Avian H9N2 viruses have wide host range among the influenza A viruses.However,knowledge of H9N2 mammalian adaptation is limited.To explore the molecular basis of the adaptation to mammals,we performed serial lung pass...Avian H9N2 viruses have wide host range among the influenza A viruses.However,knowledge of H9N2 mammalian adaptation is limited.To explore the molecular basis of the adaptation to mammals,we performed serial lung passaging of the H9N2 strain A/chicken/Hunan/8.27 YYGK3W3-OC/2018(3W3)in mice and identified six mutations in the hemagglutinin(HA)and polymerase acidic(PA)proteins.Mutations L226Q,T511I,and A528V of HA were responsible for enhanced pathogenicity and viral replication in mice;notably,HA-L226Q was the key determinant.Mutations T97I,I545V,and S594G of PA contributed to enhanced polymerase activity in mammalian cells and increased viral replication levels in vitro and in vivo.PA-T97I increased viral polymerase activity by accelerating the viral polymerase complex assembly.Our findings revealed that the viral replication was affected by the presence of PA-97I and/or PA-545V in combination with a triple-point HA mutation.Furthermore,the double-and triple-point PA mutations demonstrated antagonistic effect on viral replication when combined with HA-226Q.Notably,any combination of PA mutations,along with double-point HA mutations,resulted in antagonistic effect on viral replication.We also observed antagonism in viral replication between PA-545V and PA-97I,as well as between HA-528V and PA-545V.Our findings demonstrated that several antagonistic mutations in HA and PA proteins affect viral replication,which may contribute to the H9N2 virus adaptation to mice and mammalian cells.These findings can potentially contribute to the monitoring of H9N2 field strains for assessing their potential risk in mammals.展开更多
Identifying the cause of respiratory tract infections is important for reducing the burden of diagnosis and treatment.To assess viral etiologies of hospitalized patients with pulmonary infection,bronchoalveolar lavage...Identifying the cause of respiratory tract infections is important for reducing the burden of diagnosis and treatment.To assess viral etiologies of hospitalized patients with pulmonary infection,bronchoalveolar lavage fluid(BALF)specimens were collected from non-COVID-19 adult patients(n=333,including patients with lower respiratory tract infection,tuberculosis,lung cancer,and pulmonary nodules)between November 2020 and November 2021.Multiple common respiratory pathogens were detected using multiplex reverse-transcription polymerase chain reaction.The result showed that at least one virus was identified in 35.44%(118/333)of the cases.Among these,influenza virus was the most commonly identified,followed by the parainfluenza virus,coronavirus,human rhinoviruses,and human respiratory syncytial viruses.The tuberculosis group demonstrated the highest viral detection rate,yet paradoxically exhibited the lowest co-infection rate.In contrast,the highest co-infection frequency was observed in the pulmonary nodules group.Patients with viral infections exhibited more severe clinical symptoms compared to those without detected viral infections.However,this observation was only noted in the lower respiratory tract infection group among the different disease groups.Notably,among patients infected with a specific virus,there were no significant differences in viral load between single and co-infections.Our study identified the major causative agents in hospitalized adult patients with pulmonary infection,offering insights for precise disease diagnosis and the prevention of unnecessary use of antimicrobial drugs.展开更多
Highlights The RT-RAA-VF assay developed for the NiV P gene can perform rapid detection of NiV within 20 min at 42℃ with high specificity.This assay is capable of attaining sensitivity to a single copy of NiV RNA tra...Highlights The RT-RAA-VF assay developed for the NiV P gene can perform rapid detection of NiV within 20 min at 42℃ with high specificity.This assay is capable of attaining sensitivity to a single copy of NiV RNA transcripts.This assay effectively avoids false positives caused by aerosol contamination with a sealed disposable nucleic acid visualization test paper device.展开更多
Coxsackievirus A16(CA16) is one of the major causes of hand, foot, and mouth disease(HFMD) worldwide, which is a common illness that affects children. The frequent occurrence of HFMD outbreaks has become a serious pub...Coxsackievirus A16(CA16) is one of the major causes of hand, foot, and mouth disease(HFMD) worldwide, which is a common illness that affects children. The frequent occurrence of HFMD outbreaks has become a serious public health problem in Asia. Therefore, it is important to understand the pathogenesis and replication of CA16. In this study, a stable infectious c DNA clone of an epidemic strain of Coxsackievirus A16(CA16) was assembled, and subsequently a reporter virus(e GFP-CA16) was constructed by inserting the e GFP gene between the 5'-UTR and the N-terminus of VP4, with the addition of a 2A protease cleavage site(ITTLG) at its C-terminus. This was transfected into Vero cells to generate infectious recombinant viruses. The growth characteristics and plaque morphology, in vitro, in mammalian cells were found to be indistinguishable between the parental and recombinant viruses. Although the e GFP-CA16 showed smaller plaque size as compared to recombinant CA16, both were found to exhibit similar growth trends and EC50 of NITD008. In summary, this stable infectious c DNA clone should provide a valuable experimental system to study CA16 infection and host response. The e GFP-CA16 is expected to provide a powerful tool to monitor e GFP expression in infected cells and to evaluate the antiviral activity of potential antiviral agents in the treatment of CA16 infections.展开更多
Enteroviruses(EVs)species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand,foot and mouth disease(HFMD)in China.Mild infections are common in children;however,HFMD can...Enteroviruses(EVs)species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand,foot and mouth disease(HFMD)in China.Mild infections are common in children;however,HFMD can also cause severe illness that affects the central nervous system.To molecularly characterize EVs,a prospective HFMD virological surveillance program was performed in China between 2013 and 2016.Throat swabs,rectal swabs and stool samples were collected from suspected HFMD patients at participating hospitals.EVs were detected using generic real-time and nested reverse transcription-polymerase chain reactions(RT-PCRs).Then,the complete VP1 regions of enterovirus A71(EV-A71),coxsackievirus A16(CVA16)and CVA6 were sequenced to analyze amino acid changes and construct a viral molecular phylogeny.Of the 2836 enrolled HFMD patients,2,517(89%)were EV positive.The most frequently detected EVs were CVA16(32.5%,819),CVA6(31.2%,785),and EV-A71(20.4%,514).The subgenogroups CVA16B1 b,CVA6D3 a and EV-A71C4 a were predominant in China and recombination was not observed in the VP1 region.Sequence analysis revealed amino acid variations at the 30,29 and 44 positions in the VP1 region of EV-A71,CVA16 and CVA6(compared to the respective prototype strains Br Cr,G10 and Gdula),respectively.Furthermore,in 21 of 24(87.5%)identified EV-A71 samples,a known amino acid substitution(D31 N)that may enhance neurovirulence was detected.Our study provides insights about the genetic characteristics of common HFMD-associated EVs.However,the emergence and virulence of the described mutations require further investigation.展开更多
As a respiratory tract virus,SARS-CoV-2 infected people through contacting with the upper respiratory tract first.Previous studies indicated that microbiota could modulate immune response against pathogen infection.In...As a respiratory tract virus,SARS-CoV-2 infected people through contacting with the upper respiratory tract first.Previous studies indicated that microbiota could modulate immune response against pathogen infection.In the present study,we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough.Through metagenomic analysis of the above two groups and a healthy group from the public data,there are 6502 species identified in the samples.Specifically,the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group.Combined with the linear discriminant analysis(LDA)and the generalized linear model,eighty-one bacterial species were found with increased abundance in the COVID-19 group,where 51 species were enriched more than 8 folds.The top three enriched genera were Streptococcus,Prevotella and Campylobacter containing some opportunistic pathogens.More interestingly,through experiments,we found that two Streptococcus strains,S.suis and S.agalactiae,could stimulate the expression of ACE2 of Vero cells in vitro,which may promote SARS-CoV-2 infection.Therefore,these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host’s immune system.展开更多
Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bod...Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.展开更多
Ebola virus(EBOV) belongs to the Filoviridae family and causes severe illnesses such as hemorrhagic fever with a high mortality rate up to 90%. Now two antibody drugs termed Inmazeb and Ebanga have been approved for t...Ebola virus(EBOV) belongs to the Filoviridae family and causes severe illnesses such as hemorrhagic fever with a high mortality rate up to 90%. Now two antibody drugs termed Inmazeb and Ebanga have been approved for treating EBOV infection. However, clinical studies have demonstrated that the mortality rate of the patients who received these two antibody drugs remains above 30%. Therefore, novel therapeutics with better efficacy is still desired. The isolated human IgG1 constant domain 2(CH2 domain) has been proposed as a scaffold for the development of C-based single domain antibodies(C-sd Abs) as therapeutic candidates against viral infections and other diseases. Here, we screened and identified a novel C-sd Ab termed M24 that targets EBOV glycoprotein(GP) from a C-sd Ab phage display library. M24 neutralizes the pseudotype EBOV with IC;of 0.8 nmol/L(12 ng/mL) and has modest neutralizing activity against authentic EBOV.Epitope determination, including molecular docking and site mutation analysis, discloses that M24 binds to the internal fusion loop(IFL) within GP2, a transmembrane subunit of GP. Interestingly, we found that the binding of M24 to GP at pH5.5 has dramatically decreased compared to the binding at pH 7.5, which may lead to weak efficacy in the neutralization of authentic EBOV. Since no sd Ab against EBOV infection has been reported to date, our results not only give a proof of concept that sd Abs could be utilized for the development of potential therapeutic candidates against EBOV infection, but also provide useful information for the discovery and improvement of anti-EBOV agents.展开更多
The authors are retracting this paper owing to errors in the reported data.The paper claimed that 16 patient cases were infected with H9N2 virus.However,when the authors recently further investigated all the thirteen ...The authors are retracting this paper owing to errors in the reported data.The paper claimed that 16 patient cases were infected with H9N2 virus.However,when the authors recently further investigated all the thirteen sera samples,no anti-H9N2 antibodies were found by the haemagglutination inhibition assay.Moreover,re-sequencing of the remaining five throat swabs showed all five samples were H1N1 virus.展开更多
Dear Editor,Zika virus（ZIKV）is a mosquito-borne flavivirus that usually causes asymptomatic infections or mild illness in humans.However,the unprecedented epidemics of ZIKV in Latin America since early 2015 have mad...Dear Editor,Zika virus（ZIKV）is a mosquito-borne flavivirus that usually causes asymptomatic infections or mild illness in humans.However,the unprecedented epidemics of ZIKV in Latin America since early 2015 have made this flavivirus an international health risk（Liu and Zhang,2016）.展开更多
Wastewater-based epidemiology(WBE)has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community.Congruently,SARS-Co V-2,the etiologic agent of COVID-19,has...Wastewater-based epidemiology(WBE)has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community.Congruently,SARS-Co V-2,the etiologic agent of COVID-19,has been demonstrated to infect the gastrointestinal tissues,and be shed in feces.In the present study,SARS-Co V-2 RNA was concentrated from wastewater,sludge,surface water,ground water,sediment,and soil samples of municipal and hospital wastewater systems and related environments in Wuhan during the COVID-19 middle and low risk periods,and the viral RNA copies quantified using reverse transcription quantitative polymerase chain reaction(RT-q PCR).From the findings of this study,during the middle risk period,one influent sample and three secondary effluents collected from waste water treatment plant 2,as well as two samples from Jinyintan Hospital wastewater system influent were SARS-Co V-2 RNA positive.One sludge sample collected from Guanggu Branch of Tongji Hospital,which was obtained during the low risk period,was also positive for SARS-Co V-2 RNA.These study findings demonstrate the significance of WBE in continuous surveillance of SARS-Co V-2 at the community level,even when the COVID-19 prevalence is low.Overall,this study can be used as an important reference for contingency management of wastewater treatment plants and COVID-19 prevention and control departments of Wuhan.展开更多
Dear Editor,Bacteriophages are powerful tools for investigating and manipulating their hosts(Fernandes et al.,2014).This holds particularly true for mycobacteriophages,which have facilitated the development of mycobac...Dear Editor,Bacteriophages are powerful tools for investigating and manipulating their hosts(Fernandes et al.,2014).This holds particularly true for mycobacteriophages,which have facilitated the development of mycobacterial genetic systems and have generated tools for the clinical展开更多
Bats are natural reservoir hosts for many viruses that produce no clinical symptoms in bats.Therefore, bats may have evolved effective mechanisms to control viral replication. However, little information is available ...Bats are natural reservoir hosts for many viruses that produce no clinical symptoms in bats.Therefore, bats may have evolved effective mechanisms to control viral replication. However, little information is available on bat immune responses to viral infection. Type I interferon(IFN) plays a key role in controlling viral infections. In this study, we report the cloning, expression, and biological activity of interferon β(IFNβ) from the Chinese microbat species, Myotis davidii. We demonstrated the upregulation of IFNB and IFN-stimulated genes in a kidney cell line derived from M. davidii after treatment with poly I:C or infection with Sendai virus. Furthermore, the recombinant IFNβ inhibited vesicular stomatitis virus and bat adenovirus replication in cell lines from two bat species, M. davidii and Rhinolophus sinicus. We provide the first in vitro evidence of IFNβ antiviral activity in microbats, which has important implications for virus interactions with these hosts.展开更多
Dear Editor,It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August2018, and the epidemic situation remains severe (China News Service 2019). According to repo...Dear Editor,It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019).展开更多
The novel phage lysin PlySs2, is reported to be highly active against various bacteria, including staphylococci, streptococci and Listeria. However, the molecular mechanisms underlying its broad lytic spectrum remain ...The novel phage lysin PlySs2, is reported to be highly active against various bacteria, including staphylococci, streptococci and Listeria. However, the molecular mechanisms underlying its broad lytic spectrum remain to be established. In the present study, the lytic activity of the catalytic domain(CD, PlySc) and binding specificity of the cell wall binding domain(CBD, PlySb) of PlySs2 were examined. Our results showed that PlySc alone maintains very limited lytic activity. Enhanced green fluorescent protein(EGFP)-fused PlySb displayed high binding affinity to the streptococcal strains tested, including S.suis, S.dysgalactiae, and S.agalactiae, but not staphylococci, supporting its utility as a good CBD donor for streptococcal-targeted lysin engineering. EGFP-fused intact PlySs2 similarly displayed high affinity for streptococci, but not staphylococci. Notably, four truncated PlySb fragments showed no binding capacity. These findings collectively indicate that integrity of the PlySc and PlySb domains is an essential determinant of the broad lytic activity of PlySs2.展开更多
China is a vast territory with a wide range of animals and insects that carry complex pathogenic microorganisms.Over the past few years,a rising trend of emerging and virulent infectious diseases has been observed.The...China is a vast territory with a wide range of animals and insects that carry complex pathogenic microorganisms.Over the past few years,a rising trend of emerging and virulent infectious diseases has been observed.The outbreak of SARS in 2003 spread to over 32 regions or countries worldwide,resulting in 8422 people being infected and 919 fatalities.The recent outbreaks and endemic epidemics of hand-foot-and-mouth展开更多
Dear Editor,The avian influenza virus (AIV) H5N7 was first isolated from wild birds in North America in 2001 (Spackman et al.2007), and information on only 25 strains of this virus has been deposited in the Global Ini...Dear Editor,The avian influenza virus (AIV) H5N7 was first isolated from wild birds in North America in 2001 (Spackman et al.2007), and information on only 25 strains of this virus has been deposited in the Global Initiative on Sharing All Influenza Data (GISAID-http://platform.gisaid.org/epi3/frontend#493de3) database until October 30, 2018. Twenty viruses were identified in the United States from 2001 to2017.展开更多
Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously threatened.The coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role i...Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously threatened.The coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19.However,the efficacy is compromised by the SARS-CoV-2 evolvement and mutation.Here we report the SARS-CoV-2 S protein receptor-binding domain(RBD)inhibitor licorice-saponin A3(A3)could widely inhibit RBD of SARS-CoV-2 variants,including Beta,Delta,and Omicron BA.1,XBB and BQ1.1.Furthermore,A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells,with EC50 of 1.016μM.The mechanism was related to binding with Y453 of RBD determined by hydrogen-deuterium exchange mass spectrometry(HDX-MS)analysis combined with quantum mechanics/molecular mechanics(QM/MM)simulations.Interestingly,phosphoproteomics analysis and multi fluorescent immunohistochemistry(mIHC)respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 mitogen-activated protein kinase(MAPK)pathways and rebalancing the corresponding immune dysregulation.This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.展开更多
The chikungunya virus(CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005–2006. Starti...The chikungunya virus(CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005–2006. Starting in the middle of November 2016, CHIKV has been widely spread, and more than 4,000 cases of infections in humans were confirmed in Pakistan. Here, we report the first isolation and characterization of CHIKV from the Pakistan outbreak. Eight CHIKV strains were newly isolated from human serum samples using a cell culture procedure. A full-length genome sequence and eight complete envelope(E1) sequences of CHIKV from Pakistan were obtained in this study. Alignment of the CHIKV E1 sequences revealed that the eight new CHIKV isolates were highly homogeneous, with only two nonsynonymous substitutions found at generally conserved sites(E99 and Q235). Based on the comparison of 342 E1 sequences, the two nonsynonymous mutations were located in well-recognized domains associated with viral functions such as the cell fusion and vector specificity, suggesting their potential functional importance. Phylogenetic analysis indicated that the CHIKV strains from Pakistan originated from CHIKV circulating in the Indian region. This study helps elucidate the epidemics of CHIKV in Pakistan and also provides a foundation for studies of evolution and expansion of CHIKV in South Asia.展开更多
Dear Editor,Omsk hemorrhagic fever virus(OHFV)belongs to the tickborne virus group within Flavivirus,in Flaviviridae family(Holbrook et al.2005)which consists of several important human pathogens including tick-borne ...Dear Editor,Omsk hemorrhagic fever virus(OHFV)belongs to the tickborne virus group within Flavivirus,in Flaviviridae family(Holbrook et al.2005)which consists of several important human pathogens including tick-borne encephalitis virus(TBEV),Powassan virus(POWV),Louping ill virus(LIV),Langat virus(LGTV)and Kyasnaur Forest disease virus(KFDV)(Yoshii and Holbrook 2009).OHFV is an enveloped virus containing a single-stranded positive-sense RNA genome of approximately 11,000 nucleotides.The genome has a single open reading frame,which encodes three structural proteins[capsid(C),pre-membrane(prM)or membrane(M),and envelop(E)]and seven non-structural proteins(NS1,NS2a,NS2b,NS3,NS4a,NS4b and NS5)between the 5'untranslated region(UTR)and 3'UTR(Chambers et al.1990).展开更多
基金supported by the National Key Research and Development Program of China(NKPs)(2022YFC2604101)the National Science and Technology Major Project of China(2020ZX10001016-002)。
文摘Avian H9N2 viruses have wide host range among the influenza A viruses.However,knowledge of H9N2 mammalian adaptation is limited.To explore the molecular basis of the adaptation to mammals,we performed serial lung passaging of the H9N2 strain A/chicken/Hunan/8.27 YYGK3W3-OC/2018(3W3)in mice and identified six mutations in the hemagglutinin(HA)and polymerase acidic(PA)proteins.Mutations L226Q,T511I,and A528V of HA were responsible for enhanced pathogenicity and viral replication in mice;notably,HA-L226Q was the key determinant.Mutations T97I,I545V,and S594G of PA contributed to enhanced polymerase activity in mammalian cells and increased viral replication levels in vitro and in vivo.PA-T97I increased viral polymerase activity by accelerating the viral polymerase complex assembly.Our findings revealed that the viral replication was affected by the presence of PA-97I and/or PA-545V in combination with a triple-point HA mutation.Furthermore,the double-and triple-point PA mutations demonstrated antagonistic effect on viral replication when combined with HA-226Q.Notably,any combination of PA mutations,along with double-point HA mutations,resulted in antagonistic effect on viral replication.We also observed antagonism in viral replication between PA-545V and PA-97I,as well as between HA-528V and PA-545V.Our findings demonstrated that several antagonistic mutations in HA and PA proteins affect viral replication,which may contribute to the H9N2 virus adaptation to mice and mammalian cells.These findings can potentially contribute to the monitoring of H9N2 field strains for assessing their potential risk in mammals.
基金supported by The National Natural Science Foundation of China(82370008,32470169)National Key R&D Program of China(2023YFC260550)Major Project of Guangzhou National Laboratory(GZNL2023A01001).
文摘Identifying the cause of respiratory tract infections is important for reducing the burden of diagnosis and treatment.To assess viral etiologies of hospitalized patients with pulmonary infection,bronchoalveolar lavage fluid(BALF)specimens were collected from non-COVID-19 adult patients(n=333,including patients with lower respiratory tract infection,tuberculosis,lung cancer,and pulmonary nodules)between November 2020 and November 2021.Multiple common respiratory pathogens were detected using multiplex reverse-transcription polymerase chain reaction.The result showed that at least one virus was identified in 35.44%(118/333)of the cases.Among these,influenza virus was the most commonly identified,followed by the parainfluenza virus,coronavirus,human rhinoviruses,and human respiratory syncytial viruses.The tuberculosis group demonstrated the highest viral detection rate,yet paradoxically exhibited the lowest co-infection rate.In contrast,the highest co-infection frequency was observed in the pulmonary nodules group.Patients with viral infections exhibited more severe clinical symptoms compared to those without detected viral infections.However,this observation was only noted in the lower respiratory tract infection group among the different disease groups.Notably,among patients infected with a specific virus,there were no significant differences in viral load between single and co-infections.Our study identified the major causative agents in hospitalized adult patients with pulmonary infection,offering insights for precise disease diagnosis and the prevention of unnecessary use of antimicrobial drugs.
基金supported by the National Key Research and Development Program of China(2021YFF0703600)。
文摘Highlights The RT-RAA-VF assay developed for the NiV P gene can perform rapid detection of NiV within 20 min at 42℃ with high specificity.This assay is capable of attaining sensitivity to a single copy of NiV RNA transcripts.This assay effectively avoids false positives caused by aerosol contamination with a sealed disposable nucleic acid visualization test paper device.
基金supported by the Science and Technology Plan Projects of Wuhan (grant No. 2013060501010157)
文摘Coxsackievirus A16(CA16) is one of the major causes of hand, foot, and mouth disease(HFMD) worldwide, which is a common illness that affects children. The frequent occurrence of HFMD outbreaks has become a serious public health problem in Asia. Therefore, it is important to understand the pathogenesis and replication of CA16. In this study, a stable infectious c DNA clone of an epidemic strain of Coxsackievirus A16(CA16) was assembled, and subsequently a reporter virus(e GFP-CA16) was constructed by inserting the e GFP gene between the 5'-UTR and the N-terminus of VP4, with the addition of a 2A protease cleavage site(ITTLG) at its C-terminus. This was transfected into Vero cells to generate infectious recombinant viruses. The growth characteristics and plaque morphology, in vitro, in mammalian cells were found to be indistinguishable between the parental and recombinant viruses. Although the e GFP-CA16 showed smaller plaque size as compared to recombinant CA16, both were found to exhibit similar growth trends and EC50 of NITD008. In summary, this stable infectious c DNA clone should provide a valuable experimental system to study CA16 infection and host response. The e GFP-CA16 is expected to provide a powerful tool to monitor e GFP expression in infected cells and to evaluate the antiviral activity of potential antiviral agents in the treatment of CA16 infections.
基金supported by the National Science and Technology Major Project of China(No.2018ZX10201001-010,No.2017ZX10103009-005,No.2018ZX10713001-007)the National Natural Science Fund for Distinguished Young Scholars of China(No.81525023)+4 种基金the National Natural Science Foundation of China(No.81473031)the Program of Shanghai Academic/Technology Research Leader(No.18XD1400300)the Li Ka Shing Oxford Global Health Programme(No.B9RST00-B900.57)the Chinese Preventive Medicine Association(No:20101801)supported by CAS Pioneer Hundred Talents Program
文摘Enteroviruses(EVs)species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand,foot and mouth disease(HFMD)in China.Mild infections are common in children;however,HFMD can also cause severe illness that affects the central nervous system.To molecularly characterize EVs,a prospective HFMD virological surveillance program was performed in China between 2013 and 2016.Throat swabs,rectal swabs and stool samples were collected from suspected HFMD patients at participating hospitals.EVs were detected using generic real-time and nested reverse transcription-polymerase chain reactions(RT-PCRs).Then,the complete VP1 regions of enterovirus A71(EV-A71),coxsackievirus A16(CVA16)and CVA6 were sequenced to analyze amino acid changes and construct a viral molecular phylogeny.Of the 2836 enrolled HFMD patients,2,517(89%)were EV positive.The most frequently detected EVs were CVA16(32.5%,819),CVA6(31.2%,785),and EV-A71(20.4%,514).The subgenogroups CVA16B1 b,CVA6D3 a and EV-A71C4 a were predominant in China and recombination was not observed in the VP1 region.Sequence analysis revealed amino acid variations at the 30,29 and 44 positions in the VP1 region of EV-A71,CVA16 and CVA6(compared to the respective prototype strains Br Cr,G10 and Gdula),respectively.Furthermore,in 21 of 24(87.5%)identified EV-A71 samples,a known amino acid substitution(D31 N)that may enhance neurovirulence was detected.Our study provides insights about the genetic characteristics of common HFMD-associated EVs.However,the emergence and virulence of the described mutations require further investigation.
基金financial supports of CAS(project No 153B42KYSB20170004)the Wuhan National Biosafety Lab for this study。
文摘As a respiratory tract virus,SARS-CoV-2 infected people through contacting with the upper respiratory tract first.Previous studies indicated that microbiota could modulate immune response against pathogen infection.In the present study,we performed metagenomic sequencing of pharyngeal swabs from eleven patients with COVID-19 and eleven Non-COVID-19 patients who had similar symptoms such as fever and cough.Through metagenomic analysis of the above two groups and a healthy group from the public data,there are 6502 species identified in the samples.Specifically,the Pielou index indicated a lower evenness of the microbiota in the COVID-19 group than that in the Non-COVID-19 group.Combined with the linear discriminant analysis(LDA)and the generalized linear model,eighty-one bacterial species were found with increased abundance in the COVID-19 group,where 51 species were enriched more than 8 folds.The top three enriched genera were Streptococcus,Prevotella and Campylobacter containing some opportunistic pathogens.More interestingly,through experiments,we found that two Streptococcus strains,S.suis and S.agalactiae,could stimulate the expression of ACE2 of Vero cells in vitro,which may promote SARS-CoV-2 infection.Therefore,these enriched pathogens in the pharynxes of COVID-19 patients may involve in the virus-host interactions to affect SARS-CoV-2 infection and cause potential secondary bacterial infections through changing the expression of the viral receptor ACE2 and/or modulate the host’s immune system.
基金financial support from Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-YW-Z-0954, KSCX2-EW-Z-3)
文摘Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.
基金This work was jointly supported by the Advanced Customer Cultivation Project of Wuhan National Biosafety Laboratory,Chinese Academy of Sciences(2021ACCP-MS01,2019ACCP-ZD03)the Natural Science Foundation of Hubei Province of China(2019CFA076)the National Natural Science Foundation of China(31870926)。
文摘Ebola virus(EBOV) belongs to the Filoviridae family and causes severe illnesses such as hemorrhagic fever with a high mortality rate up to 90%. Now two antibody drugs termed Inmazeb and Ebanga have been approved for treating EBOV infection. However, clinical studies have demonstrated that the mortality rate of the patients who received these two antibody drugs remains above 30%. Therefore, novel therapeutics with better efficacy is still desired. The isolated human IgG1 constant domain 2(CH2 domain) has been proposed as a scaffold for the development of C-based single domain antibodies(C-sd Abs) as therapeutic candidates against viral infections and other diseases. Here, we screened and identified a novel C-sd Ab termed M24 that targets EBOV glycoprotein(GP) from a C-sd Ab phage display library. M24 neutralizes the pseudotype EBOV with IC;of 0.8 nmol/L(12 ng/mL) and has modest neutralizing activity against authentic EBOV.Epitope determination, including molecular docking and site mutation analysis, discloses that M24 binds to the internal fusion loop(IFL) within GP2, a transmembrane subunit of GP. Interestingly, we found that the binding of M24 to GP at pH5.5 has dramatically decreased compared to the binding at pH 7.5, which may lead to weak efficacy in the neutralization of authentic EBOV. Since no sd Ab against EBOV infection has been reported to date, our results not only give a proof of concept that sd Abs could be utilized for the development of potential therapeutic candidates against EBOV infection, but also provide useful information for the discovery and improvement of anti-EBOV agents.
文摘The authors are retracting this paper owing to errors in the reported data.The paper claimed that 16 patient cases were infected with H9N2 virus.However,when the authors recently further investigated all the thirteen sera samples,no anti-H9N2 antibodies were found by the haemagglutination inhibition assay.Moreover,re-sequencing of the remaining five throat swabs showed all five samples were H1N1 virus.
基金supported by the National Basic Research Program of China(Grants 2012CB518904)the National Natural Science Foundation of China(Grant No.81572003)+1 种基金the Core Facility and Technical Support,Wuhan Institute of VirologyWuhan Key Laboratory on Emerging Infectious Diseases and Biosafety for helpful supports during the course of the work
文摘Dear Editor,Zika virus（ZIKV）is a mosquito-borne flavivirus that usually causes asymptomatic infections or mild illness in humans.However,the unprecedented epidemics of ZIKV in Latin America since early 2015 have made this flavivirus an international health risk（Liu and Zhang,2016）.
基金supported by the Wuhan Bureau of Science and Technology(No.202002020101010022)China Geological Survey(No.DD20190282)the support team from the National Biosafety Laboratory in Wuhan,China,for the support they extended to us。
文摘Wastewater-based epidemiology(WBE)has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community.Congruently,SARS-Co V-2,the etiologic agent of COVID-19,has been demonstrated to infect the gastrointestinal tissues,and be shed in feces.In the present study,SARS-Co V-2 RNA was concentrated from wastewater,sludge,surface water,ground water,sediment,and soil samples of municipal and hospital wastewater systems and related environments in Wuhan during the COVID-19 middle and low risk periods,and the viral RNA copies quantified using reverse transcription quantitative polymerase chain reaction(RT-q PCR).From the findings of this study,during the middle risk period,one influent sample and three secondary effluents collected from waste water treatment plant 2,as well as two samples from Jinyintan Hospital wastewater system influent were SARS-Co V-2 RNA positive.One sludge sample collected from Guanggu Branch of Tongji Hospital,which was obtained during the low risk period,was also positive for SARS-Co V-2 RNA.These study findings demonstrate the significance of WBE in continuous surveillance of SARS-Co V-2 at the community level,even when the COVID-19 prevalence is low.Overall,this study can be used as an important reference for contingency management of wastewater treatment plants and COVID-19 prevention and control departments of Wuhan.
基金supported by a grant from the State Key Laboratory of Virology(PR China)Chinese Academy of Sciences(No.KJZD-EW-L02)
文摘Dear Editor,Bacteriophages are powerful tools for investigating and manipulating their hosts(Fernandes et al.,2014).This holds particularly true for mycobacteriophages,which have facilitated the development of mycobacterial genetic systems and have generated tools for the clinical
基金funded by the National Natural Science Foundation of China (No. 31321001)
文摘Bats are natural reservoir hosts for many viruses that produce no clinical symptoms in bats.Therefore, bats may have evolved effective mechanisms to control viral replication. However, little information is available on bat immune responses to viral infection. Type I interferon(IFN) plays a key role in controlling viral infections. In this study, we report the cloning, expression, and biological activity of interferon β(IFNβ) from the Chinese microbat species, Myotis davidii. We demonstrated the upregulation of IFNB and IFN-stimulated genes in a kidney cell line derived from M. davidii after treatment with poly I:C or infection with Sendai virus. Furthermore, the recombinant IFNβ inhibited vesicular stomatitis virus and bat adenovirus replication in cell lines from two bat species, M. davidii and Rhinolophus sinicus. We provide the first in vitro evidence of IFNβ antiviral activity in microbats, which has important implications for virus interactions with these hosts.
基金supported by the Research Project of African Swine Fever of Chinese Academy of Sciences (KJZD-SWL06)the National Natural Science Foundation of China (31941015)+3 种基金the National Key R&D Program of China (2016YFC1200800&2018YFC0840402)the China Mega-Project for Infectious Disease(2017ZX10103005-005)the State Key Laboratory of Veterinary Biotechnology Research Fund (SKLVBF201902)supported by Youth Innovation Promotion Association of CAS (2019091)。
文摘Dear Editor,It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019).
基金supported by the National Natural Science Foundation of China (No. 31400126)Basic Research Program of the Ministry of Science and Technology of China (No. 2012CB721102)+2 种基金Chinese Academy of Sciences (No. KJZD-EW-L02)Open Research Fund Program of the State Key Laboratory of Virology of China (No. 2014IOV002)Key Laboratory of Emerging Infectious Diseases and Biosafety, Wuhan
文摘The novel phage lysin PlySs2, is reported to be highly active against various bacteria, including staphylococci, streptococci and Listeria. However, the molecular mechanisms underlying its broad lytic spectrum remain to be established. In the present study, the lytic activity of the catalytic domain(CD, PlySc) and binding specificity of the cell wall binding domain(CBD, PlySb) of PlySs2 were examined. Our results showed that PlySc alone maintains very limited lytic activity. Enhanced green fluorescent protein(EGFP)-fused PlySb displayed high binding affinity to the streptococcal strains tested, including S.suis, S.dysgalactiae, and S.agalactiae, but not staphylococci, supporting its utility as a good CBD donor for streptococcal-targeted lysin engineering. EGFP-fused intact PlySs2 similarly displayed high affinity for streptococci, but not staphylococci. Notably, four truncated PlySb fragments showed no binding capacity. These findings collectively indicate that integrity of the PlySc and PlySb domains is an essential determinant of the broad lytic activity of PlySs2.
基金the Ministry of Science and Technology of China (Basic Work Program 2013FY113500)
文摘China is a vast territory with a wide range of animals and insects that carry complex pathogenic microorganisms.Over the past few years,a rising trend of emerging and virulent infectious diseases has been observed.The outbreak of SARS in 2003 spread to over 32 regions or countries worldwide,resulting in 8422 people being infected and 919 fatalities.The recent outbreaks and endemic epidemics of hand-foot-and-mouth
基金funded by the National Science and Technology Major Project (2018ZX10101004)the Open Research Fund Program of Wuhan National Bio-Safety Level 4 Lab of CAS (NBL2017003)+1 种基金China Ministry of Science and Technology (MOST) Key Research and Development Program (2016YFC1200800)the Shenzhen Science and Technology Research and Development Project (JCYJ20151029151932602)
文摘Dear Editor,The avian influenza virus (AIV) H5N7 was first isolated from wild birds in North America in 2001 (Spackman et al.2007), and information on only 25 strains of this virus has been deposited in the Global Initiative on Sharing All Influenza Data (GISAID-http://platform.gisaid.org/epi3/frontend#493de3) database until October 30, 2018. Twenty viruses were identified in the United States from 2001 to2017.
基金supported by National Natural Science Foundation of China(Grant Nos.:81891010/81891011,81725023,82003614,82173950,31770192,32070187,32161133003 and 82003681)China Postdoctoral Science Foundation(Grant No:2022T150029).
文摘Currently,human health due to corona virus disease 2019(COVID-19)pandemic has been seriously threatened.The coronavirus severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)spike(S)protein plays a crucial role in virus transmission and several S-based therapeutic approaches have been approved for the treatment of COVID-19.However,the efficacy is compromised by the SARS-CoV-2 evolvement and mutation.Here we report the SARS-CoV-2 S protein receptor-binding domain(RBD)inhibitor licorice-saponin A3(A3)could widely inhibit RBD of SARS-CoV-2 variants,including Beta,Delta,and Omicron BA.1,XBB and BQ1.1.Furthermore,A3 could potently inhibit SARS-CoV-2 Omicron virus in Vero E6 cells,with EC50 of 1.016μM.The mechanism was related to binding with Y453 of RBD determined by hydrogen-deuterium exchange mass spectrometry(HDX-MS)analysis combined with quantum mechanics/molecular mechanics(QM/MM)simulations.Interestingly,phosphoproteomics analysis and multi fluorescent immunohistochemistry(mIHC)respectively indicated that A3 also inhibits host inflammation by directly modulating the JNK and p38 mitogen-activated protein kinase(MAPK)pathways and rebalancing the corresponding immune dysregulation.This work supports A3 as a promising broad-spectrum small molecule drug candidate for COVID-19.
基金supported by International Cooperation on key Technologies of Biosafety along the China–Pakistan Economic Corridor(153B42KYSB20170004)Major State Basic Research Development Program(2013FY 113500)the National Natural Science Foundation of China(81572003 and 31600141)
文摘The chikungunya virus(CHIKV) is a mosquito-transmitted alphavirus, which has infected millions of people in Africa, Asia, Americas, and Europe since it reemerged in India and Indian Ocean regions in 2005–2006. Starting in the middle of November 2016, CHIKV has been widely spread, and more than 4,000 cases of infections in humans were confirmed in Pakistan. Here, we report the first isolation and characterization of CHIKV from the Pakistan outbreak. Eight CHIKV strains were newly isolated from human serum samples using a cell culture procedure. A full-length genome sequence and eight complete envelope(E1) sequences of CHIKV from Pakistan were obtained in this study. Alignment of the CHIKV E1 sequences revealed that the eight new CHIKV isolates were highly homogeneous, with only two nonsynonymous substitutions found at generally conserved sites(E99 and Q235). Based on the comparison of 342 E1 sequences, the two nonsynonymous mutations were located in well-recognized domains associated with viral functions such as the cell fusion and vector specificity, suggesting their potential functional importance. Phylogenetic analysis indicated that the CHIKV strains from Pakistan originated from CHIKV circulating in the Indian region. This study helps elucidate the epidemics of CHIKV in Pakistan and also provides a foundation for studies of evolution and expansion of CHIKV in South Asia.
基金This work was supported by the National Major Science and Technology Project(2018ZX10711001-006)the Wuhan Science and Technology Project(2018201261638501)。
文摘Dear Editor,Omsk hemorrhagic fever virus(OHFV)belongs to the tickborne virus group within Flavivirus,in Flaviviridae family(Holbrook et al.2005)which consists of several important human pathogens including tick-borne encephalitis virus(TBEV),Powassan virus(POWV),Louping ill virus(LIV),Langat virus(LGTV)and Kyasnaur Forest disease virus(KFDV)(Yoshii and Holbrook 2009).OHFV is an enveloped virus containing a single-stranded positive-sense RNA genome of approximately 11,000 nucleotides.The genome has a single open reading frame,which encodes three structural proteins[capsid(C),pre-membrane(prM)or membrane(M),and envelop(E)]and seven non-structural proteins(NS1,NS2a,NS2b,NS3,NS4a,NS4b and NS5)between the 5'untranslated region(UTR)and 3'UTR(Chambers et al.1990).
