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| 1 | Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2显示文摘Background:Coronavirus disease 2019(COVID-19)linked with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)cause severe illness and life-threatening pneumonia in humans.The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection.Therefore,the present study was aimed to design a multiepitope-based subunit vaccine(MESV)against COVID-19.Methods:Structural proteins(Surface glycoprotein,Envelope protein,and Membrane glycoprotein)of SARS-CoV-2 are responsible for its prime functions.Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B-and T-cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV.Results:Predicted epitopes suggested high antigenicity,conserveness,substantial interactions with the human leukocyte antigen(HLA)binding alleles,and collective global population coverage of 88.40%.Taken together,276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes(CTL),6 helper T lymphocyte(HTL)and 4 B-cell epitopes with suitable adjuvant and linkers.The MESV construct was non-allergenic,stable,and highly antigenic.Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3(TLR3).Furthermore,in silico immune simulation revealed significant immunogenic response of MESV.Finally,MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system,to ensure its increased expression.Conclusion:The MESV developed in this study is capable of generating immune response against COVID-19.Therefore,if designed MESV further investigated experimentally,it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19. | Muhammad Tahir ul Qamar Farah Shahid Sadia Aslam Usman Ali Ashfaq Sidra Aslam Israr Fatima Muhammad Mazhar Fareed Ali Zohaib Ling-Ling Chen | 2020 | Infectious Diseases of Poverty2020，9，5： | 2 |
| 2 | Genetic Evidence of Middle East Respiratory Syndrome Coronavirus(MERS-Cov) and Widespread Seroprevalence among Camels in Kenya显示文摘We describe the first genome isolation of Middle East respiratory syndrome coronavirus(MERS-CoV) in Kenya. This fatal zoonotic pathogen was first described in the Kingdom of Saudi Arabia in 2012. Epidemiological and molecular evidence revealed zoonotic transmission from camels to humans and between humans. Currently, MERS-CoV is classified by the WHO as having high pandemic potential requiring greater surveillance. Previous studies of MERS-CoV in Kenya mainly focused on site-specific and archived camel and human serum samples for antibodies. We conducted active nationwide cross-sectional surveillance of camels and humans in Kenya, targeting both nasal swabs and plasma samples from 1,163 camels and 486 humans collected from January 2016 to June 2018. A total of 792 camel plasma samples were positive by ELISA. Seroprevalence increased with age, and the highest prevalence was observed in adult camels(82.37%, 95%confidence interval(CI) 79.50–84.91). More female camels were significantly seropositive(74.28%, 95% CI 71.14–77.19)than male camels(P \ 0.001)(53.74%, 95% CI 48.48–58.90). Only 11 camel nasal swabs were positive for MERS-CoV by reverse transcription-quantitative PCR. Phylogenetic analysis of whole genome sequences showed that Kenyan MERSCoV clustered within sub-clade C2, which is associated with the African clade, but did not contain signature deletions of orf4 b in African viruses. None of the human plasma screened contained neutralizing antibodies against MERS-CoV. This study confirms the geographically widespread occurrence of MERS-CoV in Kenyan camels. Further one-health surveillance approaches in camels, wildlife, and human populations are needed. | Sheila Ommeh Wei Zhang Ali Zohaib Jing Chen Huajun Zhang Ben Hu Xing-Yi Ge Xing-Lou Yang Moses Masika Vincent Obanda Yun Luo Shan Li Cecilia Waruhiu Bei Li Yan Zhu Desterio Ouma Vincent Odendo Lin-Fa Wang Danielle E.Anderson Jacqueline Lichoti Erick Mungube Francis Gakuya Peng Zhou Kisa-Juma Ngeiywa Bing Yan Bernard Agwanda Zheng-Li Shi | 2018 | Virologica Sinica2018，33，6： | 1 |
| 3 | Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses显示文摘This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012–2015covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses;specifically, astroviruses(AstVs), adenoviruses(ADVs), caliciviruses(CalVs), coronaviruses(CoVs), flaviviruses, filoviruses, paramyxoviruses(PMVs), polyomaviruses(PYVs) and rotaviruses.We used family-specific primers, amplicon sequencing and further characterization by phylogenetic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions(former provinces) studied. AstVs(12.83%), CoVs(3.97%), PMV(2.4%), ADV(2.26%), PYV(1.65%), CalVs(0.29%), rotavirus(0.19%) and flavivirus(0.19%). Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A(RVA) strains detected were highly related to human strains with VP6 genotypes I2 and I16. Genotype I16 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction.Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance. | Cecilia Waruhiu Sheila Ommeh Vincent Obanda Bernard Agwanda Francis Gakuya Xing-Yi Ge Xing-Lou Yang Li-Jun Wu Ali Zohaib Ben Hu Zheng-Li Shi | 2017 | Virologica Sinica2017，32，2： | 1 |
| 4 | Countrywide Survey for MERS-Coronavirus Antibodies in Dromedaries and Humans in Pakistan显示文摘Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic pathogen capable of causing severe respiratory disease in humans. Although dromedary camels are considered as a major reservoir host, the MERS-CoV infection dynamics in camels are not fully understood. Through surveillance in Pakistan, nasal (n = 776) and serum (n = 1050)samples were collected from camels between November 2015 and February 2018. Samples were collected from animal markets, free-roaming herds and abattoirs. An in-house ELISA was developed to detect IgG against MERS-CoV. A total of 794 camels were found seropositive for MERS-CoV. Prevalence increased with the age and the highest seroprevalence was recorded in camels aged [ 10 years (81.37%) followed by those aged 3.1–10 years (78.65%) and B 3 years (58.19%).Higher prevalence was observed in female (78.13%) as compared to male (70.70%). Of the camel nasal swabs, 22 were found to be positive by RT-qPCR though with high Ct values. Moreover, 2,409 human serum samples were also collected from four provinces of Pakistan during 2016–2017. Among the sampled population, 840 humans were camel herders.Although we found a high rate of MERS-CoV antibody positive dromedaries (75.62%) in Pakistan, no neutralizing antibodies were detected in humans with and without contact to camels. | Ali Zohaib Muhammad Saqib Muhammad Ammar Athar Jing Chen Awais-ur-Rahman Sial Saeed Khan Zeeshan Taj Halima Sadia Usman Tahir Muhammad Haleem Tayyab Muhammad Asif Qureshi Muhammad Khalid Mansoor Muhammad Ahsan Naeem Bing-Jie Hu Bilal Ahmed Khan Ikram Din Ujjan Bei Li Wei Zhang Yun Luo Yan Zhu Cecilia Waruhiu Iahtasham Khan Xing-Lou Yang Muhammad Sohail Sajid Victor Max Corman Bing Yan Zheng-Li Shi | 2018 | Virologica Sinica2018，33，5： | 1 |
| 5 | Dynamic variations in COVID-19 with the SARS-CoV-2 Omicron variant in Kazakhstan and Pakistan显示文摘Background The ongoing coronavirus disease 2019(COVID-19)pandemic caused by the severe acute respiratory syndrome-coronavirus 2(SARS-CoV-2)and the Omicron variant presents a formidable challenge for control and prevention worldwide,especially for low-and middle-income countries(LMICs).Hence,taking Kazakhstan and Pakistan as examples,this study aims to explore COVID-19 transmission with the Omicron variant at different contact,quarantine and test rates.Methods A disease dynamic model was applied,the population was segmented,and three time stages for Omicron transmission were established:the initial outbreak,a period of stabilization,and a second outbreak.The impact of population contact,quarantine and testing on the disease are analyzed in five scenarios to analysis their impacts on the disease.Four statistical metrics are employed to quantify the model’s performance,including the correlation coefficient(CC),normalized absolute error,normalized root mean square error and distance between indices of simulation and observation(DISO).Results Our model has high performance in simulating COVID-19 transmission in Kazakhstan and Pakistan with high CC values greater than 0.9 and DISO values less than 0.5.Compared with the present measures(baseline),decreasing(increasing)the contact rates or increasing(decreasing)the quarantined rates can reduce(increase)the peak values of daily new cases and forward(delay)the peak value times(decreasing 842 and forward 2 days for Kazakhstan).The impact of the test rates on the disease are weak.When the start time of stage Ⅱ is 6 days,the daily new cases are more than 8 and 5 times the rate for Kazakhstan and Pakistan,respectively(29,573 vs.3259;7398 vs.1108).The impact of the start times of stageⅢon the disease are contradictory to those of stageⅡ.Conclusions For the two LMICs,Kazakhstan and Pakistan,stronger control and prevention measures can be more effective in combating COVID-19.Therefore,to reduce Omicron transmission,strict management of population movement should be employed.Moreover,the timely application of these strategies also plays a key role in disease control. | Qianqian Cui Zhengli Shi Duman Yimamaidi Ben Hu Zhuo Zhang Muhammad Saqib Ali Zohaib Baikadamova Gulnara Mukhanbetkaliyev Yersyn Zengyun Hu Shizhu Li | 2023 | Infectious Diseases of Poverty2023，12，2： | 0 |
| 6 | Antagonistic Potential of Bacterial Species against Fungal Plant Pathogens(FPP)and Their Role in Plant Growth Promotion(PGP):A Review显示文摘Since the 19th century to date,the fungal pathogens have been involved in causing devastating diseases in plants.All types of fungal pathogens have been observed in important agricultural crops that lead to significant pre and postharvest losses.The application of synthetic fungicide against the fungal plant pathogens(FPP)is a traditional management practice but at the same time these fungicides kill other beneficial microbes,insects,animal,and humans and are harmful to environment.The antagonistic microorganism such as bacteria are being used as an alternate strategy to control the FPP.These antagonistic species are cost-effective and eco-friendly in nature.These biocontrol bacteria have a broad mechanism against fungal pathogens present in the phyllosphere and rhizosphere of the plant.The antagonistic bacteria have different strategies against the FPP,by producing siderophore,biofilm,volatile organic compounds(VOCs),through parasitism,antibiosis,competition for limited resources and induce systemic resistance(ISR)in the host plant by activating the immune systems.The commercial bio-products synthesized by the major bacterial species Pseudomonas syringae,Burkholderia cepacia,Streptomyces griseoviridis,Pseudomonas fluorescens and Bacillus subtilis are used to control Fusarium,Pythium,Rhizoctonia,Penicillium,Alternaria,and Geotrichum.The commercial bio-formulations of bacteria act as both antifungal and plant growth regulators.The Plant growth-promoting rhizobacteria(PGPR)played a significant role in improving plant health by nitrogen-fixing,phosphorus solubilization,phytohormones production,minimizing soil metal contamination,and by ACC deaminase antifungal activities.Different articles are available on the specific antifungal activity of bacteria in plant diseases.Therefore,this review article has summarized the information on biocontrol activity of bacteria against the FPP and the role of PGPR in plant growth promotion.This review also provided a complete picture of scattered information regarding antifungal activities of bacteria and the role of PGPR. | Amjad Ali Yasir Iftikhar Mustansar Mubeen Haider Ali Muhammad Ahmad Zeshan Zohaib Asad Muhammad Zafar-ul-Hye Malik Abdul Rehman Mazhar Abbas Muhammad Rafique Muhammad Usman Ghani | 2022 | Phyton-International Journal of Experimental Botany2022，91，9： | 0 |
| 7 | Epidemiological trends of mosquito-borne viral diseases in Pakistan显示文摘Globally,arboviruses are public health problems.Pakistan has seen a fast-paced increase in mosquito-borne Flavivirus diseases such as dengue because of deforestation,climate change,urbanization,poor sanitation and natural disasters.The magnitude and distribution of these diseases are poorly understood due to the lack of a competitive nationwide surveillance system.In dengue-endemic countries,the recent epidemics of chikungunya(CHIKV)and human West Nile virus(WNV)have created panic among the public and are thought to provoke an outbreak of Zika virus(ZIKV)in Pakistan.Recently,hospital-based surveillance has indicated the presence of Japanese encephalitis virus(JEV),which is deeply concerned by developing countries such as Pakistan.The situation could become more devastating because of poorly developed diagnostic infrastructure.To date,no licensed vaccine has been used in Pakistan,and preventive measures are mainly based on vector control.This review provides comprehensive information concerning the association of risk factors with disease occurrence,epidemiological trends,and prediction of the spread of mosquito-borne diseases,attention to new threats of ZIKV,and future perspectives by benchmarking global health policies. | Muhammad Imran Jing Ye Muhammad K.Saleemi Iqra Shaheen Ali Zohaib Zheng Chen Shengbo Cao | 2022 | Animal Diseases2022，2，2： | 0 |
| 8 | Hyperspectral Images-Based Crop Classification Scheme for Agricultural Remote Sensing显示文摘Hyperspectral imaging is gaining a significant role in agricultural remote sensing applications.Its data unit is the hyperspectral cube which holds spatial information in two dimensions while spectral band information of each pixel in the third dimension.The classification accuracy of hyperspectral images(HSI)increases significantly by employing both spatial and spectral features.For this work,the data was acquired using an airborne hyperspectral imager system which collected HSI in the visible and near-infrared(VNIR)range of 400 to 1000 nm wavelength within 180 spectral bands.The dataset is collected for nine different crops on agricultural land with a spectral resolution of 3.3 nm wavelength for each pixel.The data was cleaned from geometric distortions and stored with the class labels and annotations of global localization using the inertial navigation system.In this study,a unique pixel-based approach was designed to improve the crops'classification accuracy by using the edge-preserving features(EPF)and principal component analysis(PCA)in conjunction.The preliminary processing generated the high-dimensional EPF stack by applying the edge-preserving filters on acquired HSI.In the second step,this high dimensional stack was treated with the PCA for dimensionality reduction without losing significant spectral information.The resultant feature space(PCA-EPF)demonstrated enhanced class separability for improved crop classification with reduced dimensionality and computational cost.The support vector machines classifier was employed for multiclass classification of target crops using PCA-EPF.The classification performance evaluation was measured in terms of individual class accuracy,overall accuracy,average accuracy,and Cohen kappa factor.The proposed scheme achieved greater than 90%results for all the performance evaluation metrics.The PCA-EPF proved to be an effective attribute for crop classification using hyperspectral imaging in the VNIR range.The proposed scheme is well-suited for practical applications of crops and landfill estimations using agricultural remote sensing methods. | Imran Ali Zohaib Mushtaq Saad Arif Abeer D.Algarni Naglaa F.Soliman Walid El-Shafai | 2023 | Computer Systems Science & Engineering2023，46，7： | 0 |
| 9 | The role of green industrial transformation in mitigating carbon emissions:Exploring the channels of technological innovation and environmental regulation显示文摘The industrial sector is vital to economic progress,yet industrial pollution poses environmental and economic concerns.The purpose of the study was to investigate the influence of green industrial transformation in re-ducing Pakistan’s carbon intensity between 1975 and 2020.Carbon emissions are considered an endogenous construct,while foreign direct investment(FDI)inflows,technological innovation,green industrial transforma-tion,environmental legislation,and research and development(R&D)investment are possible mediators.The association between variables is assessed using the robust least-squares approach.Green industrial transforma-tion is connected with lower carbon emissions,yet technical innovation,R&D investment,and inbound FDI raise a country’s carbon emissions.The findings support the pollution haven hypothesis in a country.The causality esti-mates indicate that inward FDI contributes to environmental regulations;green industrial transformation directly relates to inbound FDI and R&D expenditures;and technological innovations correspond to inbound FDI,R&D ex-penditures,industrial ecofriendly progression,and environmental standards.According to the impulse response function,environmental policies are anticipated to have a differential effect on carbon emissions in 2023,2024,2028-2030,while they are likely to decrease in the years 2025-2027 and 2031 forward.Additionally,inward FDI and technology advancements would almost certainly result in a rise in carbon emissions over time.Green industrial transitions are projected to result in a ten-year reduction in carbon emissions.The variance decomposi-tion analysis indicates that eco-friendly industrial adaptations would likely have the largest variance error shock on carbon emissions(11.747%),followed by inbound FDI,technological advancements,and regulatory changes,with R&D spending having a minimal impact over time.Pakistan’s economy should foster a green industrial revolution to avoid pollution and increase environmental sustainability to meet its environmental goals. | Saima Mehmood Khalid Zaman Shiraz Khan Zohaib Ali Haroon ur Rashid Khan | 2024 | Energy and Built Environment2024，5，3： | 0 |
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