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Discovery of novel DNA viruses in small mammals from Kenya

Virologica Sinica 2022年第4期37卷 491-502页

作者： Griphin Ochieng Ochola Bei Li Vincent Obanda Sheila Ommeh Harold Ochieng Xing-Lou Yang Samson Omondi Onyuok Zheng-Li Shi bernard agwanda Ben Hu CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan430071China Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan430074China Mammalogy Section National Museums of KenyaNairobi40658-00100Kenya University of Chinese Academy of Sciences Beijing100049China Veterinary Services Department Kenya Wildlife ServiceNairobi40241-00100Kenya Institute of Biotechnology Research Jomo Kenyatta University of Science and TechnologyNairobi62000-00200Kenya

Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health *** and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic *** surveillance programs focused more on RNA *** comparison,much less is known about DNA viruses harbored by these small *** fill this knowledge gap,tissue specimens of 232 animals including 226 rodents,five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by *** DNA sequences of adenoviruses,adeno-associated viruses,herpesviruses and polyomaviruses were *** analyses revealed that most of these viruses showed distinction from previously described viruses and formed new ***,this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys *** novel polyomavirus,named Ls Py V KY187,has less than 60%amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within *** findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal *** demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.

关键词： Kenya DNA viruses Rodents Shrews Polyomavirus

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Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses

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Virologica Sinica 2017年第2期32卷 101-114页

作者： 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 Key Lab of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Sino-Africa Joint Research Center Chinese Academy of Sciences Wuhan 430071 China Institute of Biotechnology Research Jomo Kenyatta University of Science and Technology Nairobi 00200 Kenya Veterinary Services Department Kenya Wildlife Service Nairobi 00100 Kenya Mammalogy Section National Museum of Kenya Nairobi 00100 Kenya Mammalogy Section National Museum of Kenya Nairobi 00100 Kenya

This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012-2015 covering 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 phyloge- netic 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 12 and 116. Genotype 116 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.

关键词： astroviruses (AstVs) calicivirus (CalVs) Rotavirus A 229-E-like bat coronavirus

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Genetic Evidence of Middle East Respiratory Syndrome Coronavirus(MERS-Cov) and Widespread Seroprevalence among Camels in Kenya

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Virologica Sinica 2018年第6期33卷 484-492页

作者： 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 Institute for Biotechnology Research Jomo Kenyatta University of Agriculture and TechnologyNairobi 62000-00200Kenya CAS Key Laboratory for Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China College of Biology Hunan University410006China Department of Medical Microbiology University of NairobiNairobi 30197-00100Kenya Veterinary Services Department Kenya Wildlife ServiceNairobi 40241-00100Kenya Veterinary Research Institute Kenya Agriculture and Livestock Research OrganizationNairobi 57811-00200Kenya Veterinary Services Programme in Emerging Infectious Diseases Duke-NUS Medical SchoolSingapore 169857Singapore Directorate of Veterinary Services State Department of LivestockMinistry of AgricultureLivestock Fisheries and IrrigationNairobi 34188-00100Kenya Kenya Camel Association Nairobi 30095-00100Kenya Department of Zoology National Museums of KenyaNairobi 40658-00100Kenya

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.

关键词： Middle East respiratory syndrome coronavirus(MERS-CoV) One-health Public health Zoonosis Kenya

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过去10年(2007-2017年)新蚊虫相关病毒的发现和全球分布

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中华实验和临床病毒学杂志 2019年第4期33卷 399-399页

作者：吕新军(编译) Evans Atoni Lu Zhao Samuel Karungu Vincent Obanda bernard agwanda Han Xia Zhiming Yuan Key Laboratory of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China University of Chinese Academy of Sciences Beijing China Key Laboratory of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China University of Chinese Academy of Sciences Beijing China Key Laboratory of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China University of Chinese Academy of Sciences Beijing China Veterinary Services Department Kenya Wildlife Service Nairobi Kenya Mammalogy Section National Museum of Kenya Nairobi Kenya Key Laboratory of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China Key Laboratory of Special Pathogens Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China

在过去的10年里,病毒的搜寻和发现已经加快了步伐。这一成就由三个主要因素推动:(1)测序技术的进步;(2)扩大常规虫媒病毒监测策略;(3)对新出现病原体和新病毒的“搜寻”。从大量的宿主、媒介和环境样本中发现了许多新的病毒。为了有助... 详细信息

在过去的10年里,病毒的搜寻和发现已经加快了步伐。这一成就由三个主要因素推动:(1)测序技术的进步;(2)扩大常规虫媒病毒监测策略;(3)对新出现病原体和新病毒的“搜寻”。从大量的宿主、媒介和环境样本中发现了许多新的病毒。为了有助于促进对全球蚊虫相关病毒多样性和分布的了解,并促进未来的研究,我们回顾了2007年至2017年在世界各地发现的蚊虫相关病毒。在分析期间,对属于25个家族的新发现蚊虫相关病毒和1组未分类病毒进行了分类。

关键词：虫媒病毒测序技术蚊虫环境样本病原体监测策略

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Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

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Zoological Research 2021年第4期42卷 450-460页

作者： Lin Zeng He-Qun Liu Xiao-Long Tu Chang-Mian Ji Xiao Gou Ali Esmailizadeh Sheng Wang Ming-Shan Wang Ming-Cheng Wang Xiao-Long Li Hadi Charati Adeniyi CAdeola Rahamon Akinyele Moshood Adedokun Olatunbosun Oladipo Sunday Charles Olaogun Oscar JSanke Mangbon Godwin F Sheila Cecily Ommeh bernard agwanda Jacqueline Kasiiti Lichoti Jian-Lin Han Hong-Kun Zheng Chang-Fa Wang Ya-Ping Zhang Laurent A.F.Frantz Dong-Dong Wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouHainan 571101China College of Animal Science and Technology Yunnan Agricultural UniversityKunmingYunnan 650201China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKermanPB 76169-133Iran Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Sino-Africa Joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Institute of Three-River-Source National Park Chinese Academy of SciencesXiningQinghai 810008China School of Biological and Chemical Sciences Queen Mary University of LondonLondon E14NSUK Department of Genetics Albert Einstein College of MedicineBronxNew YorkNY 10461USA Annoroad Gene Tech.(Beijing)Co. Ltd.Beijing 100176China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Federal College of Animal Health and Production Technology Moor-PlantationIbadan 234102Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi 62000-00200Kenya Department of Zoology National Museums of KenyaNairobi 40658-00100Kenya State Department of Livestock Ministry of AgricultureLivestockFisheries and IrrigationN

Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan ***,the kiang,a closely related equid species,also inhabits this *** reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan ***,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has *** assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in *** Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high *** addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan *** findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.

关键词： Kiang Donkey High altitude Adaptation Selection

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A cryptic mitochondrial DNA link between North European and West African dogs

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Journal of Genetics and Genomics 2017年第3期44卷 163-170页

作者： Adeniyi C.Adeola Sheila C.Ommeh Jiao-Jiao Song S.Charles Olaogun Oscar J.Sanke Ting-Ting Yin Guo-Dong Wang Shi-Fang Wu Zhong-Yin Zhou Jacqueline K.Lichoti bernard R.agwanda Philip M.Dawuda Robert W.Murphy Min-Sheng Peng Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University Kunming 650091 China

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, we analyse variation in mitochondrial DNA（mt DNA） D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and West Asia. All Kenyan dogs can be assigned to one of three haplogroups（matrilines; clades）： A, B, and C, while Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf（Canis lupus lupaster）. The genetic signal of a recent demographic expansion is detected in Nigerian dogs from West Africa. The analyses of mitochondrial genomes reveal a maternal genetic link between modern West African and North European dogs indicated by sub-haplogroup D1（but not the entire haplogroup D） coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,we propose that sub-haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially associated with human hunter-gatherer migration from southwestern Europe.

关键词： Dog Mitochondrial DNA Africa Haplogroup D Late-glacial dispersal Hybridization

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Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences

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Zoological Research 2020年第1期41卷 51-60页

作者： Xi-Yao Ma Tiao Ning Adeniyi CAdeola Jie Li Ali Esmailizadeh Jacqueline KLichoti bernard Ragwanda Jainagul Isakova Almaz AAldashev Shi-Fang Wu He-Qun Liu Najmudinov Tojiddin Abdulloevich Manilova Elena Afanasevna Khudoidodov Behruz Ibrohimovich Rahamon Akinyele Moshood Adedokun Sunday Charles Olaogun Oscar JSanke Godwin FMangbon Xi Chen Wei-Kang Yang Zhe Wang Min-Sheng Peng Sheila COmmeh Yan Li Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunmingYunnan 650091China Agriculture College Kunming UniversityKunmingYunnan 650214China Engineering Research Center for Urban Modern Agriculture of Higher Education in Yunnan Province Kunming UniversityKunmingYunnan 650214China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Sino-Africa Joint Research Center Chinese Academy of SciencesKunmingYunnan 650223China Department of Animal Science Faculty of AgricultureShahid Bahonar University of KermanKerman PB 76169-133Iran State Department of Livestock Ministry of Agriculture Livestock and FisheriesNairobi 00100Kenya Department of Zoology National Museums of KenyaNairobi 00100Kenya Institute of Molecular Biology and Medicine Bishkek 720040Kyrgyzstan E.N.Pavlovsky Institute of Zoology and Parasitology Academy of Sciences of Republic of TajikistanDushanbe 734025Tajikistan Department of Veterinary Medicine University of IbadanIbadan 200284Nigeria Taraba State Ministry of Agriculture and Natural Resources Jalingo 660221Nigeria Division of Veterinary Office Serti 663101Nigeria Research Center for Ecology and Environment of Central Asia Chinese Academy of SciencesUrumqiXinjiang 830011China Key Laboratory of Biogeography and Bioresource in Arid Land Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiXinjiang 830011China Department of Physiology Hebei Medical UniversityShijiazhuangHebei 050017China Hebei Key Laboratory of Animal Science Hebei Medical UniversityShijiazhuangHebei 050017China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China Animal Biotechnology Group Institute of Biotechnology ResearchJomo Kenyatta University of Agriculture and TechnologyNairob

Molecular studies on donkey mitochondrial sequences have clearly defined two distinct maternal lineages involved in ***,domestication histories of these two lineages remain *** therefore compared several population characteristics between these two lineages based on global sampling,which included 171 sequences obtained in this study(including Middle Asian,East Asian,and African samples)plus 536 published sequences(including European,Asian,and African samples).The two lineages were clearly separated from each other based on whole mitochondrial genomes and partial non-coding displacement loop(D-loop)sequences,*** Clade I lineage experienced an increase in population size more than 8000 years ago and shows a complex haplotype *** contrast,the population size of the Clade II lineage has remained relatively constant,with a simpler haplotype *** the distribution of the two lineages was almost equal across the Eurasian mainland,they still presented discernible but complex geographic bias in most parts of Africa,which are known as their domestication *** from sub-Saharan Africa tended to descend from the Clade I lineage,whereas the Clade II lineage was dominant along the East and North coasts of ***,the migration routes inferred from diversity decay suggested different expansion across China between the two ***,these differences indicated non-simultaneous domestication of the two lineages,which was possibly influenced by the response of pastoralists to the desertification of the Sahara and by the social expansion and trade of ancient humans in Northeast Africa,respectively.

关键词： Donkey lineage Domestication history Population Expansion

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The influence of pressure waves in tidal gravity records

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Geodesy and Geodynamics 2023年第1期14卷 15-25页

作者： bernard Ducarme Catholic University of Louvain Georges Lemaître Centre for Earth and Climate Research(ELI)Louvain-la-NeuveBelgium

For the reduction of atmospheric effects,observed gravity has initially been corrected by using the computed barometric admittance k of the in situ measured pressure,expressed in nms-2/hPa units and estimated by least squares ***,the local pressure changes alone cannot account for the atmospheric mass attraction and loading when the coherent pressure field exceeds a specific size,i.e.,with increasing *** overcome this difficulty,it is necessary to compute the total atmospheric effect at each station using the global pressure ***,the direct subtraction of the total gravity effect,provided by the models of pressure correction,is not yet satisfactory for S2 and other tidal components,such as K2 and P1,which include solar heating pressure *** paper identifies the origin of the problem and presents strategies to obtain a satisfactory ***,we set up a difference vector between the tidal factors of M2 and S2 after correction of the pressure and ocean tides *** vector,hereafter denoted as RES,presents the advantage of being practically insensitive to calibration *** minimum discrepancy between the tidal parameters of M2 and S2 corresponds to the minimum of the RES vector norm *** we adopt the hybrid pressure correction method,separating the local and the global pressure contribution of the models and replacing the local contribution by the pressure measured at the station multiplied by an admittance *** tested this procedure on 8 stations from the IGETS superconducting gravimeters network(former GGP network).For stations at an altitude lower than 1000 m,the value of dopt is always smaller *** discrepancy between the tidal parameters of the M2 and S2 waves is always lower than0.05% on the amplitude factors and 0.025° on the *** these stations,a correlation exists between the altitude and the value *** results at the three Central European stations Conrad,Pecny and Vienna are

关键词： Atmospheric pressure waves Atmospheric pressure correction in tidal records Atmospheric pressure models ERA5 and MERRA-2

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A Fresh Look at the Structures of Nylons and the Brill Transition

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Advanced Fiber Materials 2021年第4期3卷 203-209页

作者： bernard Lotz Institut Charles Sadron CNRS and Universitéde Strasbourg23Rue du Loess67034 StrasbourgFrance

The common knowledge of the crystal structures of nylons dates back to the early 1950s with the work of Bunn and *** describes the packing of sheets made of hydrogen-bonded stems in an extended chain *** alpha phase structures have a specific powder X-ray diffraction pattern with reflections at 4.4Åand 3.7Å.On heating,reflections trans-form progressively and merge at≈4.2Åat the so-called“Brill transition”.Other diffraction patterns have been recorded for different types of nylons and thermal *** patterns were interpreted only as indicating the existence of“variants”of the alpha ***,neither their structure,nor the origin of the Brill transition were *** structural analyses and molecular modeling approaches have provided new insights in these long-standing structural ***“variants”feature chain conformations that are“pleated”.The Brill transition does not involve the standard extended chains of the alpha phase but corresponds to a dynamic interconversion(≈10^(10)/s)between mirror conformations of these pleated stems.

关键词： Nylons Crystal structures Phase transitions Brill transition

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After Sendai:Is Africa Bouncing Back or Bouncing Forward from Disasters?

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International Journal of Disaster Risk Science 2016年第1期7卷 41-53页

作者： bernard Manyena International Disaster Management Humanitarian and Conflict Response Institute University of Manchester

The 187 countries that adopted the Sendai Framework for Disaster Risk Reduction 2015–2030 at the March 2015 UN World Conference on Disaster Risk Reduction included most African countries. Many developing regions of the world, particularly in Asia and Latin America, made considerable progress in implementing the previous Hyogo Framework for Action 2005–2015. But,despite the fact that Africa is one of the regions most vulnerable and least resilient to disasters, which continue to be exacerbated by poverty, climate change, rapid urbanization, and structural transformation, it saw only slow progress. This article considers the challenges Africa faces in implementing the Sendai Framework and recommends that besides ‘‘Africanizing'' Sendai goals and strengthening the region's political commitment to disaster risk reduction(DRR), Africa should also develop a single framework that integrates DRR, sustainable development, climate change adaptation, and conflict prevention. Equally important is the need for a strong recognition that disasters are created endogenously as well as exogenously, and thus require local solutions and local investment.

关键词： Sub-Saharan Africa Climate change adaptation Disaster risk reduction Resilience Sendai framework Sustainable development

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