Influenza A virus(IAV)shows an extensive host range and rapid genomic variations,leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species transmission....Influenza A virus(IAV)shows an extensive host range and rapid genomic variations,leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species transmission.This causes global pandemics and seasonal flu outbreaks,posing sustained threats worldwide.Thus,studying all IAVs'evolutionary patterns and underlying mechanisms is crucial for effective prevention and control.We developed FluTyping to identify IAV genotypes,to explore overall genetic diversity patterns and their restriction factors.FluTyping groups isolates based on genetic distance and phylogenetic relationships using whole genomes,enabling identification of each isolate's genotype.Three distinct genetic diversity patterns were observed:one genotype domination pattern comprising only H1N1 and H3N2 seasonal influenza subtypes,multi-genotypes cocirculation pattern including majority avian influenza subtypes and swine influenza H1N2,and hybrid-circulation pattern involving H7N9 and three H5 subtypes of influenza viruses.Furthermore,the IAVs in multi-genotypes cocirculation pattern showed region-specific dominant genotypes,implying the restriction of virus transmission is a key factor contributing to distinct genetic diversity patterns,and the genomic evolution underlying different patterns was more influenced by host-specific factors.In summary,a comprehensive picture of the evolutionary patterns of overall IAVs is provided by the FluTyping's identified genotypes,offering important theoretical foundations for future prevention and control of these viruses.展开更多
Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth.Understanding the distribution pattern of genetic diversity and its driving forces has been an import...Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth.Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology,biogeography and conservation biology since the last decade.We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China,a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia,and explored the influencing forces of environmental variables on genetic diversity.We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites,covering the range of Mountains of Southwest China and its adjoining areas.We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices.We further analyzed the variation pattern of the two indices along latitudinal,longitudinal,and elevational gradients.The correlations between the two indices and environmental variables were also evaluated.The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains,while for haplotype diversity,three hotspots were detected:the southeast edge of the Qinghai-Tibetan Plateau,the southern Hengduan Mountains and the Qinling Mountains.There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal,longitudinal or elevational gradients except for altitudinal range.Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns,including temperature,precipitation,vegetation,human influence,longitude and altitude range.Similar to the pattern of species richness,the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast,while the haplotype diversity pattern is more likely decreased from west to east.Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.展开更多
Introduction:This study aimed to characterize the genetic diversity and antimicrobial resistance patterns of Campylobacter isolates collected throughout China from 2020 to 2023.Methods:Campylobacter isolates analyzed ...Introduction:This study aimed to characterize the genetic diversity and antimicrobial resistance patterns of Campylobacter isolates collected throughout China from 2020 to 2023.Methods:Campylobacter isolates analyzed in this study were obtained from the National Pathogen Identification Network Center database,maintained by the National Institute for Infectious Disease Control and Prevention of the Chinese Center for Disease Control and Prevention.Antimicrobial susceptibility testing(AST)was performedagainsteleven antimicrobial agents.Genomic characteristics were analyzed through comprehensive genome sequence analysis.Results:Between 2020 and 2023,the National Pathogen Identification Network documented 1,077 Campylobacter jejuni(C.jejuni)and 221 Campylobacter coli(C.coli)isolates.Most isolates originated from patients presenting with diarrhea.Antimicrobial susceptibility testing was conducted on 634 C.jejuni and165C.coli isolates.The tested isolates demonstrated high resistance rates to nalidixic acid(78.22%),ciprofloxacin(78.07%),and tetracycline(71.96%).Longitudinal analysis of antimicrobial susceptibility testing results revealed a declining resistance trend from 2020 to 2023.Whole genome sequences were obtained for 540 C.jejuni and 125 C.coli isolates within the database.Virulence factors and antibiotic resistance determinants were identified using the VFDB and CARD databases,respectively.Phylogenetic relationships were established through Snippy 4.0 software analysis based on core genome comparisons.Conclusions:This comprehensive analysis.describes the antibiotic resistance profiles and genetic characteristics of Campylobacter isolates collected through the Identification Network Database from 2020 to 2023,establishing a foundational framework for campylobacteriosis control and prevention strategies in China.展开更多
Biotic invasions have a reputation for unpredictable behavior.Here,we report how slight changes in human activity responsible for the introduction and range expansion of a non-native mollusk have led to detectable dif...Biotic invasions have a reputation for unpredictable behavior.Here,we report how slight changes in human activity responsible for the introduction and range expansion of a non-native mollusk have led to detectable differences in the genetics of the invasion.Cyclope neritea is a non-predatory gastropod introduced to 2 areas of the European Atlantic:the northwest Iberian Peninsula(NWIP)and the French Atlantic coast(FAC).Shellfish seabed farming is intense in both areas but focuses on different commercial species.Using mitochondrial gene sequences,the lower genetic diversity recorded along the NWIP suggests a more homogeneous range of source populations than in the FAC.Unlike FAC,genetic diversity and haplotype composition in the NWIP correlate with the date of first occurrence of C.neritea at each site rather than with geographical location.Although this pattern evokes the genetic signature expected under a serial-founder colonization model from a single initial enclave,a comparison with samples from potential source populations suggests that the NWIP probably experienced several independent reintroductions.The jump dispersal pattern of C.neritea in the NWIP,together with the observation that populations established in the same year are genetically undifferentiated,point to human transport as the most plausible explanation for the current range expansion.Despite evidence for human-mediated dispersal,C.neritea managed to develop a seemingly non-random genetic pattern in the NWIP.It is suggested that caution must be exerted when interpreting genetic patterns in invaders.展开更多
基金supported by the National Key Plan for Scientific Research and Development of China(2021YFC2301305 and 2021YFC2302001)the National Natural Science Foundation of China(32370703,92169106,9216910042 and 32070678)+2 种基金the CAMS Innovation Fund for Medical Science(2022-I2M-1-021,2021-I2M-1-051)the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(2021-PT180-001)the Emergency Key Program of Guangzhou Laboratory(grant EKPG21-12).
文摘Influenza A virus(IAV)shows an extensive host range and rapid genomic variations,leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species transmission.This causes global pandemics and seasonal flu outbreaks,posing sustained threats worldwide.Thus,studying all IAVs'evolutionary patterns and underlying mechanisms is crucial for effective prevention and control.We developed FluTyping to identify IAV genotypes,to explore overall genetic diversity patterns and their restriction factors.FluTyping groups isolates based on genetic distance and phylogenetic relationships using whole genomes,enabling identification of each isolate's genotype.Three distinct genetic diversity patterns were observed:one genotype domination pattern comprising only H1N1 and H3N2 seasonal influenza subtypes,multi-genotypes cocirculation pattern including majority avian influenza subtypes and swine influenza H1N2,and hybrid-circulation pattern involving H7N9 and three H5 subtypes of influenza viruses.Furthermore,the IAVs in multi-genotypes cocirculation pattern showed region-specific dominant genotypes,implying the restriction of virus transmission is a key factor contributing to distinct genetic diversity patterns,and the genomic evolution underlying different patterns was more influenced by host-specific factors.In summary,a comprehensive picture of the evolutionary patterns of overall IAVs is provided by the FluTyping's identified genotypes,offering important theoretical foundations for future prevention and control of these viruses.
基金National Natural Science Foundation of China(3213000355,32070434,and 31900320)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA19050202)the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0304,2019QZKK0501)。
文摘Genetic diversity is one of the three dimensions of biodiversity and fundamental to various life forms on the Earth.Understanding the distribution pattern of genetic diversity and its driving forces has been an important topic in ecology,biogeography and conservation biology since the last decade.We investigated the genetic diversity pattern of passerine birds in the Mountains of Southwest China,a global biodiversity hotspot with the highest species richness of birds in the entire Eurasia,and explored the influencing forces of environmental variables on genetic diversity.We compiled 1189 Cytochrome b sequences of 27 passerine species from 152 geographic sites,covering the range of Mountains of Southwest China and its adjoining areas.We generated genetic diversity distribution maps using a grid-cell method based on nucleotide diversity and haplotype diversity indices.We further analyzed the variation pattern of the two indices along latitudinal,longitudinal,and elevational gradients.The correlations between the two indices and environmental variables were also evaluated.The nucleotide diversity hotspots were mostly located in the southern Hengduan Mountains,while for haplotype diversity,three hotspots were detected:the southeast edge of the Qinghai-Tibetan Plateau,the southern Hengduan Mountains and the Qinling Mountains.There was no monotonic increasing or decreasing pattern in nucleotide diversity or haplotype diversity along latitudinal,longitudinal or elevational gradients except for altitudinal range.Correlation and model selection analyses detected multiple environmental variables in driving genetic diversity patterns,including temperature,precipitation,vegetation,human influence,longitude and altitude range.Similar to the pattern of species richness,the nucleotide diversity pattern of passerine birds in the Mountains of Southwest China presents a decreasing trend from southwest to northeast,while the haplotype diversity pattern is more likely decreased from west to east.Our results indicate that the distribution pattern of genetic diversity may be derived from the complex topography and diverse microclimates in the Mountains of Southwest China.
基金Supported by the National Key Research and Development Program of China(Grant Number 2021YFC2301000)the Capital's Funds for Health Improvement and Research(No.2024-2G-7106).
文摘Introduction:This study aimed to characterize the genetic diversity and antimicrobial resistance patterns of Campylobacter isolates collected throughout China from 2020 to 2023.Methods:Campylobacter isolates analyzed in this study were obtained from the National Pathogen Identification Network Center database,maintained by the National Institute for Infectious Disease Control and Prevention of the Chinese Center for Disease Control and Prevention.Antimicrobial susceptibility testing(AST)was performedagainsteleven antimicrobial agents.Genomic characteristics were analyzed through comprehensive genome sequence analysis.Results:Between 2020 and 2023,the National Pathogen Identification Network documented 1,077 Campylobacter jejuni(C.jejuni)and 221 Campylobacter coli(C.coli)isolates.Most isolates originated from patients presenting with diarrhea.Antimicrobial susceptibility testing was conducted on 634 C.jejuni and165C.coli isolates.The tested isolates demonstrated high resistance rates to nalidixic acid(78.22%),ciprofloxacin(78.07%),and tetracycline(71.96%).Longitudinal analysis of antimicrobial susceptibility testing results revealed a declining resistance trend from 2020 to 2023.Whole genome sequences were obtained for 540 C.jejuni and 125 C.coli isolates within the database.Virulence factors and antibiotic resistance determinants were identified using the VFDB and CARD databases,respectively.Phylogenetic relationships were established through Snippy 4.0 software analysis based on core genome comparisons.Conclusions:This comprehensive analysis.describes the antibiotic resistance profiles and genetic characteristics of Campylobacter isolates collected through the Identification Network Database from 2020 to 2023,establishing a foundational framework for campylobacteriosis control and prevention strategies in China.
基金provided by the Spanish Ministerio de Educación y Ciencia grant CTM2004-04496/MAR(partially co-founded by Fondo Europeo de Desarrollo Regional)the Xunta de Galicia grant PGIDT05PXIC10302PN.
文摘Biotic invasions have a reputation for unpredictable behavior.Here,we report how slight changes in human activity responsible for the introduction and range expansion of a non-native mollusk have led to detectable differences in the genetics of the invasion.Cyclope neritea is a non-predatory gastropod introduced to 2 areas of the European Atlantic:the northwest Iberian Peninsula(NWIP)and the French Atlantic coast(FAC).Shellfish seabed farming is intense in both areas but focuses on different commercial species.Using mitochondrial gene sequences,the lower genetic diversity recorded along the NWIP suggests a more homogeneous range of source populations than in the FAC.Unlike FAC,genetic diversity and haplotype composition in the NWIP correlate with the date of first occurrence of C.neritea at each site rather than with geographical location.Although this pattern evokes the genetic signature expected under a serial-founder colonization model from a single initial enclave,a comparison with samples from potential source populations suggests that the NWIP probably experienced several independent reintroductions.The jump dispersal pattern of C.neritea in the NWIP,together with the observation that populations established in the same year are genetically undifferentiated,point to human transport as the most plausible explanation for the current range expansion.Despite evidence for human-mediated dispersal,C.neritea managed to develop a seemingly non-random genetic pattern in the NWIP.It is suggested that caution must be exerted when interpreting genetic patterns in invaders.
