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.     

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.     

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.     

Distinct strains of the re‐emergent Cassava common mosaic virus (genus: Potexvirus) infecting cassava in Argentina

Cassava common mosaic disease (CCMD) has been reported in all regions where cassava is grown in the Americas and the causal agent, Cassava common mosaic virus (CsCMV), has been identified as a mechanically transmitted potexvirus (Alphaflexiviridae). In Argentina, cassava is grown mainly in the northeast (NEA) region that shares borders with Brazil and Paraguay. Increasing incidences of CCMD were observed during the years 2014 to 2016 associated with severe leaf mosaic symptoms and yield reductions where the occurrence of CsCMV was confirmed by RT‐PCR and sequencing. In this work, the virus has been successfully purified and a double‐antibody sandwich (DAS‐) ELISA test has been developed from an Argentinean isolate of CsCMV to extend the diagnostics of the disease. A collection of 726 samples was screened and CsCMV was detected with 100% prevalence in the NEA region. Additional co‐infecting viruses were detected in some plants (64.4%); in these, CCMD symptoms correlated with CsCMV only, although more severe symptoms could be observed in mixed infected plants. Sequence analysis of the conserved RdRp domain showed a wider diversity of CsCMV isolates. Interestingly, a separate phylogenetic cluster was formed by isolates from the NEA region that only shared 77.1% to 80.3% nucleotide identity with the other clusters. These results indicate the presence of mixed strains occurring in the NEA region and suggest the presence of geographically distinct strains of CsCMV in South America.     

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.     

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     

广西局地西番莲病毒病的病原鉴定及优势病毒分析

 在广西采集表现斑驳、花叶症状疑似病毒病的西番莲叶片样品,利用小RNA测序技术,结合生物信息学分析,鉴定侵染西番莲的病毒种类。参考测序结果采用DAS-ELISA和RT-PCR方法对2015~2018年间采集的385份疑似病毒病样品进行检测,分析引发广西西番莲病毒病的优势病毒种类。结果显示:小RNA共获得20 921 061 clean reads,拼接获得560个contigs,其中99个contigs被注释为夜来香花叶病毒(telosma mosaic virus,TeMV),97个contigs被注释为黄瓜花叶病毒(cucumber mosaic virus,CMV),69个contigs被注释为东亚西番莲病毒(East Asian passiflora virus,EAPV),12个contigs被注释为大豆花叶病毒(soybean mosaic virus,SMV)。提取送测序的同批样品叶片的总RNA进行RT-PCR验证,可检测出TeMV、EAPV和CMV 3种病毒,未检出SMV。采用DAS-ELISA和RT-PCR对采集的样品进行检测,结果发现284份样品为阳性样品,检出率为73.76%,其中TeMV的检出率最高为64.16%,其次为EAPV和CMV,检出率分别为41.30%和11.43%;3种病毒存在复合侵染现象,其中TeMV+EAPV的检出率最高为24.94%,TeMV+CMV的检出率为4.16%,EAPV+CMV的检出率为0.26%,3种病毒复合侵染的检出率为4.94%。     

Variations and taxonomic status of begomoviruses causing severe epidemics of cassava mosaic disease in Kenya,Uganda, and Democratic Republic of the Congo

The molecular variability in the DNA-A of cassava-begomoviruses, East African cassava mosaic virus (EACMV), East African cassava mosaic virus – Uganda variant (EACMV-UG), African cassava mosaic virus (ACMV), and East African cassava mosaic Zanzibar virus (EACMZV) in Kenya, Uganda, and Democratic Republic of the Congo (DRC) was investigated. Most samples from western Kenya, Uganda, and eastern DRC contained EACMV-UG. Fewer than half of the samples had a mixed infection of ACMV and EACMV-UG, and a small percentage had only ACMV infections. EACMV and EACMZV were the only begomoviruses detected in samples from the Kenyan coast. The coat protein gene nucleotide (nt) and the deduced amino acid sequence analyses revealed a high degree of sequence identity within each virus type and that EACMV-UG was most related to ACMV. However, analysis of the retrieved complete DNA-A (2781–2801nt) sequences of selected virus types revealed that EACMV-UG DNA-A share more than 90% identity with EACMV and less than 80% with ACMV, confirming that the virus is a strain of EACMV.     

A general model of plant-virus disease infection incorporating vector aggregation

In plant-virus disease epidemiology, dynamical models have invariably incorporated a bilinear inoculation rate that is directly proportional to both the abundance of healthy (susceptible) hosts and the abundance of infective vectors. Similarly, the acquisition rate is usually assumed to be directly proportional to the abundance of nonviruliferous vectors and that of infectious hosts. These bilinear assumptions have been questioned for certain human diseases, and infection rates that incorporate power parameters of the variables have been proposed. Here, infection rates for plant-virus diseases that are of a more general form than the familiar bilinear terms are examined. For such diseases, the power parameter can be regarded as a measure of the spatial aggregation of the vectors or as a coefficient of interference between them, depending on the context.
Field data of cassava mosaic virus disease (CMD) incidence were examined. When vector population density and disease incidence were high, disease progress curves over the first 6 months from planting could not be explained using models with bilinear infection rates. Incorporation of the new infection terms allowed the range of observed disease progress curve types to be described. New evidence of a mutually beneficial interaction between the viruses causing CMD and the whitefly vector, Bemisia tabaci , has shown that spatial aggregation of the vectors is an inevitable consequence of infection, particularly with a severe virus strain or a sensitive host. Virus infection increases both vector fecundity and the density of vectors on diseased plants. It is postulated that this enhances disease spread by causing an increased emigration rate of infective vectors to other crops. Paradoxically, within the infected crop, vector aggregation reduces the effective contact rate between vector and host and therefore the predicted disease incidence is less than when a bilinear contact rate is used.     

Effect of pokeweed antiviral protein (PAP) on the infection of plant viruses

At a concentration of 0.4 μg purified pokeweed antiviral protein (PAP)/ml, the formation of local lesions on tobacco leaves caused by tobacco mosaic virus infection was completely inhibited and at 25 ng PAP/ ml. 68% inhibition was still obtained. PAP protected plants from infection by viruses from seven virus groups-five RNA viruses: tobacco mosaic virus, cucumber mosaic virus, alfalfa mosaic virus, potato virus X and potato virus Y; and two DNA viruses: African cassava mosaic virus (ssDNA) and cauliflower mosaic virus (dsDNA). Virus infection was probably blocked by PAP at a very early stage. PAP infiltrated into the intercellular spaces through the lower surfaces of leaves inhibited infection by virus inoculated on the upper leaf surface, and partially prevented PVY transmission by aphids. However. PAP did not show any activity against two bacterial and six fungal pathogens.     

云南美人蕉病毒病病原鉴定

In this study,the causal agents were identified from Canna indica viral diseased plants in Yunnan Province.The diseased C.indica plants mainly exhibited the symptoms like veinal chlorosis and yellowing,streak mosaic or interveinal chlorosis,while older leaves always showed veinal necrosis as well as chlorosis.Viral pathogens were detected by RT-PCR/PCR in 24 diseased C.indica samples collected from Kunming and Yuxi City in Yunnan Province.The results indicated that the main C.indica-infecting viruses were canna yellow mottle virus (CaYMV),bean yellow mosaic virus (BYMV),sugarcane mosaic virus (SCMV).CaYMV showed the highest detection rate of 87.5 %,whereas,the BYMV had the lowest rate of 16.7% in the 24 samples.Co-infections of CaYMV+SCMV,CaYMV+BYMV and CaYMV+SCMV+BYMV were also detected in the diseased samples.However,cucumber mosaic virus (CMV),tobamovirus,luteovirus,orthotospovirus,begomovirus and umbravirus were not detected in these samples.This is the first report of CaYMV and SCMV infecting C.indica in Yunnan province.     

Cassava common mosaic virus infection affects growth and yield components of cassava plants (Manihot esculenta) in Argentina

Cassava is an important crop with great economic and social significance in many countries. Most of its biomass is usable: storage roots can be destined for industry or fresh consumption, leaves are a source of protein, vitamins, and minerals, and stems can be used as propagation material. Due to its vegetative propagation, cassava yield is greatly constrained by viral diseases. Cassava common mosaic virus (CsCMV), one of the most widely spread viruses in Latin America, is the only cassava-infecting potexvirus able to cause disease in a single infection: cassava common mosaic disease (CCMD). Here, we evaluated the effect of an Argentinian strain of CsCMV on several agronomic traits. Field trials were established in north-eastern Argentina for three successive cropping seasons, 2016/17, 2017/18, and 2018/19. CsCMV presence was confirmed by PCR or ELISA tests in mechanically inoculated cassava plants. The evaluated traits were plant height (PH), total fresh weight (TFW), shoot fresh weight (SFW), diameter and FW of tuberous root per plant (TRD and FWTR), FW of each individual tuberous root (FWiTR), length and number of tuberous roots (TRL and TRN), harvest index (HI), and estimated yield of tuberous root (EY) in both infected and noninfected plants. Significant yield losses were recorded in infected plants. The most affected traits were EY and FWTR (both showing 44.3% of losses), followed by TFW, SFW, TRN, and FWiTR (37.8%, 33.5%, 29.9%, and 24.8% of losses, respectively). These losses are extremely high for Argentina, where this crop provides food security and demand for the raw material is unsatisfied.     

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.     

A Survey of Viruses of Alstroemeria in the UK and the Characterisation of Carlaviruses Infecting Alstroemeria

Alstroemeria samples collected in the UK were tested for a range of viruses using ELISA. Alstroemeria mosaic virus (AlMV), alstroemeria carlavirus (AlCV), lily symptomless virus (LSV), cucumber mosaic virus (CMV) and tobacco rattle virus (TRV) were detected either singly or in combination in 67.5% of 203 samples. AlCV and LSV isolates from Alstroemeria and lily were studied and characterised serologically using existing antisera, and by PCR, using primers to an 11kDa open reading frame (ORF) unique to carlaviruses and to the coat protein gene of LSV. Sequences of isolates of AlCV and LSV from the coat protein gene were 94–99% similar and were 99% similar in the 11kDa ORF, supporting the view that these are strains of the same virus.     

The Components and Deployment of Resistance to Cassava Mosaic Virus Disease

Cassava mosaic virus disease (CMD) is prevalent and causes serious losses in cassava (Manihot esculenta) in southern India and in many parts of sub-Saharan Africa. The disease is caused by viruses of the Geminiviridae that are transmitted by the whitefly Bemisia tabaci and disseminated in the stem cuttings used routinely for propagation. The main approach to control is through the use of virus-resistant varieties, but suitable ones are not always available and susceptible varieties are still widely grown. This explains why CMD continues to be a problem in many areas.CMD-resistant varieties have several features which are considered in this review:- They are not readily infected, even when exposed to large amounts of vector-borne inoculum. When infected they develop symptoms that tend to be inconspicuous and not associated with obvious deleterious effects on growth or yield. Moreover, the symptoms become even less conspicuous as growth proceeds and plants may eventually recover and become symptomless. Infected plants support a low virus content and they are likely to be a poor source of inoculum from which further spread can occur. Virus is not fully systemic within infected plants which can be a source of uninfected planting material when stem cuttings are collected for further propagation. This phenomenon is referred to as reversion and it has an important cleansing effect in restricting or preventing the progressive deterioration in health status that would otherwise occur during successive cycles of vegetative propagation.The available information on the different components of resistance is discussed and it is concluded that they are inter-related features of the same basic mechanism that restricts virus entry, replication and movement within the host. It is argued that the effectiveness and durability of virus-resistant varieties are likely to be influenced by the way in which they are deployed. However, this topic has received little attention from researchers and there is continuing uncertainty on the effects of CMD on the yield of resistant varieties and on the role of phytosanitation. This involves the use of virus-free planting material and the removal (roguing) of any additional diseased plants that occur. Some consider that these procedures complement the use of virus-resistant varieties and should be adopted, whereas others argue that they are unnecessary and inappropriate. It is concluded that there is considerable scope for utilizing resistant varieties more widely and more effectively than at present, but in doing so it is important to avoid eroding the genetic diversity that is currently such a marked feature of cassava cultivation in Africa.     

北京地区花生病毒病及流行规律研究

1985—1987年研究表明北京地区花生上流行的病害主要有黄瓜花叶病毒CA株系(CMV-CA)引起的黄花叶病害和花生轻斑驳病毒(PMMV)引起的轻斑驳病害。血清鉴定451份花生病害样品,黄花叶病害样品受CMV-CA侵染占95.7％,轻斑驳病害样品受PMMV侵染占91.3％,中后期病害样品受CMV-CA和PMMV复合感染较普遍。CMV种传率2％左右,种传病苗在花生出苗后开始出现,6月病害进入高峰。三年CMV-CA流行程度明显不同,主要取决于苗期蚜虫发生早晚、发生量及苗期降雨量。PMMV种传率低于1％,病苗出现稍晚,但病害扩散快,6月上旬进入高峰,7月上、中旬发病率达100％。三年流行程度差异不明显。     

侵染四川辣椒的番茄斑萎病毒和辣椒轻斑驳病毒的小RNA测序检测及鉴定

 调查发现四川省汶川县当地辣椒的病毒病严重且症状多样,病样粗提液摩擦接种辣椒、矮牵牛和三生烟,出现辣椒系统性花叶焦枯和茎尖坏死,指示植物表现局部枯斑。对3个不同症状的病果进行sRNA深度测序鉴定,发现均含有番茄斑萎病毒(Tomato spotted wilt virus,TSWV)和辣椒轻斑驳病毒(Pepper mild mottle virus,PMMoV)。通过RT-PCR技术进行验证,结果显示所有病样的果皮和部分新鲜种子以及回接寄主的病叶均检测到TSWV和PMMoV,表明该地辣椒病毒病是由TSWV和PMMoV复合侵染引起。这是TSWV侵染四川辣椒的首次报道。分别基于TSWV N基因序列和PMMoV CP基因序列构建系统发育树,汶川分离物TSWV-WC(MK468469)与贵州分离物(KP684518)亲缘关系最近,PMMoV-WC(MK408614)与北京分离物(AY859497)亲缘关系最近。推测该地辣椒病毒病可能与品种引进有关。     

Surveys of cassava plantations in Colombia for virus and virus-like diseases

The cassava common mosaic virus (CsCMV) and the frogskin (FSD) disease agent have been reported to reduce cassava yields significantly in South America. However, little information is available on the distribution and incidence of these and other cassava virus diseases in Colombia. Cassava plants collected in three principal cassava production zones of Colombia were tested for the presence of CsCMV, cassava × virus (CsXV), and the Caribbean mosaic disease (CMD) and FSD agents. Some plants were also tested for the presence of double-stranded RNA (dsRNA). CsCMV was not detected in any of the 870 plants from 86 plantations. CsXV was detected in 51% of the 150 plants collected in the Cauca Department in south-central Colombia. The virus was present on all 15 cassava plantations surveyed. The CMD agent was detected in 17% of the 138 plants sampled in the Department of Magdalena in northern Colombia. FSD root symptoms were observed on 25 and 3% of plants examined in the Departments of Cauca and Magdalena, respectively. None of the 570 plants collected in areas west of the Rio Magdalena in the Departments of Atläntico, Bolivar, Córdoba and Sucre were found to be infected with any of these disease agents. However, some plants sampled in this region were found to contain multiple dsRNA species of unknown origin.     

我国太子参主产区病毒病发生情况调查

为调查我国太子参主产区病毒病发生情况,使用RT-PCR法对采自福建省柘荣县,贵州省施秉县、丹寨县和安徽省宣城市的71份具有典型病毒病症状的太子参样品进行检测,并根据CP氨基酸序列对不同地区病毒进行系统进化分析。RT-PCR结果显示,65份样品检出病毒,检出率为91.55%,其中,56份样品检出芜菁花叶病毒Turnip mosaic virus(TuMV),49份样品检出蚕豆萎蔫病毒2号Broad bean wilt virus 2(BBWV2),9份样品检测出黄瓜花叶病毒Cucumber mosaic virus(CMV),检出率分别为78.87%、69.01%和12.68%。未检测到烟草花叶病毒Tobacco mosaic virus(TMV)。序列和系统发育进化分析显示,本研究获得的TuMV、BBWV2和CMV与NCBI数据库中的序列相似度较高,核苷酸相似度分别为98.05%～98.98%、93.61%～94.25%和98.02%～99.17%,氨基酸序列相似度分别为:96.14%～97.47%、97.33%～98.50%和98.00%～100%,分别属于World-B组、Ⅰ-a亚...