 2005.     

Cassava virus diseases and their control with special reference to southern Tanzania

Cassava is a major smallholder crop in much of Africa where it is attacked by two main virus diseases. African cassava mosaic disease (ACMD) occurs almost everywhere that the crop is grown causing severe losses in some countries. Cassava brown streak disease (CBSD) is of more restricted distribution being prevalent mainly on the east African coast and shores of Lake Malawi. Although both diseases have been known for many decades and much is known about ACMD, the aetiology and epidemiology of CBSD remain poorly understood. Control measures for African cassava mosaic virus (ACMV) have been recommended and in some cases implemented in a number of countries. Resistant varieties have been developed and national research programmes and international agencies are supporting phytosanitation programmes, based mainly on the distribution of ACMV-free planting material. It may be possible to use the same control measures against CBSD but the lack of basic information on the disease and difficulties of disease diagnosis are obstacles to the design of control strategies. ACMD is found in most areas where CBSD occurs and control measures must con sider the disease complex. This paper reviews the current knowledge about the two diseases in the context of possible integrated control     

Viruses affecting tomato crops in Serbia

In a two-year survey (2011–2012), 3220 samples were collected and analyzed in order to determine the presence and distribution of viruses in tomato crops at 56 localities of 18 districts in Serbia. Out of 12 viruses tested, Cucumber mosaic virus (CMV), Potato virus Y (PVY), Alfalfa mosaic virus (AMV), Tomato spotted wilt virus (TSWV), Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV) were detected in 42.1, 40, 11, 8.6, 2.3 and 1.3% of the total tested samples, respectively. The results revealed that CMV was prevalent in 2011 and PVY in 2012. CMV and PVY, apart from being predominant, were also the most widespread viruses. In general, single infections were the most frequent type of infection. Additionally, the most common mixed infections were double infections and the most prevalent combination was CMV and PVY. In 2011, the incidence of diseases and the percentage of all infection types were significantly higher than in 2012. Furthermore, in 2011, regardless of total single infections being prevalent compared to mixed infections, two prevailing viruses were commonly detected in mixed infections. The additional molecular testing of ELISA-negative samples using virus specific primers did not reveal the presence of Pepino mosaic virus (PepMV), Tomato yellow leaf curl virus (TYLC), Tomato infections chlorosis virus (TICV) and Tomato chlorosis virus (ToCV).     

Sequence diversity in the coat protein and 3″-untranslated region of Chinese yam necrotic mosaic virus RNA

Sixteen isolates of Chinese yam necrotic mosaic virus (ChYNMV) were collected from nine sites in Japan and one site in Korea, and 1098 nucleotides of the 3-terminal of the genome were sequenced. Identity of the coat protein gene was 95.5%–99.7% among the isolates. Substitution in the deduced amino acids of the coat protein ranged from 0 to 7, mainly in the N-terminal region. The 3-untranslated region consisted of 231 nucleotides, which had 96.5%–100% nucleotide identity among the isolates. Sequence diversity was considerably less in ChYNMV than in Yam mosaic virus or Japanese yam mosaic virus.     

Distinct association of an alphasatellite and a betasatellite with <Emphasis Type="Italic">Tomato leaf curl New Delhi virus</Emphasis> in field-infected cucurbit

Leaf samples of Cucurbita pepo with yellow mosaic disease symptoms were collected in 2012. Rolling circle amplification and PCR amplification with begomovirus-specific primers confirmed the presence of an Old World bipartite begomovirus, an alphasatellite and a betasatellite. Molecular analysis of full-length sequences showed that Tomato leaf curl New Delhi virus (DNA-A) is associated with its cognate DNA-B, Papaya leaf curl betasatellite and a novel alphasatellite. To the best of our knowledge, this is the first report of an alphasatellite and a betasatellite associated with a bipartite begomovirus.     

Symptom severity of cassava mosaic disease in relation to concentration of African cassava mosaic virus in different cassava genotypes

The concentration of African cassava mosaic virus (ACMV) was assessed by enzyme-linked immunosorbent assay in relation to symptom severity among resistant, moderately resistant and susceptible cassava genotypes. Resistant genotype NR 8083 had significantly lower symptom severity scores ( P  < 0·05) than the susceptible genotype TMS 91934, but the two genotypes contained similar levels of virus concentration. The moderately resistant genotypes TMS 30572 and NR 8082 expressed significantly lower symptom severities ( P  < 0·05) than the susceptible genotypes TMS 91934 and TME 117, but they contained significantly higher virus concentrations ( P  < 0·05) than TMS 91934 and similar virus concentration as in TME 117. However, two other resistant genotypes, TME 1 and TME 8, had low symptom severity scores and virus concentrations. There was significant interaction ( P  ≤ 0·05) between cropping season and virus concentration in all the genotypes except TMS 30572. The resistant and moderately resistant genotypes that had high virus concentrations sustained storage root yield losses. The severity of symptoms expressed was not necessarily a reflection of the virus concentration in some of the genotypes. In addition to the use of symptom severity scores to group genotypes into resistant classes, it is recommended that virus concentration should also be considered. Genotypes displaying mild symptoms, but with high levels of virus accumulation, could be an important source of inoculum in the spread of ACMV by the whitefly vectors. This suggests that each genotype should be tested for virus accumulation prior to its release to the farmers.