Diagnosis and monitoring of hepatocellular carcinoma in Hepatitis C virus patients using attenuated total reflection Fourier transform infrared spectroscopy

BACKGROUND

Current diagnostic methods for assessment of hepatitis C virus related hepatocellular carcinoma and subsequent categorization of hepatocellular carcinoma into non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma, to establish appropriate treatment strategies, are costly, invasive and requires multiple screening steps. This demands alternative diagnostic approaches that are cost-effective, time-efficient, and minimally invasive, while maintaining their efficacy for screening of hepatitis c virus related hepatocellular carcinoma. In this study, we propose that attenuated total reflection Fourier transform infrared in conjunction with principal component analysis - linear discriminant analysis and support vector machine multivariate algorithms holds a potential as a sensitive tool for the detection of hepatitis C virus-related hepatocellular carcinoma and the subsequent categorization of hepatocellular carcinoma into non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma.

METHODS

Freeze-dried sera samples collected from 31 hepatitis c virus related hepatocellular carcinoma patients and 30 healthy individuals, were used to acquire mid-infrared absorbance spectra (3500-900 cm-1) using attenuated total reflection Fourier transform infrared. Chemometric machine learning techniques were utilized to build principal component analysis - linear discriminant analysis and support vector machine discriminant models for the spectral data of hepatocellular carcinoma patients and healthy individuals. Sensitivity, specificity, and external validation on blind samples were calculated.

RESULTS

Major variations were observed in the two spectral regions i.e., 3500-2800 and 1800-900 cm-1. IR spectral signatures of hepatocellular carcinoma were reliably different from healthy individuals. Principal component analysis - linear discriminant analysis and support vector machine models computed 100% accuracy for diagnosing hepatocellular carcinoma. To classify the non-angio-invasive hepatocellular carcinoma/ angio-invasive hepatocellular carcinoma status, diagnostic accuracy of 86.21% was achieved for principal component analysis - linear discriminant analysis. While the support vector machine showed a training accuracy of 98.28% and a cross-validation accuracy of 82.75%. External validation for support vector machine based classification observed 100% sensitivity and specificity for accurately classifying the freeze-dried sera samples for all categories.

CONCLUSIONS

We present the specific spectral signatures for non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma, which were prominently differentiated from healthy individuals. This study provides an initial insight into the potential of attenuated total reflection Fourier transform infrared to diagnose hepatitis C virus related hepatocellular carcinoma but also to further categorize into non-angio-invasive and angio-invasive hepatocellular carcinoma.

Use of ATR-FTIR spectroscopy to differentiate between cirrhotic/non-cirrhotic HCV patients

BACKGROUND

Conventional techniques to diagnose (HCV) and assess non-cirrhotic/cirrhotic status of the patient for appropriate treatment regime are expensive and invasive. Present available diagnostic tests are expensive as they include multiple screening steps. Therefore, there is a need of cost-effective, less time consuming and minimally invasive alternative diagnostic approaches can be used for effective screening. We propose that (ATR-FTIR) in conjunction with (PCA-LDA),(PCA-QDA) and (SVM) multivariate algorithms can be used as a sensitive tool for detection of HCV infection and to assess non-cirrhotic/cirrhotic status of patients.

METHODS

We used 105 sera samples, of which, 55 were from healthy and 50 were from HCV positive individuals. These 50 HCV positive patients were further classified into cirrhotic and non-cirrhotic categories using serum markers and imaging techniques. These samples were freeze dried prior to spectral acquisition then multivariate data classification algorithms were employed to classify these sample types.

RESULTS

PCA-LDA and SVM model computed the diagnostic accuracy of 100% for detection of HCV infection. To further classify the non-cirrhotic/cirrhotic status of a patient, diagnostic accuracy of 90.91% for PCA-QDA and 100% for SVM was observed. Internal and external validation for SVM based classifications observed 100% sensitivity and specificity. The confusion matrix generated by PCA-LDA model computed the validation and calibration accuracy showed 100% sensitivity and specificity, by using 2 PCs for HCV infected and healthy individuals. However, when the PCA QDA analysis was done to classify the non-cirrhotic sera samples from cirrhotic sera samples the diagnostic accuracy achieved was 90.91 % based on 7 PC's. SVM was also employed for classification and developed model showed the best results with 100% sensitivity and specificity when external validation was applied.

CONCLUSIONS

This study provides an initial insight that ATR-FTIR spectroscopy in conjugation with multivariate data classification tools holds a potentialnot onlytoeffectively diagnosis HCV infection but also to assess non-cirrhotic/cirrhotic status of patients.

Chikungunya virus: Molecular epidemiology of nonstructural proteins in Pakistan

Chikungunya virus (CHIKV) is considered a public health problem due to its rapid spread and high morbidity. In 2016-2017 an outbreak of CHIKV was occurred in Pakistan but the data regarding the genomic diversity of CHIKV was not reported. Hence, the current study aimed to determine the genetic diversity of CHIKVs in Pakistan. A cross sectional study was carried out using sera of infected CHIKV patients (n = 1549) during the outbreak in Pakistan (2016-2018). Nucleotide sequencing of non-structural genes of CHIKV from eight isolates were performed followed by phylogenetic analysis using Bayesian method. Phylogenetic analysis suggested that the Pakistani CHIKV strains belonged to Indian Ocean Lineage (IOL) of genotype ECSA and C1.3a clade. Furthermore, the Pakistani isolates showed several key mutations (nsP2-H130Y, nsP2-E145D, nsP4-S55N and nsP4- R85G) corresponding to mutations reported in 2016 Indian strains of CHIKV. The molecular analysis revealed high evolutionary potential of CHIKV strains as well as better understanding of enhanced virulence and pathogenesis of this outbreak. The study highlights the need to continue surveillance in order to understand viral diversity over time and to devise preventive measures to limit diseases transmission in the region.

Adaption of distance learning to continue the academic year amid COVID-19 lockdown

This work investigates the use of distance learning in saving students' academic year amid COVID-19 lockdown. It assesses the adoption of distance learning using various online application tools that have gained widespread attention during the coronavirus infectious disease 2019 (COVID-19) pandemic. Distance learning thrives as a legitimate alternative to classroom instructions, as major cities around the globe are locked down amid the COVID-19 pandemic. To save the academic year, educational institutions have reacted to the situation impulsively and adopted distance learning platforms using online resources. This study surveyed random undergraduate students to identify the impact of trust in formal and informal information sources, awareness and the readiness to adopt distance learning. In this study, we have hypothesized that adopting distance learning is an outcome of situational awareness and readiness, which is achieved by the trust in the information sources related to distance learning. The findings indicate that trust in information sources such as institute and media information or interpersonal communication related to distance learning programs is correlated with awareness (β = 0.423, t = 12.296, p = 0.000) and contribute to readiness (β = 0.593, t = 28.762, p = 0.001). The structural model path coefficient indicates that readiness strongly influences the adoption of distance learning (β = 0.660, t = 12.798, p = 0.000) amid the COVID-19 pandemic. Our proposed model recorded a predictive relevance (Q²) of 0.377 for awareness, 0.559 for readiness, and 0.309 for the adoption of distance learning, which explains how well the model and its parameter estimates reconstruct the values. This study concludes with implications for further research in this area.

Epidemiology of Chikungunya virus isolates 2016-2018 in Pakistan

The chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it remerged in India and Indian Ocean regions in 2005-2006. The purpose of this study was to evaluate the genetic diversity and evolutionary changes in CHIKV from 2016 to 2018 in Pakistan. Blood specimens were collected and processed following the Centers for Disease Control and Prevention Trioplex Protocol. Sequencing and phylogenetic analysis of complete coding sequence of representative isolates from the CHIKV outbreak was carried out during December 2016 to July 2018, a total of 1549 samples were received, out of which 50% (n = 774) were found positive for CHIKV RNA. Mean age of chikungunya positive patients was 31.8 ± 15.7 years and most affected were between 21 and 40 years of age. The Pakistan CHIKV strains clustered with the Indian Ocean sublineage of East/Central/South African with cocirculation of some variants In the structural proteins region, two noteworthy changes (A226V and D284E) were observed in the membrane fusion glycoprotein E1. Key substitutions in the neutralizing epitopes site and a few changes indicative of adaptive to other insect cells were also detected in Pakistani strains. This study provides the emerging trend of CHIKV in the country for early identification of potential variants of high virulence and preventive measures for vector borne disease especially in the endemic areas.

Emergence of Chikungunya Virus, Pakistan, 2016-2017

During December 2016–May 2017, an outbreak of chikungunya virus infection occurred across Pakistan. The East/Central/South African genotype was predominant. This study provides baseline data on the virus strain and emphasizes the need for active surveillance and implementation of preventive interventions to contain future outbreaks.

Nanoparticles-assisted delivery of antiviral-siRNA as inhalable treatment for human respiratory viruses: A candidate approach against SARS-COV-2

The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has challenged healthcare structures across the globe. Although a few therapies are approved by FDA, the search for better treatment options is continuously on rise. Clinical management includes infection prevention and supportive care such as supplemental oxygen and mechanical ventilatory support. Given the urgent nature of the pandemic and the number of companies and researchers developing COVID-19 related therapies, FDA has created an emergency program to move potential treatments with already approved drugs to patients as quickly as possible in parallel to the development of new drugs that must first pass the clinical trials. In this manuscript, we have reviewed the available literature on the use of sequence-specific degradation of viral genome using short-interfering RNA (siRNA) suggesting it as a possible treatment against SARS-CoV-2. Delivery of siRNA can be promoted by the use of FDA approved lipids, polymers or lipid-polymer hybrids. These nanoparticulate systems can be engineered to exhibit increased targetability and formulated as inhalable aerosols.

Conventional to online education during COVID-19 pandemic: Do develop and underdeveloped nations cope alike

BACKGROUND

Educational institutes around the globe are facing challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Online learning is being carried out to avoid face to face contact in emergency scenarios such as coronavirus infectious disease 2019 (COVID-19) pandemic. Students need to adapt to new roles of learning through information technology to succeed in academics amid COVID-19.

OBJECTIVE

However, access and use of online learning resources and its link with satisfaction of students amid COVID-19 are critical to explore. Therefore, in this paper, we aimed to assess and compare the access & use of online learning of Bruneians and Pakistanis amid enforced lockdown using a five-items satisfaction scale underlying existing literature.

METHOD

For this, a cross-sectional study was done in the first half of June 2020 after the pandemic situation among 320 students' across Pakistan and Brunei with a pre-defined questionnaire. Data were analyzed with statistical software package for social sciences (SPSS) 2.0.

RESULTS

The finding showed that there is a relationship between students' satisfaction and access & use of online learning. Outcomes of the survey suggest that Bruneian are more satisfied (50%) with the use of online learning amid lockdown as compared to Pakistanis (35.9%). Living in the Urban area as compared to a rural area is also a major factor contributing to satisfaction with the access and use of online learning for both Bruneian and Pakistanis. Moreover, previous experience with the use of online learning is observed prevalent among Bruneians (P = .000), while among friends and family is using online learning (P = .000) were encouraging factors contributed to satisfaction with the use of online learning among Pakistanis amid COVID-19. Correlation results suggest that access and use factors of online learning amid COVID-19 were positively associated with satisfaction among both populations amid COVID-19 pandemic. However, Bruneian is more satisfied with internet access (r = 0.437, P < .000) and affordability of gadgets (r = 0.577, P < .000) as compare to Pakistanis (r = 0.176, P < .050) and (r = 0.152, P < .050).

CONCLUSION

The study suggested that it is crucial for the government and other policymakers worldwide to address access and use of online learning resources of their populace amid pandemic.

High somatostatin receptor expression and efficacy of somatostatin analogues in patients with metastatic Merkel cell carcinoma

BACKGROUND

Merkel cell carcinoma (MCC) is an aggressive, high-grade, cutaneous neuroendocrine tumour (NET). Agents blocking programmed death 1/programmed death ligand 1 have efficacy in metastatic MCC (mMCC), but half of patients do not derive durable benefit. Somatostatin analogues (SSAs) are commonly used to treat low- and moderate-grade NETs that express somatostatin receptors (SSTRs).

OBJECTIVES

To assess SSTR expression and the efficacy of SSAs in mMCC, a high-grade NET. Methods In this retrospective study of 40 patients with mMCC, SSTR expression was assessed radiologically by somatostatin receptor scintigraphy (SRS; n = 39) and/or immunohistochemically when feasible (n = 9). Nineteen patients (18 had SRS uptake in MCC tumours) were treated with SSA. Disease control was defined as progression-free survival (PFS) of ≥ 120 days after initiation of SSA.

RESULTS

Thirty-three of 39 patients (85%) had some degree (low 52%, moderate 23%, high 10%) of SRS uptake. Of 19 patients treated with SSA, seven had a response-evaluable target lesion; three of these seven patients (43%) experienced disease control, with a median PFS of 237 days (range 152-358). Twelve of 19 patients did not have a response-evaluable lesion due to antecedent radiation; five of these 12 (42%) experienced disease control (median PFS of 429 days, range 143-1757). The degree of SSTR expression (determined by SRS and/or immunohistochemistry) did not correlate significantly with the efficacy endpoints.

CONCLUSIONS

In contrast to other high-grade NETs, mMCC tumours appear frequently to express SSTRs. SSAs can lead to clinically meaningful disease control with minimal side-effects. Targeting of SSTRs using SSA or other novel approaches should be explored further for mMCC.

Metagenomic analysis of relative abundance and diversity of bacterial microbiota in Bemisia tabaci infesting cotton crop in Pakistan

B. tabaci species complex are among the world's most devastating agricultural pests causing economic losses by direct feeding and more importantly by transmitting plant viruses like cotton leaf curl disease (CLCuD) associated viruses to cultivated cotton in Pakistan. Taxonomic diversity of B. tabaci associated bacterial communities using NGS techniques so far is reported from insects grown on artificial diet under lab conditions. In this study 16S rDNA metagenome sequencing analysis was used to characterize bacterial compositions in wild adult B. tabaci infesting cultivated cotton in eight major cotton growing districts of southern Punjab, Pakistan. We have identified 50 known and 7 unknown genera of bacteria belonging to 10 phyla, 20 classes, 30 orders and 40 families. Beta diversity analysis of our data sets reveal that whiteflies infesting cotton in geographically distinct locations had similar bacterial diversity. These results for the first time provide insights into the microbiome diversity of wild type whiteflies infesting a cultivated crop.

Analyzing situational awareness through public opinion to predict adoption of social distancing amid pandemic COVID-19

COVID‐19 pandemic has affected over 100 countries in a matter of weeks. People's response toward social distancing in the emerging pandemic is uncertain. In this study, we evaluated the influence of information (formal and informal) sources on situational awareness of the public for adopting health‐protective behaviors such as social distancing. For this purpose, a questionnaire‐based survey was conducted. The hypothesis proposed suggests that adoption of social distancing practices is an outcome of situational awareness which is achieved by the information sources. Results suggest that information sources, formal (P = .001) and informal (P = 0.007) were found to be significantly related to perceived understanding. Findings also indicate that social distancing is significantly influenced by situational awareness, P = .000. It can, therefore, be concluded that an increase in situational awareness in times of public health crisis using formal information sources can significantly increase the adoption of protective health behavior and in turn contain the spread of infectious diseases.

Reducing mortality caused by COVID‐19 can be achieved by awareness.

Situation awareness can be increased by formal information sources.

Increased situational awareness lead to adoption of health protective behavior.

Journey of begomovirus betasatellite molecules: from satellites to indispensable partners

Betasatellites are a group of circular, single-stranded DNA molecules that are frequently found to be associated with monopartite begomoviruses of the family Geminiviridae. Betasatellites require their helper viruses for replication, movement, and encapsidation and they are often essential for induction of typical disease symptoms. The βC1 protein encoded by betasatellites is multifunctional that participates in diverse cellular events. It interferes with several cellular processes like normal development, chloroplasts, and innate immune system of plants. Recent research has indicated βC1 protein interaction with cellular proteins and its involvement in modulation of the host's cell cycle and symptom determination. This article focuses on the functional mechanisms of βC1 and its interactions with other viral and host proteins.

Identification of new spectral signatures from hepatitis C virus infected human sera

Hepatitis C virus (HCV) infection is one of the leading causes of morbidity and mortality worldwide. Mortality linked with HCV infection can be lowered with effective and prompt diagnosis in early stages of infection. In this study potential of Raman spectroscopy to differentiate between healthy and HCV infected serum samples was investigated. Clear differences were observed in the Raman spectra of HCV infected and healthy sera samples. Using the analysis of variance (ANOVA) and t-test (p < 0.001) on Raman spectra of diseased and healthy samples, we observed eleven unique Raman bands at 676, 825, 853, 936, 1029, 1105, 1155, 1305, 1620, 1654 and 1757 cm^-1 associated with only HCV infected sera and have not been reported in earlier studies. In addition, six Raman bands at 556, 585, 716, 815, 1273 and 1142 cm^-1were observed in healthy sera only. Three Raman bands at 1330, 1526 and 1572 cm^-1 were observed in both type of samples but their intensity was drastically reduced in diseased samples. Various multivariate analysis techniques were employed to demonstrate the robustness of the results. We employed multivariate and unsupervised principal component analysis (PCA) in conjunction with supervised classification linear discriminant analysis (LDA), using ten-fold jackknife cross-validation, in order to develop effective diagnostic algorithm technique (PCA-LDA). Our PCA-LDA model yielded sufficient sensitivity and specificity i.e. correctly identified all infected samples included in this study. Ours results indicate that these unique Raman bands have the potential to be used as biomarkers for optical diagnosis of HCV infection.

Raman spectroscopy based differentiation of typhoid and dengue fever in infected human sera

This study investigated the potential of Raman spectroscopy, to differentiate between two different types of human pathological conditions with some symptom similarity; typhoid and dengue. Raman spectra were recorded from 20 Salmonella Typhi infected and 22 dengue virus (DENV) infected sera samples using laser wavelength 785 nm. When Raman spectrum (540 to 1830 cm^-1) of serum samples was compared it showed significant variations. Twelve characteristic Raman bands at 562, 649, 716, 780, 838, 1099, 1144, 1156, 1260, 1386, 1556 and 1746 cm^-1 were recorded specifically in case of the typhoid infected samples, whereas four Raman bands at 756, 1218, 1672 and 1686 cm^-1 were found specifically in the DENV infected samples. For statistical differentiation principal component analysis (PCA) and linear discriminant analysis (LDA) was applied which successfully separated two sets of data. These disease specific Raman signatures may be labeled as biomarkers for identification as well as differential diagnosis of typhoid and dengue infection. Hence we propose that Raman spectroscopy has the potential to not only identify but also to differentiate between different pathological conditions, having some similar symptoms like high grade fever in this case.

Risk factors and molecular epidemiology of HBV and HCV in internally displaced persons (IDPs) of North Waziristan Agency, Pakistan

OBJECTIVE

To investigate the prevalence and transmission risks of hepatitis B virus and hepatitis C virus infections among internally displaced persons.

METHODS

This study was conducted in district Bannu, Khyber Pakhtunkhwa, Pakistan, from August 2014 to April 2015, and comprised internally displaced people from North Waziristan Agency residing in camps or settled in towns. Potential subjects were initially screened through immunochromatographic test devices. Samples detected positive were confirmed through enzyme-linked immunosorbent assay. Confirmation of the presence of viral nucleic acids and genotyping was done via real-time polymerase chain reaction. SPSS 21 was used for data analysis.

RESULTS

Of the 1,000 participants, 570(57%) were males and 430(43%) females. Seroprevalence of hepatitis B virus among the participants was 45(4.5%) and hepatitis C virus was 52(5.2%). Viral nucleic acids were present in 41(4.1%) participants in case of hepatitis B virus and 39(3.9%) in case of hepatitis C virus. No co-infection with both of these viruses was found. Dominant hepatitis B virus and hepatitis C virus genotypes were genotype-D 19(46.3%) and 3a with 20(51.2%), respectively.

CONCLUSIONS

High prevalence of hepatitis B and C virus infections was found among internally displaced people.

Prevalence and epidemiology of blood borne pathogens in health care workers of Rawalpindi/Islamabad

OBJECTIVE

To attempt to trace the molecular epidemiology of blood-borne diseases in the hospital community of Pakistan.

METHODS

The cross-sectional study was conducted at three major hospitals of Rawalpindi and Islamabad from January to May, 2014.The prevalence of three blood-borne pathogens hepatitis B and C as well as human immunodeficiency virus was investigated in hospital workers of different occupations. Initial screening was performed with immuno-chromatographic technique followed by enzyme-linked immune-sorbent assay. Positive samples were subjected to real time polymerase chain reaction amplification of specific viral sequences for amplification with universal as well as genotype-specific primers.

RESULTS

Out of total 500 subjects, there were 42(8.4%) doctors, 101(20.2%) nurses, 92(18.4%) technicians, 67(13.4%) ward boys, 41(8.2%) sweepers, 36(7.2%) security guards and 122(24.4%) administrative workers. None was positive for the presence of human immunodeficiency virus after initial screening with immuno-chromatographic technique. In case of hepatitis viruses, 9(0.18%) samples were positive for anti-hepatitis C virus and 3(0.6%) for hepatitis B surface antigen. Three (2.97%) nurses and 3(3.29%) lab technicians were at the highest risk of exposure.

CONCLUSIONS

Human immunodeficiency virus was not present among the healthcare workers, while the prevalence of hepatitis B and C viruses was far less compared to the general population.

Dengue fever in Pakistan: a paradigm shift; changing epidemiology and clinical patterns

Dengue fever has huge public health implications and affects over 100 million people worldwide. This review pictures the current situation of Dengue in Pakistan and presents a review of published literature. Pakistan has seen recurrent epidemics of Dengue Fever recently. Unfortunately, these epidemics are becoming more severe in their clinical manifestation. Pakistan experienced large epidemics of dengue fever during 2008, 2010 and 2011 affecting thousands of people and claiming hundreds of deaths. A comparison of data during these epidemics indicates a shift from mild to a more severe disease, which could be interpreted as an epidemiologic transition pattern in the country. Expansion of Dengue in Pakistan seems to be multifactorial, including the climate change, frequent natural disasters, vector resistance to insecticides and lack of resources. This highlights the need for rigorous vector control. Continuing education of primary care physicians is crucial for early appropriate management to reduce mortality.

Hurdles to the global antipolio campaign in Pakistan: an outline of the current status and future prospects to achieve a polio free world

The Global Polio Eradication Initiative to eradicate polio completely by the year 2000 has been successful, except for three endemic and some non-endemic countries. Pakistan, one of the three endemic polio reservoirs, is posing a serious threat to the success of the initiative. Currently, the expanded programme on immunisation has been geared to win the race over polio virus in Pakistan. After the remarkable decrease in polio cases from 198 in 2011 to only 58 in 2012, Pakistan seemed to be at the verge of success. However, hurdles continue to retard the campaign. The war against terrorism, misconceptions about polio vaccine, religious misinterpretations, frustration among vaccinators, lack of awareness, social considerations, natural calamities, inaccessibility, and inefficient vaccines and so on are continually rupturing the foundations of the worldwide initiative in the country. Weak health management is found at the hub of majority of the challenges. Stricter policies, well managed and supervised plans and strategic actions, risk analysis and enhanced communication may help giving the final punch to polio virus in the country. Analysis suggested that there is some literature available on the challenges to polio elimination, yet there is not a single publication up to date that considers all the possible hurdles in a single manuscript. This paper sorts out the breaches that hamper the goal of eliminating polio from Pakistan. We have evaluated all the possible barriers and explained them with a perspective that will help develop area specific strategies against polio virus and thus eradicate polio virus from the world.

Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex

Begomoviruses (family Geminiviridae) are single-stranded DNA viruses transmitted by the whitefly Bemisia tabaci. Many economically important diseases in crops are caused by begomoviruses, particularly in tropical and subtropical environments. These include the betasatellite-associated begomoviruses causing cotton leaf curl disease (CLCuD) that causes significant losses to a mainstay of the economy of Pakistan, cotton. RNA interference (RNAi) or gene silencing is a natural defense response of plants against invading viruses. In counter-defense, viruses encode suppressors of gene silencing that allow them to effectively invade plants. Here, we have analyzed the ability of the begomovirus Cotton leaf curl Multan virus (CLCuMV) and its associated betasatellite, Cotton leaf curl Multan β-satellite (CLCuMB) which, together, cause CLCuD, and the nonessential alphasatellite (Cotton leaf curl Multan alphasatellite [CLCuMA]) for their ability to suppress gene silencing in Nicotiana benthamiana. The results showed that CLCuMV by itself was unable to efficiently block silencing. However, in the presence of the betasatellite, gene silencing was entirely suppressed. Silencing was not affected in any way when infections included CLCuMA, although the alphasatellite was, for the first time, shown to be a target of RNA silencing, inducing the production in planta of specific small interfering RNAs, the effectors of silencing. Subsequently, using a quantitative real-time polymerase chain reaction assay and Northern blot analysis, the ability of all proteins encoded by CLCuMV and CLCuMB were assessed for their ability to suppress RNAi and the relative strengths of their suppression activity were compared. The analysis showed that the V2, C2, C4, and βC1 proteins exhibited suppressor activity, with the V2 showing the strongest activity. In addition, V2, C4, and βC1 were examined for their ability to bind RNA and shown to have distinct specificities. Although each of these proteins has, for other begomoviruses or betasatellites, been previously shown to have suppressor activity, this is the first time all proteins encoded by a geminiviruses (or begomovirus-betasatellite complex) have been examined and also the first for which four separate suppressors have been identified.

Identification of a major pathogenicity determinant and suppressors of RNA silencing encoded by a South Pacific isolate of Banana bunchy top virus originating from Pakistan

Five genes encoded by Banana bunchy top virus (BBTV) originating from Pakistan were expressed in Nicotiana benthamiana using a Potato virus X (PVX) vector. Expression of the master replication-associated protein (mRep) and movement protein (MP) resulted in necrotic cell death of inoculated tissues, as well as leaf curling and necrosis along the veins in newly emerging leaves. The systemic necrosis induced by the expression of MP was discolored (dark) in comparison to that induced by mRep. Expression of the cell-cycle link protein (Clink), the coat protein (CP), and the nuclear shuttle protein from the PVX vector induced somewhat milder symptoms, consisting of mild leaf curling and mosaic, although expression of the CP caused a necrotic response in inoculated leaf. The accumulation of viral RNA was enhanced by MP, Clink, and CP. Of the five BBTV-encoded gene products two, the MP and Clink, stabilized GFP-specific mRNA and reduced GFP-specific small interfering RNA in N. benthamiana line 16c when expressed under the control of the 35S promoter and co-inoculated with a construct for the expression of GFP hairpin RNA construct. These results identified MP and Clink as suppressors of RNA silencing. Taken together the ability of MP to induce severe symptoms in plants and suppress RNA silencing implicates this product as a major pathogenicity determinant of BBTV.

Genetic diversity and phylogeography of begomoviruses infecting legumes in Pakistan

Grain legumes are an important source of dietary protein across southern Asia, but they suffer extensive losses due to several viruses that are members of the genus Begomovirus (family Geminiviridae), which are collectively known as legume yellow mosaic viruses (LYMVs). Despite their economic importance, little attention has been paid to LYMVs in Pakistan and only partial sequences of virus isolates originating from this country are available in the databases. Here, a survey of LYMVs occurring across Pakistan is described. Complete sequences of 44 components (23 DNA-A, 19 DNA-B and 2 betasatellites) were determined. The results show that only the mungbean yellow mosaic India virus (MYMIV) is of agricultural significance in Pakistan having been isolated from all cultivated grain legumes examined. Mungbean yellow mosaic virus, a significant crop pathogen in India, was only identified in a weed, which together with a novel species of LYMV we reported earlier, represents the first LYMV identified in non-cultivated plants. MYMIV was shown to occur as two types in Pakistan that show phylogeographical segregation. Additionally, two begomovirus species not considered pathogens of legumes and a betasatellite were isolated. This is of grave concern since it suggests that the presumed genetic isolation of the LYMVs in legumes may be being breached. LYMVs show little, if any, evidence of interspecific recombination with non-legume infecting begomoviruses. Thus, either recombination with non-legume viruses or interaction with betasatellites, which are host range and pathogenicity determining satellites of begomoviruses, could lead to the appearance of more aggressive virus variants/strains affecting legumes.

Molecular characterisation and infectivity of a "Legumovirus" (genus Begomovirus: family Geminiviridae) infecting the leguminous weed Rhynchosia minima in Pakistan

The legume yellow mosaic viruses (LYMVs) that cause extensive losses to grain legumes across southern Asia are an evolutionarily unusual group of begomoviruses (genus Begomovirus; family Geminiviridae) with bipartite genomes. All previously identified LYMVs were isolated from leguminous crop species. Here we have identified a virus related to the LYMVs in a common weed, the legume Rhynchosia minima originating from Pakistan. Analysis of the sequence of the virus shows it to be a typical bipartite begomovirus. Sequence comparisons to all other begomovirus sequences available in the databases show the virus from R. minima to be distinct, with the highest level of sequence identity (69.5%) to an isolate of Mungbean yellow mosaic virus. This indicates that the virus identified here is a new species in the genus Begomovirus for which we propose the name Rhynchosia yellow mosaic virus (RhYMV). By Agrobacterium-mediated inoculation we show that, in common with the other LYMVs, the clones of RhYMV are not infectious to the experimental host Nicotiana benthamiana. In soybean, the results of inoculation depended upon the variety. In soybean var. Ig6 the symptoms were mild and plants recovered from infection. However, in var. FS-85, symptoms were severe and progressed to necrosis, indicative of a hypersensitive response. These results indicate that there is resistance to RhYMV in the soybean germplasm. The significance of these results is discussed.

A Severe Leaf Curl Disease on Chilies in Pakistan is Associated with Multiple Begomovirus Components

Chili leaf curl disease is an important limiting factor for chilies in the Indian subcontinent and is associated with begomoviruses (2,3). Field visits of commercially grown chilies in 2007 and 2008 identified a very severe leaf curl disease with 100% incidence and severe yield losses at several locations in Faisalabad District, Punjab, Pakistan. Symptoms of the disease were severe leaf curl with cup-shaped, upward curling, yellowing, and stunted plant growth. To identify the causative agent, symptomatic plant samples were collected from 10 locations and total DNA was extracted with a cetyltrimethylammoniumbromide method. Universal primers that amplify begomovirus DNA A, Begomo F (ACGCGT GCCGTGCTGCTGCCCCCATTGTCC) and Begomo R (ACGCGT ATGGGCTGYCGAAGTTSAGAC), were used in PCR. A PCR product of the expected size (approximately 2.8 kb) was amplified from all symptomatic plants, and no amplification products of the expected size were obtained from healthy or asymptomatic plants, confirming the association of a begomovirus with the disease. When used as a probe in Southern hybridization, a full-length clone of Cotton leaf curl Multan virus detected characteristic viral DNA forms and further confirmed the association of begomovirus with the disease. To identify the begomovirus associated with the disease at the species level, the PCR product obtained with universal primers was cloned into a TA cloning vector and five clones were partially sequenced. Comparison of the DNA sequence of the coat protein gene of clones resulted in identification of two begomovirus species; the first clone (GenBank Accession No. FN179278) showed 94% DNA sequence identity with the bipartite virus Tomato leaf curl New Delhi virus (ToLCNDV), while the second clone (GenBank Accession No. FN252382) showed 97% sequence identity with the monopartite begomovirus Chili leaf curl Multan virus (ChLCMV). Rolling circle amplification was used to clone the DNA B of ToLCNDV from samples showing typical chili leaf curl disease symptoms. Sequence analysis of the DNA B clone (GenBank Accession No. FN179276) in the intergenic region and movement protein gene showed 94% identity with ToLCNDV DNA B. To confirm association of betasatellite with the disease, universal primers (β-01 and β-02) were used for the amplification of betasatellite by PCR (1). DNA sequence analysis of betasatellite (GenBank Accession No. FN179279) associated with the disease showed 90% identity with the previously cloned chili leaf curl betasatellite (1). No evidence for the association of alphasatellite with the disease was found. The multiple infection of a begomovirus complex, consisting of a monopartite virus with a bipartite begomovirus where DNA B is maintained in the presence of betasatellite, presents yet another example of rapid changes in begomovirus complexes that infect important crops in the region. The appearance of chili leaf curl disease at a higher incidence and symptom severity may be attributed to the synergistic action of geminivirus disease complex comprising a monopartite and a bipartite begomovirus along with DNA betasatellite. High yield losses resulting from this severe disease threatens chili cultivation in the area and is forcing farmers to grow other crops. References: (1) R. W. Briddon et al. Virology 312:106, 2003. (2) B. Chattopadhyay et al. Arch Virol. 10:7, 2007. (3) M. Hussain et al. Plant Pathol. 53:794, 2004.

Molecular characterisation of banana bunchy top virus (BBTV) from Pakistan

Banana bunchy top disease is caused by a single-stranded circular DNA virus, banana bunchy top virus (BBTV), which is a member of the genus Babuvirus (family Nanoviridae). We have cloned and sequenced five components (DNA-R, DNA-S, DNA-N, DNA-M and DNA-C) of a BBTV isolate originating from Pakistan. In addition, the DNA-R and several other components of five further isolates, originating from geographically distinct sites across the banana-growing area of Sindh province, Pakistan, were cloned and sequenced. Analysis of the sequences indicates that BBTV present in Pakistan belongs to the "South Pacific" group of isolates and that the genetic diversity of the virus in the country is very low. The virus shows the highest levels of sequence identity to BBTV isolates originating from Egypt, India and Australia. The significance of these results with respect to the possible origin of the virus in Pakistan and the prospects for obtaining genetically engineered resistance to the virus are discussed.

Molecular characterisation of banana bunchy top virus (BBTV) from Pakistan

Banana bunchy top disease is caused by a single-stranded circular DNA virus, banana bunchy top virus (BBTV), which is a member of the genus Babuvirus (family Nanoviridae). We have cloned and sequenced five components (DNA-R, DNA-S, DNA-N, DNA-M and DNA-C) of a BBTV isolate originating from Pakistan. In addition, the DNA-R and several other components of five further isolates, originating from geographically distinct sites across the banana-growing area of Sindh province, Pakistan, were cloned and sequenced. Analysis of the sequences indicates that BBTV present in Pakistan belongs to the "South Pacific" group of isolates and that the genetic diversity of the virus in the country is very low. The virus shows the highest levels of sequence identity to BBTV isolates originating from Egypt, India and Australia. The significance of these results with respect to the possible origin of the virus in Pakistan and the prospects for obtaining genetically engineered resistance to the virus are discussed.

Contribution of the satellite encoded gene betaC1 to cotton leaf curl disease symptoms

Cotton leaf curl disease (CLCuD) is caused by one of seven begomoviruses in conjunction with a specific satellite; CLCuD DNA beta. Associated with some monopartite begomoviruses, DNA beta components encode a single gene (betaC1) which mediates satellite functions. We have investigated the contribution the satellite, specifically betaC1, makes to CLCuD symptoms in the absence of the helper begomovirus. Systemic expression of CLCuD-betaC1 from a Potato virus X (PVX) vector induces bona fide CLCuD disease symptoms in Nicotiana tabacum plants, including enations, swollen veins and vein darkening. These contrast with the mild symptoms of PVX in this host. Analysis of thin sections across enations induced by PVX expressing betaC1 shows the structure of the enation to be identical to those induced by CLCuD DNA beta in conjunction with a helper begomovirus. These results demonstrate that CLCuD betaC1 is the major determinant of symptoms for the CLCuD complex.

Legume yellow mosaic viruses: genetically isolated begomoviruses

SUMMARY

The yellow mosaic diseases of a number of legumes across Southern Asia are caused by four species of whitefly-transmitted geminiviruses (genus Begomovirus, family Geminiviridae): Mungbean yellow mosaic virus, Mungbean yellow mosaic India virus, Dolichos yellow mosaic virus and Horsegram yellow mosaic virus. They cause losses to a number of important pulse crops, a major source of dietary protein in the region. The viruses have host ranges limited to plants of the family Fabaceae and efforts to limit losses are hampered by limited availability of conventional resistance sources and/or the lack of durability of the resistance that has been identified. There is ample evidence for genetic interaction between these begomoviruses within the legumes, in the form of both classical recombination and component exchange, but little evidence for interaction with viruses that infect other plants. This is indicative of genetic isolation, the viruses in legumes evolving independently of the begomoviruses in plant species of other families. This has implications for the development of engineered resistance in legumes, which holds the promise of durability but has yet to be transferred to the field.

TAXONOMY

The viruses causing yellow mosaic diseases of legumes across southern Asia, four of which have been identified so far, are bipartite begomoviruses (genus Begomovirus, family Geminiviridae): Mungbean yellow mosaic virus, Mungbean yellow mosaic India virus, Horsegram yellow mosaic virus and Dolichos yellow mosaic virus. Physical properties: The legume yellow mosaic viruses (LYMVs), like all members of the Geminiviridae, have geminate (twinned) particles, 18-20 nm in diameter, 30 nm long, apparently consisting of two incomplete T = 1 icosahedra joined together in a structure with 22 pentameric capsomers and 110 identical protein subunits.

DISEASE SYMPTOMS

Symptoms caused by LYMVs are largely dependent on host species and susceptibility. Initially symptoms appear as small yellow specks along the veins and then spread over the leaf. In severe infections the entire leaf may become chlorotic. In blackgram the chlorotic areas sometimes turn necrotic. Infections of French bean usually do not produce a mosaic but instead induce a downward leaf curling.

DISEASE CONTROL

Control is based mainly on preventing the establishment of the whitefly vector, Bemisia tabaci, in the crop by application of insecticides. Changes in agricultural practices, such as moving the cropping period out of periods of high vector incidence (the wet period in late summer) to times of low vector incidence (dry season in early summer) have met with some, albeit short-term, benefits. The use of natural, host plant resistance is efficacious, although the available sources of resistance in most legume crops are limited. In mungbean the resistance is attributed to two recessive genes which are used effectively to control the disease.

USEFUL WEBSITES

http://www.danforthcentre.org/iltab/geminiviridae/, http://www.iwglvv.org/

A PCR-Based Method, With Internal Control, for the Detection of Banana Bunchy Top Virus in Banana

Banana bunchy top disease is a major constraint to banana production in most regions where this crop is grown. The disease is caused by Banana bunchy top virus (BBTV), a multicomponent, single-stranded DNA virus of the family Nanoviridae. We have designed primers to a conserved region of the master replication-associated protein that are useful for the polymerase chain reaction (PCR)-mediated detection of BBTV. In addition, primers to banana genomic sequence are used as an internal control, overcoming the uncertainty (owing to false-negatives) inherent in PCR diagnostics. Together these primer sets are a valuable tool in the effort to control BBTV, particularly in screening micropropagated banana plantlets for the absence of virus before release to farmers.