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| 1 | 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 |
| 2 | 过去10年(2007-2017年)新蚊虫相关病毒的发现和全球分布显示文摘在过去的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。 | 吕新军(编译) Evans Atoni Lu Zhao Samuel Karungu Vincent Obanda Bernard Agwanda Han Xia Zhiming Yuan | 2019 | 中华实验和临床病毒学杂志2019，33，4： | 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 | Discovery of novel DNA viruses in small mammals from Kenya显示文摘Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority.Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses.Many surveillance programs focused more on RNA viruses.In comparison,much less is known about DNA viruses harbored by these small mammals.To 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 PCR.Diverse DNA sequences of adenoviruses,adeno-associated viruses,herpesviruses and polyomaviruses were detected.Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters.Furthermore,this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species.This 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 Betapolyomavirus.Our 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 reservoirs.It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa. | Griphin Ochieng Ochola Bei Li Vincent Obanda Sheila Ommeh Harold Ochieng Xing-Lou Yang Samson Omondi Onyuok Zheng-Li Shi Bernard Agwanda Ben Hu | 2022 | Virologica Sinica2022，37，4： | 0 |
| 5 | Correction to: Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses显示文摘 | Cecilia Waruhiu Sheila Ommeh Vincent Obanda Bernard Agwandas Francis Gakuya Xing-Yi Ge Xing-Lou Yang Li-Jun Wu Ali Zohailb Ben Hu Zheng-Li Shi | 2018 | Virologica Sinica2018，33，3： | 0 |
| 6 | Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation显示文摘Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We 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 kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our 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. | 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 | 2021 | Zoological Research2021，42，4： | 0 |
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