First record of Grapevine Pinot gris virus infecting Vitis vinifera in the United Kingdom

Grapevine Pinot gris virus (GPGV) is a member of the genus Trichovirus, and was first identified in grapevine (Vitis vinifera) cv. Pinot Gris in Italy in 2012 (Giampetruzzi et al., 2012). Since then GPGV has been reported in several European countries as well as Australia, Canada, China, Korea and the USA (Bertazzon et al., 2016). In April 2017, a survey of four geographically separated vineyards in the UK was done to investigate the presence of GPGV. A dormant cane was sampled at random from each of the four locations (Pinot Noir clones 119, 336, 792 and 924, reciprocally grafted upon Gravesac, SO4 or 3309 Couderc rootstocks)

Associations of obesity and circulating insulin and glucose with breast cancer risk: a Mendelian randomization analysis.

BACKGROUND: In addition to the established association between general obesity and breast cancer risk, central obesity and circulating fasting insulin and glucose have been linked to the development of this common malignancy. Findings from previous studies, however, have been inconsistent, and the nature of the associations is unclear. METHODS: We conducted Mendelian randomization analyses to evaluate the association of breast cancer risk, using genetic instruments, with fasting insulin, fasting glucose, 2-h glucose, body mass index (BMI) and BMI-adjusted waist-hip-ratio (WHRadj BMI). We first confirmed the association of these instruments with type 2 diabetes risk in a large diabetes genome-wide association study consortium. We then investigated their associations with breast cancer risk using individual-level data obtained from 98 842 cases and 83 464 controls of European descent in the Breast Cancer Association Consortium. RESULTS: All sets of instruments were associated with risk of type 2 diabetes. Associations with breast cancer risk were found for genetically predicted fasting insulin [odds ratio (OR) = 1.71 per standard deviation (SD) increase, 95% confidence interval (CI) = 1.26-2.31, p  =  5.09  ×  10-4], 2-h glucose (OR = 1.80 per SD increase, 95% CI = 1.3 0-2.49, p  =  4.02  ×  10-4), BMI (OR = 0.70 per 5-unit increase, 95% CI = 0.65-0.76, p  =  5.05  ×  10-19) and WHRadj BMI (OR = 0.85, 95% CI = 0.79-0.91, p  =  9.22  ×  10-6). Stratified analyses showed that genetically predicted fasting insulin was more closely related to risk of estrogen-receptor [ER]-positive cancer, whereas the associations with instruments of 2-h glucose, BMI and WHRadj BMI were consistent regardless of age, menopausal status, estrogen receptor status and family history of breast cancer. CONCLUSIONS: We confirmed the previously reported inverse association of genetically predicted BMI with breast cancer risk, and showed a positive association of genetically predicted fasting insulin and 2-h glucose and an inverse association of WHRadj BMI with breast cancer risk. Our study suggests that genetically determined obesity and glucose/insulin-related traits have an important role in the aetiology of breast cancer

Yams (Dioscorea spp.) from the South Pacific Islands contain many novel badnaviruses: Implications for international movement of yam germplasm

Yam (Dioscorea spp.) samples (n = 690) from seven South Pacific Islands were screened for badnavirus infection by ELISA using two antisera to African badnaviruses. Positive readings were obtained for 26.4–34.6% of samples representing both known (D. bulbifera, D. nummularia and D. pentaphylla) and unreported host species (D. alata, D. esculenta, D. rotundata and D. trifida) in this region. Total DNAs were extracted from 25 ELISA-positive plants and 4 ELISA-negative controls and subjected to PCR amplification with badnavirus-specific primers targeting the reverse transcriptase (RT)–RNaseH genes. All 29 samples yielded the expected size PCR-product for badnaviruses, which were cloned and sequenced. Phylogenetic analyses of the resulting 45 partial (500–527 bp) RT–RNaseH sequences revealed 11 new sequence groups with <79% nucleotide identity to each other or any EMBL sequence. Three sequences (two groups) were highly divergent to the other nine new South Pacific yam badnavirus groups (47.9–57.2% identity) and probably represent either new Caulimoviridae genera or endogenous pararetrovirus sequences. Some sequence groups appeared specific to particular Dioscorea host species. Four 99.9% identical RT–RNaseH sequences possessing nine amino acid deletions from D. esculenta from three islands represent a putative integrated sequence group. The distribution of sequence groups across the islands indicates that badnaviruses have spread extensively between islands and continents through infected germplasm

Molecular characterization of potyviruses infecting potato and vegetables in Iraq

The genetic diversity of potyviruses infecting potato and vegetables in Iraq was determined by reverse transcription polymerase chain reaction (RT-PCR) targeting the 3´ terminal part of the genome. RT-PCR products were cloned and sequenced. Sequence analysis confirmed the occurrence of potyviruses, namely Bean yellow mosaic virus (BYMV) in broad bean, Potato virus Y (PVY) in potato and tomato, and Zucchini yellow mosaic virus (ZYMV) in zucchini squash. BYMV sequences showed maximum nucleotide sequence identity (97.2-98.7%) with isolates from Australia and Japan. Most PVY sequences were very closely related (ca. 99% nucleotide sequence identity) to PVYO: N isolates from USA and Canada, whereas other sequences showed nucleotide identities (98.5-98.7%) with PVYNTN isolates from Poland, UK and Syria. ZYMV sequences showed maximum nucleotide identity (97.9%) with an isolate from Israel. The low genetic diversity amongst Iraqi potyviruses, alongside their high sequence identities with potyviruses from other countries, suggests a relatively recent introduction to Iraq through imported planting materials

East African cassava mosaic Zanzibar virus – a recombinant begomovirus species with a mild phenotype

Cassava plants exhibiting mild symptoms of cassava mosaic disease (CMD) were collected from Unguja island, Zanzibar. Cuttings grown from these plants in the glasshouse produced similar symptoms, which were milder than those caused by other known cassava mosaic geminiviruses (CMGs). The whitefly vector, Bemisia tabaci (Gennadius), transmitted the putative virus to 27.7% (nthinsp=thinsp18) of target plants. Total DNA extracted from diseased leaves did not yield diagnostic PCR-bands using virus-specific primers to known CMGs. Degenerate primers, however, produced a diagnostic band indicating the presence of a begomovirus. Full-length DNA-A (2785 nucleotides) and DNA-B (2763 nucleotides) components were subsequently PCR-amplified, cloned and sequenced. Phylogenetic analyses of DNA-A and -B sequences showed that they were most similar to strains of East African cassava mosaic virus from Tanzania and Uganda at 83% and 86% nucleotide identities, respectively. The number and arrangement of open reading frames were similar to those of bipartite begomoviruses from the Old World. DNA-A was predicted to have recombined in the intergenic region (IR), AC1 and AC4 genes, and DNA-B in the IR. A maximum nucleotide identity of 83% in the DNA-A component with other sequenced begomoviruses, together with different biological properties allows this virus to be recognised as belonging to a new species named East African cassava mosaic Zanzibar virus (EACMZV)

Host range, vector relationships and sequence comparison of a begomovirus infecting hibiscus in India

Hibiscus leaf curl disease (HLCuD) occurs widely in India. Infected hibiscus plants show vein thickening, upward curling of leaves and enations on the abaxial leaf surface, reduction in leaf size and stunting. The commonly occurring weeds (Ageratum conyzoides, Croton bonplandianum and Euphorbia geniculata), Nicotiana benthamiana, Nicotiana glutinosa and Nicotiana tabacum (var. Samsun, Xanthi), cotton and tomato were shown to be susceptible to HLCuD. One of the four species of hibiscus (Hibiscus rosa-sinensis) and 75 of the 101 commercial hybrids/varieties grown in the Bangalore area of southern India were also susceptible. Two virus isolates associated with HLCuD from Bangalore, South India (Ban), and Bhubaneswar, North India (Bhu), were detected serologically and by PCR-mediated amplification of virus genomes. The isolates were characterised by sequencing a fragment of DNA-A component (1288 nucleotides) and an associated satellite DNA molecule of 682 nucleotides. Phylogenetic analyses of these DNA-A sequences clustered them with Old World cotton-infecting begomoviruses and closest to Cotton leaf curl Multan virus (CLCuMV) at 95–97% DNA-A nucleotide identities. The 682-nucleotide satellite DNA molecules associated with the HLCuD samples Ban and Bhu shared 96.9% sequence identity with each other and maximum identity (93.1–93.9% over positions 158–682) with ;1350-nucleotide DNA-b satellite molecules associated with cotton leaf curl disease in Pakistan and India (accession nos AJ298903, AJ316038). HLCuD in India, therefore, appears to be associated with strains of CLCuMV, a cotton-infecting begomovirus from Pakistan, which is transmitted in a persistent manner by Bemisia tabac

Assessment of yam mild mosaic virus coat protein gene sequence diversity reveals the prevalence of cosmopolitan and African group of isolates in Ghana and Nigeria

Open Access Journal; Published online: 19 May 2020This study analyzed the genetic diversity of 18 Yam mild mosaic virus (YMMV, genus Potyvirus) isolates collected from field surveys in Ghana (N = 8) and Nigeria (N = 10) in 2012−13. The full coat protein (CP) encoding region of the virus genome was sequenced and used for comparison and phylogenetic analysis of the YMMV isolates available in the NCBI nucleotide database. The mean nucleotide (nt) diversity was 13.4% among the 18 isolates (17 from D. alata and one from D. rotundata), 11.4% within the isolates of Ghana and 7.4% within the isolates of Nigeria. The phylogenetic clustering of the 18 YMMV isolates did not show correlation with the country of origin, and they aligned with the reference sequences of four of the 11 YMMV monophyletic groups representing the cosmopolitan group and the African group of YMMV isolates. High sequence homology of 99% between the YMMV sequence from Nigeria (CP12-DaN6-1) and a previously reported sequence from Togo (GenBank Accession Number AF548514) suggests a prevalence of seed-borne virus spread within the region. Understanding YMMV sequence diversity in West Africa aid in the improvement of diagnostic assays necessary for virus indexing and seed certification

Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus

Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10× cheaper (£0.53 = US$0.80 per sample) than the RNeasy method (£5.91 = US$8.86 per sample). A two-step RT-PCR (£1.34 = US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (£4.48 = US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100–400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7–1.7%, respectively. CBSV was detected at 10−4-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV

Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: Analyses to support safe germplasm movement

The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high