Dear Editor,Severe acute respiratory syndrome coronavirus(SARSCo V)is the causative agent of the 2002–2003 SARS pandemic,which resulted in more than 8000 human infections worldwide and an approximately 10%fatality ra...Dear Editor,Severe acute respiratory syndrome coronavirus(SARSCo V)is the causative agent of the 2002–2003 SARS pandemic,which resulted in more than 8000 human infections worldwide and an approximately 10%fatality rate(Ksiazek et al.2003;Peiris et al.2004).The virus infects both upper airway and alveolar epithelial cells,resulting in mild to severe lung injury in展开更多
Bats,probably the most abundant,diverse and geographically dispersed vertebrates on earth,have recently been shown to be the reservoir hosts of a number of emerging viruses responsible for severe human and livestock d...Bats,probably the most abundant,diverse and geographically dispersed vertebrates on earth,have recently been shown to be the reservoir hosts of a number of emerging viruses responsible for severe human and livestock disease outbreaks. Flying foxes have been demonstrated to be the natural reservoir for Hendra and Nipah viruses. Evidence supporting the possibility of bats as potential reservoirs for SARS coronavirus(SARS-CoV) and Ebola virus has also been reported. The recent discovery of these viruses and other viruses occurring naturally in the bat population provides a unique insight into a diverse pool of potentially emergent and pathogenic viruses. The factors which influence the ability of zoonotic viruses to effectively cross the species barrier from bats to other animal populations are poorly understood. A brief review is provided here on the recently emerged bat viruses and on current and future strategies for research in this area.展开更多
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 m...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.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
The ongoing coronavirus disease 2019(COVID-19)pandemic is a global public health crisis,causing social and economic disasters in many countries.In China,two-consecutive negative results of nucleic acid tests for SARS-...The ongoing coronavirus disease 2019(COVID-19)pandemic is a global public health crisis,causing social and economic disasters in many countries.In China,two-consecutive negative results of nucleic acid tests for SARS-CoV-2 from the respiratory samples are required to end the quarantine of COVID-19 patients.However,clinicians face a dilemma in case of patients with long-term viral shedding.This report described an unusual COVID-19 case who had persistent viral RNA positivity for more than 4 months after initial illness in the presence of low neutralizing antibodies,but without prolonged clinical symptoms.Multiple anti-viral drug treatments had no impact and there was no evidence of re-infection.When the patient was self-quarantined at home,no infection occurred to the three family members living with her for 15 to 19 days.Sputum viral culture in BSL-3 laboratory on the 102nd day after symptom onset was negative.From the 129th day on,8 continuous nucleic acid tests of sputum samples showed negative results.The patient was discharged on 137th days since symptom onset.In conclusion,viral RNA shedding in the sputum of the COVID-19 patient may last over 4 months.As no evidence shows the existence of infectious virus,two-consecutive negative nucleic acid tests may not be the prerequisite for ending quarantine of COVID-19 patients with prolonged viral shedding.展开更多
As the only mammalian group capable of powered flight,bats have many unique biological traits.Previous comparative genomic studies in bats have focused on long-term evolution.However,the microevolutionary processes dr...As the only mammalian group capable of powered flight,bats have many unique biological traits.Previous comparative genomic studies in bats have focused on long-term evolution.However,the microevolutionary processes driving recent evolution are largely under-explored.Using resequencing data from 50 black flying foxes(Pteropus alecto),one of the model species for bats,we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species.Demographic inference reveals strong population fluctuations(>100 fold)coinciding with multiple historical events including the last glacial change and Toba super eruption,suggesting that the black flying fox is a very resilient species with strong recovery abilities.While long-term adaptation in the black flying fox is enriched in metabolic genes,recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category.The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience.Taken together,this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.展开更多
Bat SARS-Iike coronavirus （SL-CoV） has a genome organization almost identical to that of SARS-CoV, but the N-terminus of the Spike （S） proteins, which interacts with host receptor and is a major target of neutrali...Bat SARS-Iike coronavirus （SL-CoV） has a genome organization almost identical to that of SARS-CoV, but the N-terminus of the Spike （S） proteins, which interacts with host receptor and is a major target of neutralizing antibodies against CoVs, of the two viruses has only 63-64% sequence identity. Although there have been reports studying the overall immunogenicity of SsL, knowledge on the precise location of immunodominant determinants for SSL is still lacking. In this study, using a series of truncated expressed SsL fragments and SsL specific mouse sera, we identified two immunogenic determinants for SSL. Importantly, one of the two regions seems to be located in a region not shared by known immunogenic determinants of the SSARS. This finding will be of potential use in future monitoring of SL-CoV infection in bats and spillover animals and in development of more effective vaccine to cover broad protection against this new group of coronaviruses.展开更多
Dear Editor,Zika virus(ZIKV),a pathogen within the genus Flavivirus,family Flaviviridae brought an international public health emergency due to its association with neonatal microcephaly case(Platt and Miner 2017).Cur...Dear Editor,Zika virus(ZIKV),a pathogen within the genus Flavivirus,family Flaviviridae brought an international public health emergency due to its association with neonatal microcephaly case(Platt and Miner 2017).Currently the most reliable diagnostic test is PCR detection of ZIKV RNA from body fluid samples.Unfortunately,the short viremia window and asymptomatic/mild infections greatly reduce the success rate of PCRs(de Vasconcelos et al.2018).展开更多
Multiple Omicron sub-lineages have emerged,with Omicron XBB and XBB.1.5 subvariants becoming the dominant variants globally at the time of this study.The key feature of new variants is their ability to escape humoral ...Multiple Omicron sub-lineages have emerged,with Omicron XBB and XBB.1.5 subvariants becoming the dominant variants globally at the time of this study.The key feature of new variants is their ability to escape humoral immunity despite the fact that there are limited genetic changes from their preceding variants.This raises the question of whether Omicron should be regarded as a separate serotype from viruses serologically clustered with the ancestral severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus.Here,we present cross-neutralization data based on a pseudovirus neutralization test using convalescent sera from naïve individuals who had recovered from primary infection by SARS-CoV-1 and SARS-CoV-2 strains/variants including the ancestral virus and variants Beta,Delta,Omicron BA.1,Omicron BA.2 and Omicron BA.5.The results revealed no significant cross-neutralization in any of the three-way testing for SARS-CoV-1,ancestral SARS-CoV-2 and SARS-CoV-2 Omicron subvariants.The data argue for the assignment of three distinct serotypes for the currently known human-infecting SARS-related coronaviruses.展开更多
IS THERE A NEED FOR SEROTYPING?The emergence and rapid selection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)immune escape variants have exerted significant challenges in many different ways,from pub...IS THERE A NEED FOR SEROTYPING?The emergence and rapid selection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)immune escape variants have exerted significant challenges in many different ways,from public health response to vaccine boosting strategy and monitoring of herd immunity against future variants or related severe acute respiratory syndrome(SARS)related coronaviruses(SARSr-CoVs).The Omicron sub-variants,which differ substantially from the pre-Omicron variants,are circulating worldwide and continuing to evolve extensively through mutations and/or recombination predominantly in the spike protein,mainly due to immune-selective pressure.Despite their phylogenetically close relationship to ancestral SARS-CoV-2,antigenically,Omicron variants are very different from the original strain.It is therefore very natural to raise the question whether we need a better way to classify and differentiate those CoVs which are genetically very similar,but antigenically quite distinct.Serotyping of viruses is a common practice for many known virus groups,most notably for human papillomavirus(HPV)and dengue virus(DENV)[1,2].The concept of CoV serotypes was not new and has been applied to study the antigenicity of feline CoVs[3].The possibility of establishing distinctive serotypes for the SARS-CoV-2 virus was first raised by Simon-Loriere and Schwartz in 2022[4].Serotyping SARS-CoV-2 is expected to help more scientifically define the differences between variants and facilitate more targeted diagnostics,therapeutics,and vaccine development.展开更多
基金funded by the National Natural Science Foundation of China Grant (81290341) to ZLSthe National Institute of Allergy and Infectious Diseases of the National Institutes of Health (Award Number R01AI110964) to PD and ZLS+2 种基金United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT project Grant (Cooperative Agreement No. AID-OAA-A-14-00102) to PDSingapore NRFCRP Grant (NRF2012NRF-CRP001–056)CD-PHRG Grant (CDPHRG/0006/2014) to LFW
文摘Dear Editor,Severe acute respiratory syndrome coronavirus(SARSCo V)is the causative agent of the 2002–2003 SARS pandemic,which resulted in more than 8000 human infections worldwide and an approximately 10%fatality rate(Ksiazek et al.2003;Peiris et al.2004).The virus infects both upper airway and alveolar epithelial cells,resulting in mild to severe lung injury in
文摘Bats,probably the most abundant,diverse and geographically dispersed vertebrates on earth,have recently been shown to be the reservoir hosts of a number of emerging viruses responsible for severe human and livestock disease outbreaks. Flying foxes have been demonstrated to be the natural reservoir for Hendra and Nipah viruses. Evidence supporting the possibility of bats as potential reservoirs for SARS coronavirus(SARS-CoV) and Ebola virus has also been reported. The recent discovery of these viruses and other viruses occurring naturally in the bat population provides a unique insight into a diverse pool of potentially emergent and pathogenic viruses. The factors which influence the ability of zoonotic viruses to effectively cross the species barrier from bats to other animal populations are poorly understood. A brief review is provided here on the recently emerged bat viruses and on current and future strategies for research in this area.
基金funded by Sino-Africa Joint Research Center (SAJC201313 and SAJC201605)External Cooperation Program of CAS (153211KYSB20160001)National Science and Technology Major Project (2018ZX0101004)
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.
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.
文摘The ongoing coronavirus disease 2019(COVID-19)pandemic is a global public health crisis,causing social and economic disasters in many countries.In China,two-consecutive negative results of nucleic acid tests for SARS-CoV-2 from the respiratory samples are required to end the quarantine of COVID-19 patients.However,clinicians face a dilemma in case of patients with long-term viral shedding.This report described an unusual COVID-19 case who had persistent viral RNA positivity for more than 4 months after initial illness in the presence of low neutralizing antibodies,but without prolonged clinical symptoms.Multiple anti-viral drug treatments had no impact and there was no evidence of re-infection.When the patient was self-quarantined at home,no infection occurred to the three family members living with her for 15 to 19 days.Sputum viral culture in BSL-3 laboratory on the 102nd day after symptom onset was negative.From the 129th day on,8 continuous nucleic acid tests of sputum samples showed negative results.The patient was discharged on 137th days since symptom onset.In conclusion,viral RNA shedding in the sputum of the COVID-19 patient may last over 4 months.As no evidence shows the existence of infectious virus,two-consecutive negative nucleic acid tests may not be the prerequisite for ending quarantine of COVID-19 patients with prolonged viral shedding.
基金supported in part by the National Natural Science Foundation of China(32293190,32293192)National Key R&D Program of China(2019YFA0709501)+4 种基金M.L.is supported in part by the National Natural Science Foundation of China(11971459)W.Z.is supported in part by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB17)the National Natural Science Foundation of China(31970566)National Key R&D Program of China(2018YFC1406902 and 2018YFC0910400)The Duke-NUS team was supported in part by a grant from the Singapore National Research Foundation(NRFCRP10-2012-05).
文摘As the only mammalian group capable of powered flight,bats have many unique biological traits.Previous comparative genomic studies in bats have focused on long-term evolution.However,the microevolutionary processes driving recent evolution are largely under-explored.Using resequencing data from 50 black flying foxes(Pteropus alecto),one of the model species for bats,we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species.Demographic inference reveals strong population fluctuations(>100 fold)coinciding with multiple historical events including the last glacial change and Toba super eruption,suggesting that the black flying fox is a very resilient species with strong recovery abilities.While long-term adaptation in the black flying fox is enriched in metabolic genes,recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category.The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience.Taken together,this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.
基金funded by the State Key Program for Basic Research Grant (2010CB530100,2011CB504700)special project for infectious diseases(2009ZX10004-109) from the Chinese Ministry of Science and Technology
文摘Bat SARS-Iike coronavirus （SL-CoV） has a genome organization almost identical to that of SARS-CoV, but the N-terminus of the Spike （S） proteins, which interacts with host receptor and is a major target of neutralizing antibodies against CoVs, of the two viruses has only 63-64% sequence identity. Although there have been reports studying the overall immunogenicity of SsL, knowledge on the precise location of immunodominant determinants for SSL is still lacking. In this study, using a series of truncated expressed SsL fragments and SsL specific mouse sera, we identified two immunogenic determinants for SSL. Importantly, one of the two regions seems to be located in a region not shared by known immunogenic determinants of the SSARS. This finding will be of potential use in future monitoring of SL-CoV infection in bats and spillover animals and in development of more effective vaccine to cover broad protection against this new group of coronaviruses.
基金funded in part by NMRC Grant ZRRF16006CDPHRG Grant CDPHRG/0006/2014
文摘Dear Editor,Zika virus(ZIKV),a pathogen within the genus Flavivirus,family Flaviviridae brought an international public health emergency due to its association with neonatal microcephaly case(Platt and Miner 2017).Currently the most reliable diagnostic test is PCR detection of ZIKV RNA from body fluid samples.Unfortunately,the short viremia window and asymptomatic/mild infections greatly reduce the success rate of PCRs(de Vasconcelos et al.2018).
基金supported in part by grants from the National Medical Research Council(COVID19RF-001,COVID19RF-003,COVID19RF-0008,COVID19RF-0014,COVID19RF-0018,COVID19RF3-0060,MOH-000535/MOH-OFYIRG19nov-0002 and MOH-000505-02)SingHealth Duke-NUS Academic Medicine COVID-19 Rapid Response Research Grant(AM/COV001/2020)+3 种基金Collaborative Research Fund(C2103-20GF)Wellcome COVID-19 Grant on Understanding the Biological Significance SARS-CoV-2 Variants(226120/Z/22/Z)National Institute of Health NIAID(R01AI163118 and 5U01AI151797)National Public Health COVID Program of the Government of Monaco.
文摘Multiple Omicron sub-lineages have emerged,with Omicron XBB and XBB.1.5 subvariants becoming the dominant variants globally at the time of this study.The key feature of new variants is their ability to escape humoral immunity despite the fact that there are limited genetic changes from their preceding variants.This raises the question of whether Omicron should be regarded as a separate serotype from viruses serologically clustered with the ancestral severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus.Here,we present cross-neutralization data based on a pseudovirus neutralization test using convalescent sera from naïve individuals who had recovered from primary infection by SARS-CoV-1 and SARS-CoV-2 strains/variants including the ancestral virus and variants Beta,Delta,Omicron BA.1,Omicron BA.2 and Omicron BA.5.The results revealed no significant cross-neutralization in any of the three-way testing for SARS-CoV-1,ancestral SARS-CoV-2 and SARS-CoV-2 Omicron subvariants.The data argue for the assignment of three distinct serotypes for the currently known human-infecting SARS-related coronaviruses.
文摘IS THERE A NEED FOR SEROTYPING?The emergence and rapid selection of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)immune escape variants have exerted significant challenges in many different ways,from public health response to vaccine boosting strategy and monitoring of herd immunity against future variants or related severe acute respiratory syndrome(SARS)related coronaviruses(SARSr-CoVs).The Omicron sub-variants,which differ substantially from the pre-Omicron variants,are circulating worldwide and continuing to evolve extensively through mutations and/or recombination predominantly in the spike protein,mainly due to immune-selective pressure.Despite their phylogenetically close relationship to ancestral SARS-CoV-2,antigenically,Omicron variants are very different from the original strain.It is therefore very natural to raise the question whether we need a better way to classify and differentiate those CoVs which are genetically very similar,but antigenically quite distinct.Serotyping of viruses is a common practice for many known virus groups,most notably for human papillomavirus(HPV)and dengue virus(DENV)[1,2].The concept of CoV serotypes was not new and has been applied to study the antigenicity of feline CoVs[3].The possibility of establishing distinctive serotypes for the SARS-CoV-2 virus was first raised by Simon-Loriere and Schwartz in 2022[4].Serotyping SARS-CoV-2 is expected to help more scientifically define the differences between variants and facilitate more targeted diagnostics,therapeutics,and vaccine development.
