Bats are the natural reservoir hosts for SARS-related coronavirus(SARSr-CoV)and other highly pathogenic microorganisms.Therefore,it is conceivable that an individual bat may harbor multiple microbes.However,there is l...Bats are the natural reservoir hosts for SARS-related coronavirus(SARSr-CoV)and other highly pathogenic microorganisms.Therefore,it is conceivable that an individual bat may harbor multiple microbes.However,there is limited knowledge on the overall co-circulation of microorganisms in bats.Here,we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts.Among these,76 individual samples were selected for further metagenomics analysis.We found a complex microenvironment characterized by the general cocirculation of microbes from two different sources:mammal-associated viruses or environment-associated microbes.The later includes commensal bacteria,enterobacteria-related phages,and insect or fungal viruses of food origin.Results showed that 25%(19/76)of the samples contained at least one another mammal-associated virus,notably alphacoronaviruses(13/76)such as AlphaCoV/YN2012,HKU2-related CoV and AlphaCoV/Rf-HuB2013,along with viruses from other families.Notably,we observed three viruses co-circulating within a single bat,comprising two coronavirus species and one picornavirus.Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats.Furthermore,we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples,some of which formed new evolutionary lineages.Collectively,our study reveals the complex microenvironment of bat microbiome,facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.展开更多
The family Hepeviridae has seen an explosive expansion in its host range in recent years,yet the evolutionary trajectory of this zoonotic pathogen remains largely unknown.The emergence of rat hepatitis E virus(HEV)has...The family Hepeviridae has seen an explosive expansion in its host range in recent years,yet the evolutionary trajectory of this zoonotic pathogen remains largely unknown.The emergence of rat hepatitis E virus(HEV)has introduced a new public health threat due to its potential for zoonotic transmission.This study investigated2?464 wild small mammals spanning four animal orders,eight families,21 genera,and 37 species in Yunnan Province,China.Using broadly reactive reverse transcription-polymerase chain reaction(RT-PCR),we systematically screened the presence and prevalence of Orthohepevirus and identified 192 positive specimens from10 species,corresponding to an overall detection rate of7.79%.Next-generation sequencing enabled the recovery of 24 full-length genomic sequences from eight host species,including Bandicota bengalensis,Eothenomys eleusis,and Episoriculus caudatus,representing newly reported host species for Orthohepevirus strains.Phylogenetic and sequence analyses revealed extensive genetic diversity within orthohepeviruses infecting rodents and shrews.Notably,among the identified strains,20 were classified as Rocahepevirus ratti C1,two as C3,and one as Rocahepevirus eothenomi,while the remaining strain exhibited significant divergence,precluding classification.Evolutionary analyses highlighted close associations between orthohepeviruses and their respective host taxa,with distinct phylogenetic clustering patterns observed across different host orders.These findings emphasize the critical roles of co-speciation and cross-species transmission in shaping the evolutionary trajectories of the genera Paslahepevirus and Rocahepevirus.展开更多
The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China...The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-Co V-2 epidemics in several large cities or provinces of China. However,information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-Co V-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-Co V-2 transmission profiles. Genomic epidemiology revealed multiple SARS-Co V-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size.Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-Co V-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-Co V-2 strains during the early COVID-19 epidemic in China.展开更多
Dear Editor,The ongoing COVID-19 disease,caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),has led to over 112 million confirmed cases and 2.4 million deaths in more than 220 countries as of 25 Fe...Dear Editor,The ongoing COVID-19 disease,caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),has led to over 112 million confirmed cases and 2.4 million deaths in more than 220 countries as of 25 February 2021(WHO 2021).Hospital-admitted patients show clinical features including fever,dry cough,fatigue,dyspnea,lymphopenia,and pneumonia with radiological groundglass lung opacities(Huang et al.2020;Guan et al.2020).SARS-Co V-2 was quickly isolated and could be detected in clinical samples,such as nasopharyngeal swabs,sputum,alveolar lavage fluid,and feces,as well as occasionally in seminal fluid and tears among other sources(Bhat et al.2020;Li et al.2020),which means that it can infect a variety of human tissues and organs.展开更多
基金supported by the National Key R&D Program of China(2021YFC2300901 to P.Z.)China Natural Science Foundation for outstanding scholars(82325032 to P.Z.)+1 种基金the Self-Supporting Program of Guangzhou Laboratory(SRPG22-001 to P.Z.GZNL2023A01001 to ZLS).
文摘Bats are the natural reservoir hosts for SARS-related coronavirus(SARSr-CoV)and other highly pathogenic microorganisms.Therefore,it is conceivable that an individual bat may harbor multiple microbes.However,there is limited knowledge on the overall co-circulation of microorganisms in bats.Here,we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts.Among these,76 individual samples were selected for further metagenomics analysis.We found a complex microenvironment characterized by the general cocirculation of microbes from two different sources:mammal-associated viruses or environment-associated microbes.The later includes commensal bacteria,enterobacteria-related phages,and insect or fungal viruses of food origin.Results showed that 25%(19/76)of the samples contained at least one another mammal-associated virus,notably alphacoronaviruses(13/76)such as AlphaCoV/YN2012,HKU2-related CoV and AlphaCoV/Rf-HuB2013,along with viruses from other families.Notably,we observed three viruses co-circulating within a single bat,comprising two coronavirus species and one picornavirus.Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats.Furthermore,we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples,some of which formed new evolutionary lineages.Collectively,our study reveals the complex microenvironment of bat microbiome,facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.
基金supported by the National Natural Science Foundation of China (U2002218,81874274)Yunnan Health Training Project of High Level Talents (L-2017027)+3 种基金Project of Cross-border Control and Quarantine Innovation Group of Zoonosis of Dali University (ZKPY2019302)to Y.Z.ZOpen Project of Yunnan Key Laboratory of Biodiversity Information (BIKF22-02)Youth Innovation Promotion Association of the Chinese Academy of SciencesYunnan Revitalization Talent Support Program Young Talent Project to X.L.Y。
文摘The family Hepeviridae has seen an explosive expansion in its host range in recent years,yet the evolutionary trajectory of this zoonotic pathogen remains largely unknown.The emergence of rat hepatitis E virus(HEV)has introduced a new public health threat due to its potential for zoonotic transmission.This study investigated2?464 wild small mammals spanning four animal orders,eight families,21 genera,and 37 species in Yunnan Province,China.Using broadly reactive reverse transcription-polymerase chain reaction(RT-PCR),we systematically screened the presence and prevalence of Orthohepevirus and identified 192 positive specimens from10 species,corresponding to an overall detection rate of7.79%.Next-generation sequencing enabled the recovery of 24 full-length genomic sequences from eight host species,including Bandicota bengalensis,Eothenomys eleusis,and Episoriculus caudatus,representing newly reported host species for Orthohepevirus strains.Phylogenetic and sequence analyses revealed extensive genetic diversity within orthohepeviruses infecting rodents and shrews.Notably,among the identified strains,20 were classified as Rocahepevirus ratti C1,two as C3,and one as Rocahepevirus eothenomi,while the remaining strain exhibited significant divergence,precluding classification.Evolutionary analyses highlighted close associations between orthohepeviruses and their respective host taxa,with distinct phylogenetic clustering patterns observed across different host orders.These findings emphasize the critical roles of co-speciation and cross-species transmission in shaping the evolutionary trajectories of the genera Paslahepevirus and Rocahepevirus.
基金supported by the China National Science Foundation (Excellent Scholar Grants 81822028 and 82041013 to P.Z.)Ministry of Science and Technology of China (grant 2020YFC0840900 to P.Z.)Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDB29010101 to Z.-L. S.)。
文摘The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-Co V-2 epidemics in several large cities or provinces of China. However,information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-Co V-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-Co V-2 transmission profiles. Genomic epidemiology revealed multiple SARS-Co V-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size.Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-Co V-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-Co V-2 strains during the early COVID-19 epidemic in China.
基金supported by the China Natural Science Foundation(32070180 to X.-L.Y.,31770175 to Z.-L.S.)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB29010101 to Z.-L.S.)a Youth innovation promotion association of CAS(2019328 to X.-L.Y.)。
文摘Dear Editor,The ongoing COVID-19 disease,caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2),has led to over 112 million confirmed cases and 2.4 million deaths in more than 220 countries as of 25 February 2021(WHO 2021).Hospital-admitted patients show clinical features including fever,dry cough,fatigue,dyspnea,lymphopenia,and pneumonia with radiological groundglass lung opacities(Huang et al.2020;Guan et al.2020).SARS-Co V-2 was quickly isolated and could be detected in clinical samples,such as nasopharyngeal swabs,sputum,alveolar lavage fluid,and feces,as well as occasionally in seminal fluid and tears among other sources(Bhat et al.2020;Li et al.2020),which means that it can infect a variety of human tissues and organs.
