Evidence of Grapevine enamovirus 1 Infecting Grapevine (Vitis vinifera L.) in Canada.

Grapevine enamovirus 1 (GEV1) belongs to the genus Enamovirus, in the family Solemoviridae. It has been reported from several countries infecting grapevines including Brazil (Silva et al. 2017), China (Ren et al. 2021) and France (Hily et al. 2022). To assess the prevalence and diversity of economically important grapevine viruses in nine Canadian vineyards, total RNA and double-stranded RNA (dsRNA) (Fall et al. 2020) were extracted from 30 and 100 composite samples respectively, with each consisting of five vines of the same cultivars. The cultivars included in this study are Frontenac noir (n=34), Vidal (n=32), Marquette (n=33), Riesling (n=31), and Pinot noir (n=31). The total RNA and dsRNA samples were subsequently multiplexed and diagnosed by high-throughput sequencing (HTS) on NovaSeq (600 S4 PE100) and MiSeq (2 × 250 cycle PE) respectively. From NovaSeq and MiSeq sequencing, an average of 410,000 to 1.3 million reads/sample were obtained, respectively, with mapped viral reads representing 10.92% to 12.48% of the total reads. After sequence quality was verified using Trimmomatic v.0.40 (Bolger et al. 2014), the clean sequences were screened against all possible viruses in the databases using the Virtool (Rott et al. 2017) and VirFind virus detection pipelines (Ho and Tzanetakis 2014). GEV1 was detected in clean sequences from two, three, and two leaf samples of cultivars 'Marquette' 'Riesling' and 'Frontenac noir' respectively. Six of the seven HTS-assembled GEV1 genomes were partial, ranging from 4,523 to 6,000 nucleotide (nt) with genome coverage varying from 71% to 89%. Only one 6,314 nt long assembled contig (Accession No. OR021829), represented a nearly complete genome, being only 53 and 3 nt shorter than Sd-CG (MT536978) at 5' and 3' untranslated regions (UTR), respectively. Isolate 3- Riesling-CAN (OR021829) shares 90.56 to 94.19% nt identities with several GEV1isolates at 96-99% of query coverage. Phylogenetically, OR021829 is closer to GEV1 isolates from France and China (Figure S1). To validate the HTS results, the developed primer pair SetF and Set1R (Silva et al., 2017) was used for RT-PCR detection. The amplicons from all seven HTS-positive samples were sequenced using Sanger sequencing, confirming the presence of GEV-1 in three studied grape cultivars in Canadian vineyards. Symptoms associated with the specific GEV1-infected vines could not be explained as composite samples were used. Each of the combined samples HTS library also tested positive for at least one of the known grape virus/viroids, namely grapevine leafroll associated-virus -3, grapevine pinot gris virus, grapevine rupestris stem pitting-associated virus, Marafivirus syrahense grapevine Syrah virus-1 and hop stunt viroid. To our knowledge, this is the first report of GEV1 being detected in grapevines in Canada, or in any North American vineyard. GEV1 is a relatively new virus, and its biology remains largely unknown. Based on this sequence new GEV1 primers can be developed to know the genetic variability among GEV-1 and improve the detection of this virus in vineyards.

Quantitative insights into grapevine anthracnose (Elsinoë ampelina) epidemiology: impact of temperature and leaf age on incubation, lesion development, and sporulation.

Grapevine anthracnose, caused by Elsinoe ampelina, is one of the most devastating diseases for wine and table grapes, particularly in hot, humid regions. This study explores how temperature and leaf age affect incubation and how temperature affects lesion development and sporulation. The influence of temperature and leaf age on incubation period (days) was tested under controlled conditions. Leaves from 1 to 8 days old were inoculated and maintained at temperatures of 5, 10, 15, 20, 25, and 30°C. The time elapsed between inoculation and the emergence of initial lesions was recorded. The effect of temperature on lesion development and sporulation was investigated under vineyard conditions. This was achieved through artificial inoculations, with 17, 11, and 11 inoculations conducted in 2016, 2017, and 2018, respectively. The average incubation period, considering all leaf ages, was 27.50 days at 5°C, 15.10 days at 10°C, 9.70 days at 15°C, 5.90 days at 20°C, 3.70 days at 25°C, and 2.26 days at 30°C. Regardless of temperature, the average incubation period was 3.6, 5.9, 8.3, 9.8, 11.9, 13.4, 15.6, and 17.1 days for leaves 1, 2, 3, 4, 5, 6, 7, and 8 days old respectively. The exponential decay model accurately describes the incubation period as a function of both temperature and leaf age. On average, the relative lesion development (RLD) were 0.00, 0.00, 0.23, 0.47, 0.72, 0.93 0.92, 0.90, 0.94, and 1.0 at 0, 1, 2, 3, 4, 5, 6, 7, 8, and 9 days after inoculation, respectively. The average relative sporulation (RSPO) was 0.03, 0.36, 0.82, 0.96, and 1.0 at 5, 10, 15, 20, and 25 days after inoculation, respectively. Both RDL and RSPO as a function of degree-days (Tbase= 0°C) since inoculation were well described by the logistic function. The rates of change in relative lesion development and relative sporulation were 0.055 and 0.032, respectively. The results of this study provide new quantitative insights into three important stages (monocyclic processes) in the development of grapevine anthracnose caused by E. ampelina.

Strength development and self-desiccation of saline cemented paste backfill.

Given that many mines around the world are located in areas where fresh water is scarce, and companies are being held to increasingly stringent sustainability and environmental responsibility standards, many mines are looking to use locally available saline groundwater or seawater as mixing water in cemented paste backfill (CPB). However, the impacts of this decision on key engineering properties of CPB (e.g. strength and self-desiccation) that affect its mechanical stability need to be better understood to allow confident selection of this practical and more sustainable solution. Thus, the effect of mixing water salinity and binder type on the strength (unconfined compressive strength, UCS) development and self-desiccation (measured by suction and volumetric water content) of CPB is explored in this research. NaCl concentrations from 0 to 300 g/L were used in CPB made with silica tailings and Portland cement type I (PC). Concentrations of 10 and 35 g/L were found to moderately increase UCS, while a concentration of 100 g/L had comparable UCS to non-saline CPB and a concentration of 300 g/L was found to significantly decrease UCS over all curing times. The overall trend is 10 g/L > 35 g/L > 0 g/L > 100 g/L > 300 g/L. The UCS of the 60-day-old CPB with a NaCl of 300 g/L is significantly lower, registering a 26% decrease compared to the UCS of the 60-day-old CPB without salt. In contrast, the UCS of the 60-day-old CPBs containing 10 g/L and 35 g/L of salt exhibits a notable improvement, being 15% and 10% higher, respectively, than the UCS of the 60-day-old CPB without salt. Water content and suction monitoring were conducted up to 28 days of curing time, and it was found that suction only slightly contributed to UCS gain of the saline CPB, and high salt contents (100 and 300 g/L) significantly inhibited the self-desiccation ability of CPB due to inhibition of cement hydration by the excessive amount of salt. The increase in strength of both saline and non-saline samples was attributed primarily to the increase in cement hydration products, while the increased strength of the samples with salinities of 10 and 35 g/L was mainly attributed to the enhancement of the binder hydration due to the low amount of salt and the presence of Friedel's salt in the pores. The effect of PC replacement by 25 to 75% with slag on CPB with 35 g/L mixing water salinity was also studied. Slag replacement of 50% and higher resulted in significantly higher UCS over most curing times. Suction likely moderately contributed to UCS of the saline CPB with slag, in addition to the presence of Friedel's salt in the pores and the acceleration of cement and slag hydration by the presence of NaCl.

NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection.

There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common.

A Decade of Hidden Phytoplasmas Unveiled Through Citizen Science.

Climate change is impacting agriculture in many ways, and a contribution from all is required to reduce the imminent losses related to it. Recently, it has been shown that citizen science could be a way to trace the impact of climate change. However, how can citizen science be applied in plant pathology? Here, using as an example a decade of phytoplasma-related diseases reported by growers, agronomists, and citizens in general, and confirmed by a government laboratory, we explored how to better value plant pathogen monitoring data. Through this collaboration, we found that in the last decade, 34 hosts have been affected by phytoplasmas; 9, 13, and 5 of these plants were, for the first time, reported phytoplasma hosts in eastern Canada, all of Canada, and worldwide, respectively. Another finding of great impact is the first report of a 'Candidatus Phytoplasma phoenicium'-related strain in Canada, while 'Ca. P. pruni' and 'Ca. P. pyri' were reported for the first time in eastern Canada. These findings will have a great impact on the management of phytoplasmas and their insect vectors. Using these insect-vectored bacterial pathogens, we show the need for new strategies that can allow fast and accurate communication between concerned citizens and those institutions confirming their observations.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

First report of Alstroemeria necrotic streak virus infecting greenhouse bell pepper (Capsicum annuum) in Canada.

Alstroemeria necrotic streak virus (ANSV) is an Orthotospovirus that has been isolated from symptomatic Alstroemeria plant in 2010 (Hassani-Mehraban et al. 2010). It has been shown to infect crops of bell pepper (Capsicum annuum) and tomato (Solanum lycopersicum) (Olaya et al. 2017) which are two of the three biggest greenhouse crops in Canada in terms of production volume and value (Statistic Canada. 2020). In July of 2022, the entire production of bell pepper (all plants) from a greenhouse in Québec was presenting necrotic rings and discoloration in fruit and seemingly healthy leaves. Samples from these infected bell pepper were found to be negative for twenty two common viruses infecting bell pepper by ELISA immunoassay by the Laboratoire d'expertise et de diagnostic en phytoprotection (LEDP) (Québec, Canada). To identify the causal agent, double-stranded RNA was extracted from leaf and fruit of one plant to form two separate samples (leaf and fruit) and used for cDNA library preparations with Nextera XT DNA Sample Prep kit (Illumina, USA). The libraries were sequenced using Illumina Miseq (Fall et al. 2020). The same dsRNA were also sequenced with MinION nanopore sequencing method as described previously (Javaran et al. 2021; Javaran et al. 2023). The obtained raw FASTQ data were processed following the methodology described in Fall et al. 2020 and Javaran et al. 2023. The Miseq sequencing yielded over 2 million reads per sample with a percentage of mapped viral reads ranging from 26.92 to 47.29% of the total number of reads. The leaf samples were positive to Bell pepper endornavirus (BPEV) with the full genome covered 16713 times and Alstroemeria necrotic streak virus (ANSV) with 98% of the genome covered 4929 times. The MinION sequencing yielded 1,028,460 reads and the same viruses were detected with 1288 long reads (mean length of 745bp) assigned to ANSV genome. Both viruses were detected in the leaf and fruit samples. The complete ANSV genome comprising three segments (L, M, and S) was assembled and deposited in GenBank: (OQ261731-OQ261733). These L, M and S segments shown 99% nt identity with an isolate from the Columbia (GenBank: MF469036, MF469037, MF469038). It is interesting that read coverage at near the 2000th position of the S segment, was very low. This phenomenon may suggest a cleavage site nearby by a viral or host factor. ANSV was mainly found in leaf samples and very low numbers of reads in fruit samples. The presence of ANSV was confirmed by RT-PCR using the primers specific to the ANSV nucleocapsid gene Tospo_S_F (5'- CAG AAT CAG GCT GCA TTT AAT TTC C-3') and Tospo_S_R (5'-CAA CGC TTC CTT TAG CAT TAG G-3') (Gallo et al. 2019). The sequences of ∼600 bp amplicons were determined using Sanger sequencing and showed 100% nt identity with Miseq-derived sequences of ANSV. The virus has previously been detected in Colombia (Hassani-Mehraban et al. 2010) and then in California in 2018 (Tian et al. 2020). This is to our knowledge the first detection of ANSV in Canada. Bell pepper is one of the most important crops in Canada and the ANSV vector, the western flower thrips (Frankliniella occidentalis), known to spread the tomato spotted wilt virus (TSWV) is established in Canada (Allen et al. 1986). The detection of ANSV in Canada is line with the hypothesis of an international spread of this virus (Tian et al. 2020) as is it not known to spread through seeds.

Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada.

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada.

Assessment of the global toxicity of marine sediments from the Dakar peninsula (Senegal, West Africa).

Marine pollution in West Africa is major threat particularly around coastal megacities. We assess the chemical and ecotoxicological quality of the marine sediments in various submerged sampling sites of Dakar. Analysis revealed that sediments were slightly basic in which fine and coarse sands predominated. High percentages of total organic carbon were found sometime above 6%. Higher levels of heavy metal were reported than in previous studies. Chromium and nickel were above the Probable Effect Concentration. Low trophic level appeared not affected by the overall toxicity, while medium trophic level was more affected. Indeed, the vast majority (91%) of sites studied revealed a net percentage of Magallana gigas embryolarval developmental abnormality over 20%. The assessment of the global toxicity of marine sediments from the Dakar sites Studied (n = 11) seemed, almost, as a whole, to be in a poor ecotoxicological state calling to take measures to improve the sanitary condition of this marine feature.

Household level of air pollution and its impact on the occurrence of Acute Respiratory Illness among children under five: secondary analysis of Demographic and Health Survey in West Africa.

BACKGROUND: One out of ten deaths of children under five are attributable to indoor air pollution. And Acute Respiratory Illness (ARI) is among the direct causes. OBJECTIVE: This study showed the possibilities of characterizing indoor air pollution in West African Economic and Monetary Union (WAEMU) area and it also made it possible to estimate its impact on the occurrence of ARI in children under five. METHODS: It has been a secondary analysis based on Demographic and Health Surveys (DHSs) from WAEMU countries' data.. "Household level of air pollution" is the created composite variable, from questions on the degradation factors of indoor air quality (domestic combustion processes) which served to characterize indoor air pollution and to measure its impact by a logistic regression. RESULTS: Burkina Faso stands out with a greater number of households with a high level of pollution (63.7%) followed by Benin (43.7%) then Togo (43.0%). The main exposure factor "Household level of air pollution" was associated with ARI symptoms (Togo: prevalence = 51.3%; chi-squared test's p-value < 0.001). Exposure to high level of pollution constitutes a risk (AOR [95 CI]), even though it is not significant ( Ivory Coast: 1.29 [0.72-2.30], Senegal: 1.39 [0.94-2.05] and Togo: 1.15 [0.67-1.95]) and this could be explained by the high infectious etiology of the ARI.

Water, sanitation, and hygiene access in Senegal and its impact on the occurrence of diarrhea in children under 5 years old.

Diarrheal diseases are the second leading cause of child mortality worldwide, occurring in about one in every nine child deaths, and were associated with water, sanitation, and hygiene (WASH) access. In this study, we provided an overview of WASH indicators' evolution from 2000 to 2017 and their impact on the occurrence of diarrhea in children under 5 years old in Senegal. It was a retrospective cross-sectional study, in which we did a secondary analysis of data from the Joint Monitoring Program (JMP) for water supply and sanitation and from the Senegal Demographic and Health Survey 2018. Our results showed that access to safely managed services increased by 18.1 and 19.1%, respectively, for water and sanitation. The prevalence of diarrhea estimated at 18.16% was associated with straining water through a cloth (adjusted odds ratio (AOR) [95% confidence interval (CI)]: 1.21 [1.00-1.45]) and getting water supplies from a source not located in a dwelling (AOR [95% CI]: 1.59 [1.21-2.09]). The prevalence of diarrhea among children under 5 years old was still relatively high in Senegal and was significantly associated with a lack of WASH access. Although the latter continues to increase, additional efforts to make water safer to drink will significantly reduce the occurrence of diarrheal diseases among children under 5 years old in Senegal.

Competition Between Plasmopara viticola Clade riparia and Clade aestivalis: A Race to Lead Grape Downy Mildew Epidemics.

There is evidence of five clades of Plasmopara viticola in the world. Only two clades, riparia and aestivalis, have been identified as responsible for downy mildew epidemics in Quebec, Canada. It was reported in 2021 that epidemics caused by clade riparia start 2 or 3 weeks before those caused by clade aestivalis and that clade aestivalis was more aggressive than clade riparia. The objective of this work was to study the competition between P. viticola clade riparia (A) and clade aestivalis (B) and to compare the aggressiveness of both clades in mono- and coinfection situations. Suspensions of sporangia from both clades with six percentage combinations (AB 100-0; AB 89-11; AB 74-26; AB 46-54; AB 23-77; and AB 0-100) were inoculated on leaf discs (cultivar Vidal), and three other combinations (AB 88-12; AB 68-32; and AB 47-53) were inoculated on living leaves of grape plants (cultivar Vidal). Then, sporangium production, expressed as the percentage of sporangia produced by each clade, was estimated on leaf discs after eight cycles of infection-sporulation and then validated on living grape leaves after five cycles. The aggressiveness of clades in monoinfection situations on leaf discs was compared with that in coinfection situations. The results show that the percentage of sporangia produced by clade aestivalis increases with the infection-sporulation cycle while that produced by clade riparia decreases. The area under the sporangium production progress curve (AUSPPC) of clade aestivalis was significantly higher than that of clade riparia. The aggressiveness of P. viticola clades riparia and aestivalis in coinfection situations was different from that in monoinfection situations and was strongly influenced by the percentage of each clade in competition. These results suggest that, on the grapevine cultivar Vidal, P. viticola clade aestivalis is more competitive than clade riparia and that the percentage of each clade present in the vineyard should be considered for management of downy mildew.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Speciation of metals by sequential extractions of agricultural soils located near a dumpsite for prediction of element availability to vegetables.

In this paper heavy metal pollution has been investigated by comparing total concentrations and speciation of heavy metals (Cr, Cu, Mn, Zn, Pb and Sr) in soils from four agricultural fields (S1, S2, S3, S4) located in the direct vicinity of the largest landfill in Senegal. The sequential test allowed discriminating between various fractions of heavy metals, namely the acid-extractable fraction, the fraction bound to Fe oxides, the fraction bound to organic matter and the residual fraction. It was proven that the most important fractions of metals (Cr, Cu, Pb, Mn, Sr and Zn) are bound to the residual fraction, more than 50% for most sites, and thus they may be relatively hardly liberated into the environment. The results also showed that the metal pollution in S3 and S4 were more severe than in other sampling sites, especially for Mn and Zn. In addition, the exchangeable fraction, which is the most available, represents from 10 to 47% of the total concentration for Sr, Mn and Zn, indicating that a non-negligible part of these elements may be easily released. Matrix correlation between soil characteristics and the elemental concentrations was tested to study and to detect a possible trend of metal mobilization from organic matter or oxides to agricultural soils. Vegetable grown from the four sampling sites were analyzed, Cr, Zn and Pb concentrations were high in many studied foodstuffs, (up to 54 mg/kg; 45.8 mg/kg and 3.4 mg/kg for Mn, Zn and Pb respectively) and higher than the threshold values of FAO/WHO. Calculation of hazard indexes suggested no potential health risks associated with consuming the vegetables with the exception of cassava and cassava leaves.

Investigating the metal contamination status from recycling e-waste sites from Dakar, Senegal.

In Senegal, processes employed for recycling e-wastes result in release of so-called heavy metals in the environment. In this study, the metal distribution and concentrations of soils collected from four e-waste recycling areas located in the Dakar area are presented. Measurements are performed using portable X-ray fluorescence and laser-induced breakdown spectroscopy (LIBS) to obtain a complete analysis of the soil, including major and trace elements (i.e., mg/kg). Levels of zinc, copper, manganese, and iron in soils are high but contrasted ranging from 66 mg/kg for Cu in Mbeubeuss landfill to more than 1000 mg/kg for Mn and 10,000 mg/kg for Zn. Lower values are obtained for chromium and lead (Cr = 207 mg/kg and Pb = 181 mg/kg). The most elevated average lead values (i.e., 2935 mg/kg and 1427 mg/kg) are obtained from the e-waste recycling sites located in the urban area of Dakar: Reubeuss and Pikine, respectively. Specific element fingerprints are obtained from each of the studied areas. To evaluate human exposure to the main metals, vegetables grown outside the large e-waste landfill were analyzed. The values obtained for Cr, Cu, Fe, Mn, Sr, and Zn are low, ranging from 0.11 to 9.66 mg/kg for chromium in turnip and iron in beetroots, respectively. The calculated health risk index remains below unit for all vegetables, which means no potential risk of vegetable consumption for human health. The data provided useful information to estimate contaminations and their origin. Therefore, in order to ensure food safety, continuous monitoring of the vegetables grown in the vicinity of recycling areas is needed.

Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics.

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for the direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses, the principle of third-generation sequencing platforms, and the application of nanopore sequencing technology in grapevine virus detection, virus-plant interactions, as well as the characterization of viral RNA modifications.

Dynamic response of thickened tailings in shaking table testing.

In this study, an instrumented thickened tailings deposit model was designed, built and employed to evaluate the behaviour of layered thickened tailings to dynamic loading by using a shaking table equipment. The thickened tailings were deposited subsequently in three thin layers in a flexible laminar shear box mounted on top of the shaking table. Cyclic loading with a peak horizontal acceleration of 0.13 g and a frequency of 1 Hz was applied to the layered tailings deposit. Different types of sensors were placed to monitor the accelerations, displacements, volumetric water content and pore water pressures at the intermediate depth of each layer. Results indicated that the acceleration for the bottom and middle layers were similar to that of the base of the shaking table; but, this was not the case for the top layer. The measurements of vertical displacements indicated that all layers of thickened tailings experienced initially contraction and subsequently dilation during the shaking. The excess pore water pressure ratios were found to exceed unity through all layers of thickened tailings when the shaking ended. In other words, the results showed that the layered thickened tailings are susceptible to liquefaction under the considered testing conditions. It is also found that upward pore water migration to the top layer and downward pore water flow to the bottom layer occurred in the thickened tailings deposit. This water migration generated additional pore water pressure and also impacted the vertical displacement and liquefaction susceptibility of the thickened tailings material. The results of this study give a better understanding of the dynamic behaviour of thickened tailings, which is crucial for the safety of thickened tailings systems as well as sustainable mining.

First report of Grapevine yellow speckle viroid 1 infecting grapevine (Vitis vinifera L.) in Canada.

Quebec is the third largest wine grape producer in Canada in acreage, tonnage, and wine grape sales (Carisse et al. 2017; Ben Moussa et al. 2019). To evaluate the diversity of viruses infecting grapevine in Quebec, a total of 77 leaf tissue samples (cv. Vidal) were collected from July to October in 2020 in three different vineyards located in Frelighsburg, Hemmingford and Saint-Jacques-le-Mineur in Quebec, Canada. Double-stranded RNA was extracted from each sample and used for cDNA library preparation with the Nextera XT DNA Library Preparation Kit (Illumina) as described previously (Kesanakurti et al. 2016). High-throughput sequencing (HTS, 2x300 bp) was conducted on dual-indexed libraries in a v3 flow cell using the Illumina MiSeq platform (Adkar-Purushothama et al. 2020). The obtained raw FASTQ data was de-multiplexed into 154 separate sequence files, and the adapters and barcode sequences were trimmed. The quality of the sequences was verified using Trimmomatic V.0.32 and the "clean" sequences were analyzed using Virtool and VirFind virus detection pipelines described elsewhere (Ho and Tzanetakis 2014; Rott et al. 2017) to screen for all possible viruses in the databases. Over 100,000 reads per sample were obtained with a percentage of mapped viral reads ranging from 1.47 to 19.43% of total number of reads. Out of 77 samples, 16 revealed the sequence of grapevine yellow speckle viroid 1 (GYSVd-1), for which the length coverage ranged from 98.5 to 99.1%; the depth ranged from 2X to 856X. The GYSVd-1 positive sequence files were subjected to whole genome assembly on CLC genomics Workbench v20.0.4 with the isolate SY-BR from Brazil (KU880715) used as reference. Seven complete genomes of GYSVd-1 of 366-368 nucleotides (nt) in size were deposited (GenBank Acc. MW732682 to MW732688). BLASTN analysis of the sequences showed 98-100% nt identities with isolate SY-BR. Other viruses and viroids such as Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine rupestris vein feathering virus and Hop stunt viroid were also detected. To confirm GYSVd-1 presence in Quebec vineyards, seven of the 16 HTS-positive grapevine leaf tissue samples were subjected to total RNA extraction, followed by RT-PCR assay as before (Adkar-Purushothama et al. 2015; Sahana et al. 2013); all were positive by RT-PCR. The PCR products were directly Sanger-sequenced, and they showed 100% nt identity to the HTS derived sequences. Three of the seven GYSVd-1 positive grapevines exhibited yellow leaf spots and flecks and tiny yellow leaves, but their mixed infection status makes definitive symptoms association difficult to determine. Previously, Hop stunt viroid was reported from grapevines in Canada (Xiao et al. 2019; Fall et al. 2020) but to the best of our knowledge, this is the first report of GYSVd-1 infecting grapevines in Canada, specifically in the province of Quebec. Further research is required to assess the GYSVd-1 related yield loss. Monitoring and testing for GYSVd-1 infection is necessary to prevent propagation of infected materials, spread, and potential negative impact for the Canadian grapevine industry.

High HIV-1 Virological Failure and Drug Resistance among Adult Patients Receiving First-Line ART for At least 12 Months at a Decentralized Urban HIV Clinic Setting in Senegal before the Test-and-Treat.

BACKGROUND: The feasibility of antiretroviral therapy (ART) monitoring remains problematic in decentralized HIV clinic settings of sub-Saharan Africa. We assessed the rates and correlates of HIV-1 virological failure (VF) and drug resistance (DR) in 2 pre-test-and-treat urban clinic settings of Senegal. METHODS: Consenting HIV-1-infected adults (⩾18 years) receiving first-line ART for ⩾12 months were cross-sectionally enrolled between January and March 2015, at the referral outpatient treatment center of Dakar (n = 151) and decentralized regional hospital of Saint-Louis (n = 127). In the 12 months preceding plasma specimens' collection patients at Saint-Louis had no viral load (VL) testing. Significant predictors of VF (VL ⩾ 1000 copies/ml) and DR (clinically relevant mutations) were determined using binomial logistic regression in R software. RESULTS: Of the 278 adults on EFV-/NVP-based regimens, 32 (11.5% [95%CI: 8.0-15.9]) experienced VF. Failing and non-failing patients had comparable median time [interquartile] on ART (69.5 [23.0-89.5] vs 64.0 [34.0-99.0] months; P = .46, Mann-Whitney U-test). Of the 27 viraemic isolates successfully genotyped, 20 (74.1%) carried DR mutations; most frequent were M184VI (55.6%), K103N (37.1%), thymidine analog mutations (29.6%), Y181CY (22.2%). The pattern of mutations did not always correspond to the ongoing treatment. The adjusted odds of VF was significantly associated with the decentralized clinic site (P < .001) and CD4 < 350 cells/mm3 (P < .006). Strong correlates of DR also included Saint-Louis (P < .009), CD4 < 350 cells/mm3 (P <. 001), and nevirapine-based therapies (comparator: efavirenz-based therapies; P < .027). In stratification analyses by site, higher rate of VF at Saint-Louis (20.5% [95%CI: 13.8-28.5] vs 4.0% [95%CI: 1.5-8.5] in Dakar) was associated with nevirapine-based therapies (OR = 3.34 [1.07-11.75], P = .038), self-reported missing doses (OR = 3.30 [1.13-10.24], P = .029), and medical appointments (OR = 2.91 [1.05-8.47], P = .039) in the last 1 and 12 months(s), respectively. The higher rate of DR at Saint-Louis (12.9% [95%CI: 7.6-20.1] vs 2.7% [95%CI: 0.7-6.7] in Dakar) was associated with nevirapine-based therapies (OR = 5.13 [1.12-37.35], P = .035). CONCLUSION: At decentralized urban settings, there is need for enhanced virological monitoring and adherence support. HIV programs in Senegal should intensify early HIV diagnosis for effective test-and-treat. These interventions, in addition to the superiority of efavirenz-based therapies provide a favorable framework for transitioning to the recommended potent drug dolutegravir, thereby ensuring its long-term use.

Renal impairment assessment on adults living nearby a landfill: Early kidney dysfunction biomarkers linked to the environmental exposure to heavy metals.

The aim of this study was to assess the integrity and kidney overall functional capacity of subjects exposed to landfill emissions. Urine and blood levels of Pb and Cd, and several of the newly biomarkers of nephrotoxicity (Kim Injury Molecule 1 (KIM-1), alpha-1 Microglobulin (α1 M), beta-2 Microglobulin (ß2 M), Cystatin-C (Cyst C), Clusterin, alpha-glutathione S-transferase (GSTα), pi-glutathione S-transferase (GSTπ), Tissue Inhibitor of Metalloproteinase-1 (TIMP1), Calbindin, Neutrophil Gelatinase-Associated Lipocalin (NGAL), Osteopontin (OPN), (Retinol Binding Protein(RBP), Liver-type Fatty Acid-Binding Protein (FABP-1), Trefoil Factor 3 (TFF3), Collagen VI) were measured in order to assess glomerular and tubule damage in adults living near a landfill. Our results indicate glomerular dysfunction in exposed subjects, and supported evidence of necrosis of proximal and distal tubule epithelial cells as specific biomarkers began to appear in the urine. Positive correlation by Pearson test were obtained between : blood Pb and B-OPN, B-Cyst C, Calbindin, U-KIM-1, TIMP1, U-OPN, and U-Clusterin; and also, between urinary Cd and TIMP1, B-Clusterin, U-OPN, FABP-1, Albumin, and U-Clusterin. The relation between biomarkers of Cd/Pb exposure and early effect biomarkers in this study clearly predicts the future risk of severe kidney injury in subjects living close to the landfill.

A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA Sequencing.

Quebec is the third-largest wine grape producing province in Canada, and the industry is constantly expanding. Traditionally, 90% of the grapevine cultivars grown in Quebec were winter hardy and largely dominated by interspecific hybrid Vitis sp. cultivars. Over the years, the winter protection techniques adopted by growers and climate changes have offered an opportunity to establish V. vinifera L. cultivars (e.g., Pinot noir). We characterized the virome of leafroll-infected interspecific hybrid cultivar and compared it to the virome of V. vinifera cultivar to support and facilitate the transition of the industry. A dsRNA sequencing method was used to sequence symptomatic and asymptomatic grapevine leaves of different cultivars. The results suggested a complex virome in terms of composition, abundance, richness, and phylogenetic diversity. Three viruses, grapevine Rupestris stem pitting-associated virus, grapevine leafroll-associated virus (GLRaV) 3 and 2 and hop stunt viroid (HSVd) largely dominated the virome. However, their presence and abundance varied among grapevine cultivars. The symptomless grapevine cultivar Vidal was frequently infected by multiple virus and viroid species and different strains of the same virus, including GLRaV-3 and 2. Our data show that viruses and viroids associated with the highest number of grapevines expressing symptoms included HSVd, GLRaV-3 and GLRaV-2, in gradient order. However, co-occurrence analysis revealed that the presence of GLRaV species was randomly associated with the development of virus-like symptoms. These findings and their implications for grapevine leafroll disease management are discussed.