Phylogeny, genetic diversity and population structure of Faba bean necrotic yellows virus based on the nucleotide sequence of DNA-M.

Faba bean necrotic yellows virus (FBNYV) has a circular ssDNA genome possibly consisting of several components of about 1 kb each. The complete nucleotide sequence of one component of FBNYV (FBNYV DNA 1) containing a putative replicase gene is presented. This component consists of 1002 nucleotides and, in the virion orientation, contains one large open reading frame (ORF1) potentially encoding a 32.3 kDa replicase with the NTP-binding motif GGEGKS. No obvious functions could be assigned to two smaller ORFs (7.4 and 9.3 kDa) occurring in the complementary orientation. Amino acid sequence comparisons of the putative replicase of FBNYV with that of other similar ssDNA viruses yielded higher homologies to subterranean clover stunt virus than to banana bunchy top and coconut foliar decay viruses. A potential stem-loop structure and a TATA box were identified within the noncoding region. Two oligonucleotides derived from FBNYV DNA 1 were used for direct sequencing of the virion ssDNA to determine its virion polarity and for amplifying part of this component by immunocapture PCR in extracts from from FBNYV-infected plants.

Multipartite viruses contain more than one distinctive genome component, and the origin of multipartite viruses has been suggested to evolve from a non-segmented wild-type virus. To explore whether recombination also plays a role in the evolution of the genomes of multipartite viruses, we developed a systematic approach that employs motif-finding tools to detect conserved motifs from divergent genomic regions and applies statistical approaches to select high-confidence motifs. The information that this approach provides helps us understand the evolution of viruses. In this study, we compared our motif-based strategy with current alignment-based recombination-detecting methods and applied our methods to the analysis of multipartite single-stranded plant DNA viruses, including bipartite begomoviruses, Banana bunchy top virus (BBTV) (consisting of 6 genome components) and Faba bean necrotic yellows virus (FBNYV) (consisting of 8 genome components). Our analysis revealed that recombination occurred between genome components in some begomoviruses, BBTV and FBNYV. Our data also show that several unusual recombination events have contributed to the evolution of BBTV genome components. We believe that similar approaches can be applied to resolve the evolutionary history of other viruses.

The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.

Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses

In Sudan yellowing viruses are key production constraints in pulse crops. Field surveys were carried out to identify luteovirids affecting chickpea crops in the major production regions (Gezira Scheme and River Nile State). A total of 415 chickpea plant samples with yellowing and stunting symptoms were collected during the 2013, 2015 and 2018 growing seasons. Serological results (Tissue-blot immunoassays) showed that Luteoviridae and Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) were the most common viruses, with rare infections with Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae). Some samples reacted only with a broad-spectrum luteovirid monoclonal antibody (5G4-MAb), and others showed cross reactions between the specific monoclonal antibodies, suggesting the occurrence of new luteovirid variants. Serological results were confirmed by amplification with reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of the partial coat protein gene. Molecular analyses provided a basic, sufficient and reliable characterization for four viruses affecting chickpea that belong to Polerovirus (family Luteoviridae). These were Cucurbit aphid-borne yellows virus (CABYV), Pepper vein yellows virus (PeVYV), Pepo aphid-borne yellows virus (PABYV) and Cotton leafroll dwarf virus (CLRDV), that shared high similarity with the type sequences. Phylogenetic analyses also revealed high similarity to luteovirid species. This study has established reliable, rapid and sensitive molecular tools for the detection of luteovirid species.

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.

s PLoS Medicine, Daniel Reidpath and Kit Yee Chan challenge the widely cited link between HIV-related stigma and the spread of the epidemic [1].This is an important question, given the heavy emphasis on stigma in policies of the World Health Organization, the Joint United Programme on HIV/AIDS, and other public health institutions, but in making their argument Reidpath and Chan misrepresent the connections that other authors have made between stigma and viral transmission, ignore evidence that does suggest an association, and propose a model of their own for which they offer no evidence.HIV infection establishes itself fi rst in certain high-risk groups-men who have sex with men, intravenous drug users, sex workers, mobile populations-and only later moves into the general population.In the early stages of the epidemic, stigma facilitates transmission within high-risk groups, because these already marginalized groups receive little attention from policy makers and the health-care community and are further discriminated against when they are identifi ed with HIV and AIDS [2].Stigma also prevents or makes it more diffi cult for members of high-risk groups to access preventive services, including HIV antibody testing [3].Reidpath and Chan distort this dynamic by describing a model in which stigma leads to fear which leads to unsafe behavior.We know of no one who suggests that stigma causes sex between men or intravenous drug use.Instead, there is evidence that HIV-related stigma makes it diffi cult for people to take actions to reduce their risks; for example, by accessing HIV education [4], exchanging needles [5], and negotiating condom use [6].Stigma may even lead women who know they are HIV positive to breast-feed their infants rather than arouse suspicion of their serostatus through formula feeding [7].This undoubtedly increases the risk of vertical viral transmission.Reidpath and Chan go on to propose that stigma may actually "slow the spread of infection from those [highrisk] groups to the general population."Although there is a plausible logic to this suggestion, there is no evidence for it.Even if stigma does reduce the opportunities that marginalized groups have to transmit HIV to the broader population, this would have little effect on the dynamics of a generalized epidemic.While they recognize that stigma presents a barrier to the treatment and care of people living with HIV, Reidpath and Chan fail to recognize the association this may have with increased transmission.HIV-related stigma discourages people from disclosing their status, entering care, and adhering to antiretroviral regimens, all of which represent missed opportunities for prevention.Around the world HIV capitalizes on and reinforces social stigma and discrimination, especially the low status of women.Defeating the epidemic requires an honest examination of all these phenomena and interventions that target both the virus itself and its widespread social impacts.

Introduction: Dentistry is the field that brings back one’s smile. It is this field that teaches about the importance of oral hygiene. Dental education varies in all Southeast Asian and South Asian countries. Aim: To compare dental education concerning fee structure, dentist population ratio, and year of graduation between South Asian and Southeast Asian countries. Methodology: This study was conducted to the comparison of dental education in South Asian and Southeast Asian countries. Southeast Asian countries were classified as Group A and South Asian countries were classified as Group B. Data was retrieved from manual and electronic databases using search engines (Pubmed, google scholar, Web of Science). In this study, the keywords were Dentistry, Southeast Asian, South Asian, Dental colleges, and Dentist population ratio used in the search. Result: This study determined the difference between dental education, dentist population ratio, and the dentist’s average salary among Group A and B. The number of Dental colleges was the maximum in India (71%) among all other Group A and B. Conclusion: Nevertheless South Asia had a plethora of colleges, and high-paying dental jobs were possible only in Southeast Asian countries. Hence substantial numbers of dental colleges with proper apportionment and job contentment is obligatory for better treatment outcome of patients.

South and South-East Asian countries report a great liability for the world's road traffic injuries (RTIs) and deaths. A vast number of research studies tested various interventions including specific protective devices to prevent accidents, but no review papers have been conducted to find out the prevalence of RTIs in South-East and South Asian countries. This review paper was an attempt to find out the prevalence of RTIs and their associated factors in South-East and South Asian countries. Following the guidelines of Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA), we searched the articles in the electronic databases of PubMed/Medline, Scopus, CINAHL, ProQuest, and Web of Science. Articles were selected if they reported the prevalence of RTI, or road traffic accident (RTA) deaths. In addition, a data quality assessment was done. Out of the 10,818 article hits from the literature search, ten articles found the eligibility and inclusion criteria. Most of the studies reported that males are involved in the RTIs more than females. The male mortality rate is more than the female mortality in RTI mortality. Young adult males are the major victims when compared with the different age groups of male victims. Two-wheelers are the major contributors to the accident rate. Religious or national festivals are not free from accident-prone times. Climatic seasons and nighttime have a major influence on the RTIs. RTIs are increasing due to the sudden and huge increase in the number of motor vehicles and the development of cities and towns. Accidents are non-predictable but controllable disasters in society. Overspeeding, bad conditions on road, the vulnerability of the vehicles, and careless driving are the major reported reasons for RTIs. Making and implementing strict laws can help us to control RTAs. The major effect on the reduction of RTI can be assured only with the presence of responsible people. That can be achieved only by creating awareness in society about traffic rules and responsibilities.

Background Menopausal symptoms can have a significant impact on a woman's quality of life. Information on availability of menopausal hormone therapy (MHT) in National Essential Medicines Lists (NEMLs) of South Asian (SA) countries has not been widely studied. Objective To review the availability of non-injectable MHT included in NEMLs of SA countries and to assess differences in availability compared to the recommended MHT preparations in the World Health Organization (WHO) model essential medicines list and the list of MHT available to women of a developed country in the Asia Pacific Region, while comparing with the healthcare expenditure and country's economic status. Methods Most recent NEMLs were obtained from all eight SA counties by visiting the Ministry of health/regulatory website of the respective country. Latest WHO model essential medicines list and Pharmaceuticals Benefits Scheme (PBS) schedule from Australia were obtained from the WHO and PBS websites respectively. Per capita health expenditure was obtained from The WHO Global Health Expenditure Database. Two investigators extracted the non-injectable MHT preparations independently from NEMLs and conducted the comparison. Results Except in two countries, in all other SA coun­tries NEMLs were updated within the preceding five years. According to available data, seven SA countries had at least one separate preparation of oestrogen suitable for MHT while all countries had a separate progesterone preparation suitable for MHT. The oestrogen preparations available in the SA NEMLs were limited to either ethinyl estradiol or conjugated oestrogen tablets whilst in the WHO model, oestrogen preparations were not specified. In Australia, estradiol tablets were the only available oral oestrogen while there were four more different dosage forms of oestrogens available through the PBS Scheme. Progesterone preparations found in SA countries, WHO list and PBS schedule were similar, but oestrogen progesterone combination MHT preparations were only available in the PBS schedule. Per capita health expenditure was much higher in Australia compared to SA countries where a wide variation was observed. Conclusions The available evidence suggests that a larger population of SA women have access only to a very limited number of options if in need of MHT. In contrast, importance of MHT is highlighted in PBS Schedule. Although per capita health expenditure was low in SA countries, given that MHT products are relatively low cost and that there is a large proportion of women in menopausal age in this region, it would be imperative to update the WHO model list and NEMLs of SA countries to address the growing need of safe MHT and to improve the quality of life of postlnenopausal women in our region.

Epizootic Hemorrhagic Disease Virus (EHDV) is an arbovirus, transmitted to wild and domestic ruminants through Culicoides biting midges. Since 2006, high morbidity and mortality cases of EHDV have been reported among cattle and deer populations in several Mediterranean countries. The temporal and geographic origins of these incursions remained unclear. In this study, we aimed to investigate the evolutionary history of EHDV in the Mediterranean region and highlight the epidemiological features of viruses in relationship with genetic diversity and viral ecology. We extracted from GenBank the EHDV VP2 and VP5 segments isolated in the mediterranean region during the period 2006 to 2023 and blasted them to obtain a final dataset of 68 and 91 nucleotide sequences. Using these datasets, we conducted a Bayesian phylodynamic analysis, which inferred discrete models of "geographic origin," "Serotype" and "Host" by employing the BEAST package. RSPP and TMRCA analyses showed that the Mediterranean EHDV has as ancestral root the North America strains that circulated in the 17th century. Our study suggested that the first EHDV incursions in the Mediterranean region started in France and Tunisia during the 1800s. The latter countries were epicenters of EHDV in the region. Significant transition routes (BF>3) were detected revealing virus transmission between North African and European countries. Serotype model study revealed VP5 multiple inter-serotype events involving serotypes 1, 2, 6, 7, and 8 with high statistical support (BF>100). Significant virus transmission was detected for Cattle-deer and Culicoides-Cattle transition routes. The virus transmission was intense between North African and European countries of the Mediterranean region. EHDV spread in this region seems to be influenced mainly by vector/host distribution and abundance, ruminants' trade and prevailing winds.

Genetic diversity in Schistosoma mansoni populations can impact the prevalence of resistance-conferring alleles, affecting treatment outcomes and control measures. Understanding how parasites are structured across and within populations is important to monitor and manage treatment impacts and the spread of drug resistance. This study assessed the genetic diversity and structure of S. mansoni populations under treatment using multi-locus microsatellite markers. Egg-positive stool samples from school-aged children in schistosomiasis-endemic communities were analyzed to obtain a binary matrix for GenAlEx 6.502 analysis. The markers were 78.57% polymorphic, with a mean allele number ranging from 2.50 to 4.75. Average population metrics were as follows: different alleles (Na) = 3.179, effective alleles (Ne) = 2.282, expected heterozygosity (He) = 0.442, and genetic identity (I) = 0.800, indicating high diversity. Diversity indices were particularly high in Tomefa (I = 0.931, He = 0.499), Manheam (I = 1.074, He = 0.557), and Adakope (I = 0.778, He = 0.448). Analysis of molecular variance revealed low differentiation among populations (4% of total variance, P = 0.001) and high differentiation among individuals (88% of total variance, P = 0.001), with FST = 0.04 and high gene flow (Nm = 5.959). A neighbor-joining tree and principal coordinate analysis indicated low population structuring. The Mantel test showed no significant correlation between genetic and geographic distances (r = 0.006, P = 0.148). The findings suggest high genetic diversity and gene flow, supporting the potential spread of alleles that may confer traits like drug resistance. An integrated approach is needed to achieve sustainable control of schistosomiasis.IMPORTANCEThis study is crucial as it provides a detailed analysis of Schistosoma mansoni genetic diversity and population structure in schistosomiasis-endemic communities under treatment. By employing multi-locus microsatellite markers, the research highlights significant genetic variation within and among populations, revealing high levels of genetic diversity and gene flow, as well as the presence of private alleles. These findings emphasize the potential for the emergence and spread of drug resistance and virulence traits, which can impact treatment efficacy and control measures. The absence of significant geographic isolation in population structure further emphasizes the need for a comprehensive approach to schistosomiasis control, as genetic factors rather than geographic barriers may drive resistance dynamics. This study informs strategies for sustainable control by integrating genetic insights into disease management efforts.

South Asians have high rates of acute myocardial infarction (AMI) at younger ages compared with individuals from other countries but the reasons for this are unclear. To evaluate the association of risk factors for AMI in native South Asians, especially at younger ages, compared with individuals from other countries. Standardized case-control study of 1732 cases with first AMI and 2204 controls matched by age and sex from 15 medical centers in 5 South Asian countries and 10,728 cases and 12,431 controls from other countries. Individuals were recruited to the study between February 1999 and March 2003. Association of risk factors for AMI. The mean (SD) age for first AMI was lower in South Asian countries (53.0 [11.4] years) than in other countries (58.8 [12.2] years; P<.001). Protective factors were lower in South Asian controls than in controls from other countries (moderate- or high-intensity exercise, 6.1% vs 21.6%; daily intake of fruits and vegetables, 26.5% vs 45.2%; alcohol consumption > or =once/wk, 10.7% vs 26.9%). However, some harmful factors were more common in native South Asians than in individuals from other countries (elevated apolipoprotein B(100) /apolipoprotein A-I ratio, 43.8% vs 31.8%; history of diabetes, 9.5% vs 7.2%). Similar relative associations were found in South Asians compared with individuals from other countries for the risk factors of current and former smoking, apolipoprotein B100/apolipoprotein A-I ratio for the top vs lowest tertile, waist-to-hip ratio for the top vs lowest tertile, history of hypertension, history of diabetes, psychosocial factors such as depression and stress at work or home, regular moderate- or high-intensity exercise, and daily intake of fruits and vegetables. Alcohol consumption was not found to be a risk factor for AMI in South Asians. The combined odds ratio for all 9 risk factors was similar in South Asians (123.3; 95% confidence interval [CI], 38.7-400.2] and in individuals from other countries (125.7; 95% CI, 88.5-178.4). The similarities in the odds ratios for the risk factors explained a high and similar degree of population attributable risk in both groups (85.8% [95% CI, 78.0%-93.7%] vs 88.2% [95% CI, 86.3%-89.9%], respectively). When stratified by age, South Asians had more risk factors at ages younger than 60 years. After adjusting for all 9 risk factors, the predictive probability of classifying an AMI case as being younger than 40 years was similar in individuals from South Asian countries and those from other countries. The earlier age of AMI in South Asians can be largely explained by higher risk factor levels at younger ages.

Lentil landraces from South Asia exhibit a low diversity and discordance with landraces from other countries according to a combination of qualitative and quantitative agromorphological characters. They exhibit specific phenological adaptation to the South Asian environment which precludes the direct use of alien germplasm in breeding programs in South Asia. An understanding of the genetic relationships and diversity of South Asian lentil landraces, in relation to landraces from other countries, is important in attempting to widen the genetic base of germplasm in the region. The objectives of this study were to investigate the genetic relationships between lentil landraces from 3 South Asian countries (India, Nepal and Pakistan) and those from 13 other countries and to determine their relative genetic diversities, using both isozyme electrophoresis and random amplified polymorphic DNA (RAPD) analysis. Polymorphisms were observed for 7 isozyme loci (16 alleles) and 22 RAPD loci. According to Nei's genetic distance, germplasm from Afghanistan clustered with that from the South Asian countries. The germplasm from these countries was striking different to that from the other countries studied. Based on genetic distance estimates from RAPD analysis, the countries with the lowest diversity were Pakistan, Afghanistan and Nepal. These data support evidence at the morphological level of a genetic bottleneck in lentil landraces from South Asia. Genetic relationships between countries outside the South Asian group are discussed. Classification into macrosperma and microsperma types did not reflect overall country relationships.

The genus Helicoverpa (Lepidoptera: Noctuidae) includes phytophagous and polyphagous agricultural insect pests. In the Americas, a native pest, Helicoverpa zea (Boddie), and an invasive pest, Helicoverpa armigera (Hübner), are causing severe damage in vegetable and agronomic crops. The population structure of both species in South America is poorly understood, and the phylogenetic relatedness of H. armigera and H. zea suggests natural interspecific gene flow between these species. Using microsatellite loci, we investigated: 1) the genetic diversity and gene flow of H. armigera specimens from Brazil; 2) the genetic diversity and gene flow between H. zea specimens from Brazil and the United States; and 3) the possibility of interspecific gene flow and the frequency of putative hybrids in Brazil. We detected high intraspecific gene flow among populations collected in the same country. However, there is a geographic limit to gene flow among H. zea individuals from South and North America. Pairwise Fst and private alleles showed that H. armigera is more similar to H. zea from Brazil than H. zea from the United States. A comparative STRUCTURE analysis suggests natural hybridization between H. armigera and H. zea in Brazil. High gene flow and natural hybridization are key traits to population adaptation in new and disturbed environments, which can influence the management of these pests in the American continent.