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genetic diversity and occult hepatitis B infection in Africa: A comprehensive review

World Journal of Hepatology 2024年第5期16卷 843-859页

作者： Michee M Bazie Mahamoudou Sanou Florencia Wendkuuni Djigma Tegwinde Rebeca Compaore Dorcas Obiri-Yeboah Benoît Kabamba Bolni Marius Nagalo Jacques Simpore Rasmata Ouédraogo Department of Medicine Transmissible Diseases LaboratoryUniversitéJoseph KI-ZERBOOuagadougou 0000Burkina Faso Department of Biochemistry and Microbiology Molecular Biology and Genetics LaboratoryUniversity Joseph KI-ZERBOOuagadougou 0000Burkina Faso Infectious and parasitic disease Laboratory Health Sciences Research InstituteIRSS/CNRSTNational Center for Scientific and Technological ResearchOuagadougou 0000Burkina Faso Department of Microbiology and Immunology School of Medical SciencesUniversity of Cape CoastPMBCape Coast 0000Ghana Department of Clinical Biology Virology LaboratoryCliniques Universitaires Saint LucUniversitéCatholique de LouvainBruxelles 0000Belgium Division of Hematology and Oncology Mayo ClinicAZ 0000United States

BACKGROUND Occult hepatitis B infection(OBI)is a globally prevalent infection,with its frequency being influenced by the prevalence of hepatitis B virus(HBV)infection in a particular geographic region,including Africa.OBI can be transmitted th-rough blood transfusions and organ transplants and has been linked to the development of hepatocellular carcinoma(HCC).The associated HBV genotype influences the infection.AIM To highlight the genetic diversity and prevalence of OBI in Africa.METHODS This systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and involved a comprehensive search on PubMed,Google Scholar,Science Direct,and African Journals Online for published studies on the prevalence and genetic diversity of OBI in Africa.RESULTS The synthesis included 83 articles,revealing that the prevalence of OBI varied between countries and population groups,with the highest prevalence being 90.9%in patients with hepatitis C virus infection and 38%in blood donors,indicating an increased risk of HBV transmission through blood transfusions.Cases of OBI reactivation have been reported following chemotherapy.Genotype D is the predominant,followed by genotypes A and E.CONCLUSION This review highlights the prevalence of OBI in Africa,which varies across countries and population groups.The study also demonstrates that genotype D is the most prevalent.

关键词： Occult hepatitis B infection Blood transfusion genetic diversity

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genetic diversity of the S-type small subunit ribosomal RNA gene of Plasmodium knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia

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Asian Pacific Journal of Tropical Medicine 2024年第2期17卷 84-90页

作者： Eric Tzyy Jiann Chong Joveen Wan Fen Neoh Tiek Ying Lau Kek Heng Chua Yvonne Ai-Lian Lim Ping-Chin Lee Biotechnology Research Institute Universiti Malaysia SabahJalan UMS88400 Kota KinabaluSabahMalaysia Department of Biomedical Science Faculty of Medicine BuildingUniversity of Malaya50603 Kuala LumpurMalaysia Centre of Excellence for Research in AIDS(CERiA) University of Malaya50603 Kuala LumpurMalaysia Faculty of Science and Natural Resources Universiti Malaysia SabahJalan UMS88400 Kota KinabaluSabahMalaysia

Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.

关键词： Plasmodium knowlesi S-type small subunit ribosomal RNA genetic diversity Natural selection Haplotype

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Epidemiological Surveillance: genetic diversity of Rotavirus Group A in the Pearl River Delta, Guangdong, China in 2019

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Biomedical and Environmental Sciences 2024年第3期37卷 278-293页

作者： JIANG Jie Ying LIANG Dan WANG Li XIAO Yun LIANG Yu Feng KE Bi Xia SU Juan XIAO Hong WANG Tao ZOU Min LI Hong Jian KE Chang Wen School of Public Health Shantou UniversityShantou 515063GuangdongChina Guangdong Provincial Center for Disease Control and Prevention Guangdong Workstation for Emerging Infectious Disease Control and PreventionGuangzhou 511430GuangdongChina Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan UniversityGuangzhou 510632GuangdongChina School of Public Health Sun Yat-sen UniversityGuangzhou 510275GuangdongChina School of Public Health Southern Medical UniversityGuangzhou 510515GuangdongChina Shantou University Medical College Shantou 515041GuangdongChina

Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.

关键词： Infectious diarrheal disease Rotavirus Phylogenetic analysis Gene rearrangement Codon usage bias genetic diversity

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genetic diversity of food-medicinal Lycium spp. in China: Insights from chloroplast genome

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Chinese Herbal Medicines 2024年第3期16卷 401-411页

作者： Ruyu Yao Bin Wang Michael Heinrich Qiuling Wang Peigen Xiao Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Institute of Botany Chinese Academy of Sciences Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine Hainan Branch of the Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences and Peking Union Medical College Research Group 'Pharmacognosy and Phytotherapy' UCL School of PharmacyUniversity of London

Objective:Goji(fruits of Lycium spp.) is commonly consumed as food and medicine.The increasing market demand for goji has led to its wide cultivation and broad breeding,which might cause loss of genetic diversity.This study aims to uncover the genetic diversity of the cultivated and wild Lycium.Methods:The chloroplast genome(CPG) of 34 accessions of Chinese food-medicinal Lycium spp., including the popular cultivars and their wild relatives,was re-sequenced and assembled,based on which the genetic diversity was evaluated.Results:Sequence structural comparison shows that CPG is comparatively conserved within species.Phylogenetic analysis indicates that CPG is sufficient for the discrimination of Lycium species;combined with nuclear ribosomal internal transcribed spacer(Nr ITS) sequences,materials with mixed genetic backgrounds can be identified.Nucleotide diversity analysis reveals that the modern cultivars are probably with a common maternal parent,while the wild accessions are with higher level of genetic diversity.Conclusion:For the first time this study reveals the intraspecies genetic diversity of Lycium spp.using CPG,highlighting the urgent conservation demand of wild genetic resources of Lycium.Our study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity conservation.This CPG-based technology will contribute to the sustainable development of medicinal plants broadly.

关键词： chloroplast genome cultivar food-medicine genetic diversity goji wild relative

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Genome-wide SNP markers provided insights into the reproductive strategy and genetic diversity of the green tide causative species Ulva prolifera in China

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Journal of Oceanology and Limnology 2024年第2期42卷 533-543页

作者： Song SUN Weiwei MA Nan WANG Song FENG Yan SUN CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdao 266071China Laboratory for Marine Ecology and Environmental Science Laoshan LaboratoryQingdao 266237China Jiaozhou Bay Marine Ecosystem Research Station Chinese Academy of SciencesQingdao 266071China University of Chinese Academy of Sciences Beijing 100049China

Ulva prolifera is the causative species of the annually occurring large-scale green tides in China since 2007.Its specific biological features on reproductivity strategies,as well as intra-species genetic diversity,are still largely unknown,especially at the genome level,despite their importance in understanding the formation and outbreak of massive green tides.In the present study,the restriction site-associated DNA genotyping approach(2b-RAD)was adopted to identify the genome-wide single-nucleotide polymorphisms(SNPs)of 54 individual thalli including samples collected from Subei Shoal in 2019 and Qingdao coast from 2019 to 2021.SNPs genotype results revealed that most of the thalli in 2019 and 2020 were haploid gametophytes,while only half of the thalli were gametophytes in 2021,indicating flexibility in the reproductive strategies for the formation of the green tides among different years and the dominance of asexual and vegetative reproductive mode for the floating period.Besides,population analysis was conducted,and it revealed a very low genetic diversity among samples from Subei Shoal and the Qingdao coast in the same year and a higher divergence among samples in different years.The results showed the efficiency of 2b-RAD in the exploration of SNPs in U.prolifera and provided the first genome-wide scale evidence for the origin of the large-scale green tides on the Qingdao coast.This study improved our understanding of the reproductive strategy and genetic diversity of the green tide causative species and will help further reveal the biological causes of the green tide in China.

关键词： green tide Ulva prolifera 2b-RAD single-nucleotide polymorphism(SNP) reproductive strategy genetic diversity

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genetic diversity of Jute Mallow (Corchorus spp.) Accessions Based on ISSR Markers

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American Journal of Plant Sciences 2024年第5期15卷 316-328页

作者： Munguatosha Ngomuo Tsvetelina Stoilova Tileye Feyissa Patrick A. Ndakidemi School of Life Sciences Nelson Mandela African Institute of Science and Technology Arusha Tanzania Tanzania Official Seed Certification Institute (TOSCI) Arusha Tanzania AVRDC— World Vegetable Centre Arusha Tanzania Institute of Biotechnology Addis Ababa University Addis Ababa Ethiopia

Jute mallow is a nutritious leafy vegetable. The leaves are rich in proteins, vitamins and essential amino acids. Molecular characterization of Jute mallow with focus on improvement of leaf yield is scarcely reported. In the present study, inter sequence simple repeats (ISSR) molecular markers were employed to assess genetic diversity and relationships of 83 accessions of Jute mallow from different parts of Africa and Asia conserved at the World Vegetable Center East and Southern Africa. A total of 89 bands were amplified by 8 ISSR primers. Number of polymorphic bands per primer ranged from 2 to 6 with an average of 2.75 bands per primer. Polymorphic information content (PIC) values ranged from 0.390 to 0.760 with average of 0.53. Average Nei’s gene diversity (h) and Shannon’s information index (I) were 0.335 and 0.494 respectively. The highest pairwise genetic distance was 0.431 observed in a population from East Africa accessions. PC1 and PC2 axis explained 21.69% and 11.66% of the total variation respectively. UPGMA cluster analysis grouped the accessions into six main clusters at genetic similarity coefficient of 0.53 as standard value for classification. These results have important implications for jute mallow breeding and conservation.

关键词： Corchorus spp. genetic diversity ISSRs Jute Mallow Leafy Vegetable

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genetic diversity in Cowpea (Vigna unguiculata (L.) Walp) under Two Growing Conditions^*

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Advances in Bioscience and Biotechnology 2024年第5期15卷 310-324页

作者： Omotola Oluwakemi Dairo Department of Plant Breeding and Seed Technology Federal University of Agriculture Abeokuta Nigeria College of Education and Liberal Art Wilmington University Delaware USA

This study explores the use of genetic variability for advancing the genetic improvement of Cowpea (Vigna unguiculata (L.) Walp), particularly in response to insect infestation stress. Over a period spanning 2015 to 2017, forty accessions of cowpeas were evaluated to determine their variability under both insecticide spray and no insecticide spray conditions at the Teachings and Research Farms, Federal University of Agriculture, Abeokuta. The experimental design was a randomized complete block design in three replicates. The accessions were evaluated for plant height, leaf length, leaf width, number of days of 50% flowering, number of pods per plant, pod length, number of seeds per plant, 100-seed weight, and seed yield. Data collected were subjected to principal component and single linkage cluster analyses. Principal axis I (PCA1) accounted for 39% and 35% under insecticide spray and no insecticide spray respectively to the total variation in the accessions. Plant height with a factor score of 0.38, leaf length (0.41), number of leaves (0.37), and 100-seed, weight (0.30) was related to PCAI under insecticide spray while leaf width (0.32). Pod length (0.37) and number of seeds/plant (0.38) were significant to PCA1 under no insecticide spray. Notably, accessions such as SAMPEA6, SAMPEA10, IFE-Brown, and IFE-BPE exhibited consistent performance across both conditions, while others displayed condition-specific attributes. For instance, NGB1063, NGB1152, and NGB1093 demonstrated distinct traits under insecticide spray, while NGB1146 and NGB1124 exhibited notable characteristics under no insecticide spray conditions. Therefore, identifying these forty accessions with desirable traits hold promise for future genetic improvement efforts of cowpea cultivation in Nigeria and beyond.

关键词： Cowpea Vigna Unguiculata genetic diversity Cowpea Accessions

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genetic diversity,Antibiotic Resistance,and Pathogenicity of Aeromonas Species from Food Products in Shanghai,China

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Biomedical and Environmental Sciences 2022年第9期35卷 842-853页

作者： QU Feng Tian WANG Wen Qing LIU Qian ZHOU Hai Jian HU Jin Rui DU Xiao Li WANG Yue XUE Jia Qi CUI Zhi Gang XIE Gui Lin MENG Shuang College of Life Science Northeast Agricultural UniversityHa’erbin 150000HeilongjiangChina State Key Laboratory of Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Shanghai Pudong New Area Center for Disease Control and Prevention Shanghai 200136China Laboratory Medicine Beijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing 100730China Clinic Medical College North China University of Science and TechnologyTangshan 063000HebeiChina

Objective Aeromonas has recently been recognized as an emerging human pathogen.Aeromonasassociated diarrhea is a phenomenon occurring worldwide.This study was designed to determine the prevalence,genetic diversity,antibiotic resistance,and pathogenicity of Aeromonas strains isolated from food products in Shanghai.Methods Aeromonas isolates(n=79)collected from food samples were analyzed using concatenated gyrB-cpn60 sequencing.The antibiotic resistance of these isolates was determined using antimicrobial susceptibility testing.Pathogenicity was assessed usingβ-hemolytic,extracellular protease,virulence gene detection,C.elegans liquid toxicity(LT),and cytotoxicity assays.Results Eight different species were identified among the 79 isolates.The most prevalent Aeromonas species were A.veronii[62(78.5%)],A.caviae[6(7.6%)],A.dhakensis[3(3.8%)],and A.salmonicida[3(3.8%)].The Aeromonas isolates were divided into 73 sequence types(STs),of which 65 were novel.The isolates were hemolytic(45.6%)and protease-positive(81.0%).The most prevalent virulence genes were act(73.4%),fla(69.6%),aexT(36.7%),and ascV(30.4%).The results of C.elegans LT and cytotoxicity assays revealed that A.dhakensis and A.hydrophila were more virulent than A.veronii,A.caviae,and A.bivalvium.Antibiotic resistance genes[tetE,blaTEM,tetA,qnrS,aac(6)-Ib,mcr-1,and mcr-3]were detected in the isolates.The multidrug-resistance rate of the Aeromonas isolates was 11.4%,and 93.7%of the Aeromonas isolates were resistant to cefazolin.Conclusion The taxonomy,antibiotic resistance,and pathogenicity of different Aeromonas species varied.The Aeromonas isolates A.dhakensis and A.hydrophila were highly pathogenic,indicating that food-derived Aeromonas isolates are potential risks for public health and food safety.The monitoring of food quality and safety will result in better prevention and treatment strategies to control diarrhea illnesses in China.

关键词： Aeromonas genetic diversity Antibiotic resistance Virulence gene Cytotoxicity assay Multidrug-resistance

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genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

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Journal of Forestry Research 2022年第2期33卷 611-621页

作者： Qi Guo Sen Cao Li Dong Xiuyu Li Jiangtao Zhang Yuanshuai Zhang Zijie Zhang Yuhan Sun Cui Long Yingming Fan Chao Han Peiyao Han Xiaodi Liu Yun Li Beijing Advanced Innovation Center for Tree Breeding By Molecular Design Engineering Technology Research Center of Black Locust of National Forestry and Grassland AdministrationCollege of Biological Sciences and TechnologyNational Engineering Laboratory for Tree BreedingBeijing Forestry UniversityBeijing 100083P.R.China College of Agriculture Henan University of Science and TechnologyLuoyang 471023P.R.China Henan Academy of Forestry Zhengzhou 450008P.R.China Feixian County State Owned Daqingshan Forest Farm Linyi 273400P.R.China

Robinia pseudoacacia is an important afforesta-tion tree introduced to China in 1878.In the present study,we examined the genetic diversity among 687 strains rep-resenting four improved varieties and two secondary prov-enances,comprising 641 clones and 46 seedlings.Ninety-one simple sequence repeats(SSRs)were selected through segregation analysis and polymorphism characterization,and all sampled individuals were genotyped using well-characterized SSR markers.After excluding loci with non-neutral equilibrium,missing locus data and null alleles,we used 36 primer pairs to assess the genetic diversity of these germplasm resources,revealing vast genetic differentiation among the samples,with an average of 8.352 alleles per locus and a mean Shannon′s index of 1.302.At the popula-tion level,the partitioning of variability was assessed using analysis of molecular variance,which revealed 93%and 7%variation within and among collection sites,respectively.Four clusters were detected using structure analysis,indi-cating a degree of genetic differentiation among the six populations.Insights into the genetic diversity and structure of R.pseudoacacia provide a theoretical basis for the con-servation,breeding and sustainable development in China.

关键词： Robinia pseudoacacia genetic diversity genetic differentiation Microsatellite Population structure Black locust

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genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica rice(Oryza sativa L.)in Northeast China

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Journal of Integrative Agriculture 2022年第6期21卷 1539-1550页

作者： XU Xin YE Jun-hua YANG Ying-ying LI Ruo-si LI Zhen WANG Shan SUN Yan-fei ZHANG Meng-chen XU Qun FENG Yue WEI Xing-hua YANG Yao-long State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311400P.R.China

Milling and appearance quality are important contributors to rice grain quality.Abundant genetic diversity and a suitable environment are crucial for rice improvement.In this study,we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning,Jilin and Heilongjiang provinces in Northeast China.Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions.An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality,whereas cultivars from Heilongjiang tended to exhibit superior appearance quality.Single-and multi-locus genome-wide association studies(GWAS)were conducted to identify loci associated with milling and appearance quality-related traits.Ninety-nine significant single-nucleotide polymorphisms(SNPs)were detected.Three common SNPs were detected using the mixed linear model(MLM),mrMLM,and FASTmrMLM methods.Linkage disequilibrium decay was estimated and indicated three candidate regions(qBRR-1,qBRR-9 and qDEC-3)for further candidate gene analysis.More than 300 genes were located in these candidate regions.Gene Ontology(GO)analysis was performed to discover the potential candidate genes.genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding.These results provide information that will be valuable for the improvement of grain quality in rice breeding.

关键词： rice grain quality GWAS genetic diversity

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