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.

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 (ß = 0.423, t = 12.296, p = 0.000) and contribute to readiness (ß = 0.593, t = 28.762, p = 0.001). The structural model path coefficient indicates that readiness strongly influences the adoption of distance learning (ß = 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.

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.

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.

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.

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.

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.

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 ßC1 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 ßC1 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 ßC1 and its interactions with other viral and host proteins.

Evaluation of freeze-dried human sera as a novel approach for ATR-FTIR spectroscopic analysis as compared to conventionally used thin dry film sera.

OBJECTIVE: Evaluation of the diagnostic potential of freeze dried sera in comparison to thin dry film analysis for recording ATR-FTIR spectra. RESULTS: For this purpose, we compared our novel sample preparation technique i.e. freeze dried with conventional technique i.e. thin dry film sera. Using both methods ATR-FTIR spectra were recorded from Salmonella Typhi infected and healthy control human sera samples. When PCA was applied PC1 scores showed more inter-class variation among infected and healthy controls when freeze dried sample was used (90 %) as compared to thin dry film method (46 %). CONCLUSIONS: Potential of ATR-FTIR for discrimination of bio-molecules between two classes of samples is enhanced when freeze dried sera instead of thin dry film method is used.

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 of Blood-Borne Viruses in Health Care Workers of a Northern District in Pakistan: Risk Factors and Preventive Behaviors.

Background. Blood-borne viral infections like viral hepatitis are highly prevalent in Pakistan. There is also a potential threat of human immunodeficiency virus (HIV) spread in the country. Health care workers (HCWs) are a high risk population for acquiring such viral infections and potential spread to the patients. This study aimed to determine the frequency of three blood-borne viruses: HCV, HBV, and HIV in HCWs of district Malakand in northern Khyber Pakhtunkhwa (KPK) province of Pakistan. Moreover, risk factors and preventive behaviors among HCWs were investigated in detail. Materials and Methods. Prevalence was investigated using serological assays followed by real time polymerase chain reaction (RT-PCR) based characterization. A total of 626 health care workers working at 17 different health care units, belonging to 6 different job categories, were included in this study. Results. HIV was not detected in the HCWs while rate of prevalence of HCV and HBV was far less (0.8 % and 0.64 %, resp.) as compared to general population (4.7%-38%). The majority of HCWs were aware of the mode of spread of these viruses and associated risk factors. Needle stick injury was found to be the most important risk factor for possible acquisition of these infections.

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.