This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012-2015 covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study w...This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012-2015 covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses; specifically, astroviruses （AstVs）, adenoviruses （ADVs）, caliciviruses （CalVs）, coronaviruses （CoVs）, flaviviruses, filoviruses, paramyxoviruses （PMVs）, polyomaviruses （PYVs） and rotaviruses. We used family-specific primers, amplicon sequencing and further characterization by phyloge- netic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions （former provinces） studied. AstVs （12.83%）, CoVs （3.97%）, PMV （2.4%）, ADV （2.26%）, PYV （1.65%）, CalVs （0.29%）, rotavirus （0.19%） and flavivirus （0.19%）. Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A （RVA） strains detected were highly related to human strains with VP6 genotypes 12 and 116. Genotype 116 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction. Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance.展开更多
Infectious diseases caused by arboviruses are a public health concern in Pakistan.However,studies on data prevalence and threats posed by arboviruses are limited.This study investigated the seroprevalence of arbovirus...Infectious diseases caused by arboviruses are a public health concern in Pakistan.However,studies on data prevalence and threats posed by arboviruses are limited.This study investigated the seroprevalence of arboviruses in a healthy population in Pakistan,including severe fever with thrombocytopenia syndrome virus(SFTSV),Crimean-Congo hemorrhagic fever virus(CCHFV),Tamdy virus(TAMV),and Karshi virus(KSIV)based on a newly established luciferase immunoprecipitation system(LIPS)assays,and Zika virus(ZIKV)by enzyme-linked immunosorbent assays(ELISA).Neutralizing activities against these arboviruses were further examined from the antibody positive samples.The results showed that the seroprevalence of SFTSV,CCHFV,TAMV,KSIV,and ZIKV was 17.37%,7.58%,4.41%,1.10%,and 6.48%,respectively,and neutralizing to SFTSV(1.79%),CCHFV(2.62%),and ZIKV(0.69%)were identified,as well as to the SFTSV-related Guertu virus(GTV,0.83%).Risk factors associated with the incidence of exposure and levels of antibody response were analyzed.Moreover,co-exposure to different arboviruses was demonstrated,as thirty-seven individuals were having antibodies against multiple viruses and thirteen showed neutralizing activity.Males,individuals aged40 years,and outdoor workers had a high risk of exposure to arboviruses.All these results reveal the substantial risks of infection with arboviruses in Pakistan,and indicate the threat from co-exposure to multiple arboviruses.The findings raise the need for further epidemiologic investigation in expanded regions and populations and the necessity to improve health surveillance in Pakistan.展开更多
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic pathogen capable of causing severe respiratory disease in humans. Although dromedary camels are considered as a major reservoir host, the MERS-CoV ...Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic pathogen capable of causing severe respiratory disease in humans. Although dromedary camels are considered as a major reservoir host, the MERS-CoV infection dynamics in camels are not fully understood. Through surveillance in Pakistan, nasal (n = 776) and serum (n = 1050)samples were collected from camels between November 2015 and February 2018. Samples were collected from animal markets, free-roaming herds and abattoirs. An in-house ELISA was developed to detect IgG against MERS-CoV. A total of 794 camels were found seropositive for MERS-CoV. Prevalence increased with the age and the highest seroprevalence was recorded in camels aged [ 10 years (81.37%) followed by those aged 3.1–10 years (78.65%) and B 3 years (58.19%).Higher prevalence was observed in female (78.13%) as compared to male (70.70%). Of the camel nasal swabs, 22 were found to be positive by RT-qPCR though with high Ct values. Moreover, 2,409 human serum samples were also collected from four provinces of Pakistan during 2016–2017. Among the sampled population, 840 humans were camel herders.Although we found a high rate of MERS-CoV antibody positive dromedaries (75.62%) in Pakistan, no neutralizing antibodies were detected in humans with and without contact to camels.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
Globally,arboviruses are public health problems.Pakistan has seen a fast-paced increase in mosquito-borne Flavivirus diseases such as dengue because of deforestation,climate change,urbanization,poor sanitation and nat...Globally,arboviruses are public health problems.Pakistan has seen a fast-paced increase in mosquito-borne Flavivirus diseases such as dengue because of deforestation,climate change,urbanization,poor sanitation and natural disasters.The magnitude and distribution of these diseases are poorly understood due to the lack of a competitive nationwide surveillance system.In dengue-endemic countries,the recent epidemics of chikungunya(CHIKV)and human West Nile virus(WNV)have created panic among the public and are thought to provoke an outbreak of Zika virus(ZIKV)in Pakistan.Recently,hospital-based surveillance has indicated the presence of Japanese encephalitis virus(JEV),which is deeply concerned by developing countries such as Pakistan.The situation could become more devastating because of poorly developed diagnostic infrastructure.To date,no licensed vaccine has been used in Pakistan,and preventive measures are mainly based on vector control.This review provides comprehensive information concerning the association of risk factors with disease occurrence,epidemiological trends,and prediction of the spread of mosquito-borne diseases,attention to new threats of ZIKV,and future perspectives by benchmarking global health policies.展开更多
Background:Coronavirus disease 2019(COVID-19)linked with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)cause severe illness and life-threatening pneumonia in humans.The current COVID-19 pandemic demands a...Background:Coronavirus disease 2019(COVID-19)linked with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)cause severe illness and life-threatening pneumonia in humans.The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection.Therefore,the present study was aimed to design a multiepitope-based subunit vaccine(MESV)against COVID-19.Methods:Structural proteins(Surface glycoprotein,Envelope protein,and Membrane glycoprotein)of SARS-CoV-2 are responsible for its prime functions.Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B-and T-cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV.Results:Predicted epitopes suggested high antigenicity,conserveness,substantial interactions with the human leukocyte antigen(HLA)binding alleles,and collective global population coverage of 88.40%.Taken together,276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes(CTL),6 helper T lymphocyte(HTL)and 4 B-cell epitopes with suitable adjuvant and linkers.The MESV construct was non-allergenic,stable,and highly antigenic.Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3(TLR3).Furthermore,in silico immune simulation revealed significant immunogenic response of MESV.Finally,MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system,to ensure its increased expression.Conclusion:The MESV developed in this study is capable of generating immune response against COVID-19.Therefore,if designed MESV further investigated experimentally,it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.展开更多
Background The ongoing coronavirus disease 2019(COVID-19)pandemic caused by the severe acute respiratory syndrome-coronavirus 2(SARS-CoV-2)and the Omicron variant presents a formidable challenge for control and preven...Background The ongoing coronavirus disease 2019(COVID-19)pandemic caused by the severe acute respiratory syndrome-coronavirus 2(SARS-CoV-2)and the Omicron variant presents a formidable challenge for control and prevention worldwide,especially for low-and middle-income countries(LMICs).Hence,taking Kazakhstan and Pakistan as examples,this study aims to explore COVID-19 transmission with the Omicron variant at different contact,quarantine and test rates.Methods A disease dynamic model was applied,the population was segmented,and three time stages for Omicron transmission were established:the initial outbreak,a period of stabilization,and a second outbreak.The impact of population contact,quarantine and testing on the disease are analyzed in five scenarios to analysis their impacts on the disease.Four statistical metrics are employed to quantify the model’s performance,including the correlation coefficient(CC),normalized absolute error,normalized root mean square error and distance between indices of simulation and observation(DISO).Results Our model has high performance in simulating COVID-19 transmission in Kazakhstan and Pakistan with high CC values greater than 0.9 and DISO values less than 0.5.Compared with the present measures(baseline),decreasing(increasing)the contact rates or increasing(decreasing)the quarantined rates can reduce(increase)the peak values of daily new cases and forward(delay)the peak value times(decreasing 842 and forward 2 days for Kazakhstan).The impact of the test rates on the disease are weak.When the start time of stage Ⅱ is 6 days,the daily new cases are more than 8 and 5 times the rate for Kazakhstan and Pakistan,respectively(29,573 vs.3259;7398 vs.1108).The impact of the start times of stageⅢon the disease are contradictory to those of stageⅡ.Conclusions For the two LMICs,Kazakhstan and Pakistan,stronger control and prevention measures can be more effective in combating COVID-19.Therefore,to reduce Omicron transmission,strict management of population movement should be employed.Moreover,the timely application of these strategies also plays a key role in disease control.展开更多
基金funded by SinoAfrica Joint Research Center (SAJC201313 and SAJC 201605)
文摘This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012-2015 covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses; specifically, astroviruses （AstVs）, adenoviruses （ADVs）, caliciviruses （CalVs）, coronaviruses （CoVs）, flaviviruses, filoviruses, paramyxoviruses （PMVs）, polyomaviruses （PYVs） and rotaviruses. We used family-specific primers, amplicon sequencing and further characterization by phyloge- netic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions （former provinces） studied. AstVs （12.83%）, CoVs （3.97%）, PMV （2.4%）, ADV （2.26%）, PYV （1.65%）, CalVs （0.29%）, rotavirus （0.19%） and flavivirus （0.19%）. Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A （RVA） strains detected were highly related to human strains with VP6 genotypes 12 and 116. Genotype 116 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction. Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance.
基金supported by the National Key Research and Development Programme of China[Grant Number 2021YFC2300900,2022YFC2302700]International Partnership Programme of the Bureau of International Cooperation,Chinese Academy of Sciences[Grant Number 153B42KYSB20200013]+1 种基金National Natural Science Foundation of China[Grant Number U22A20363]Biological Resources Programme,Chinese Academy of Sciences[Grant Number KFJ-BRP-017-74].
文摘Infectious diseases caused by arboviruses are a public health concern in Pakistan.However,studies on data prevalence and threats posed by arboviruses are limited.This study investigated the seroprevalence of arboviruses in a healthy population in Pakistan,including severe fever with thrombocytopenia syndrome virus(SFTSV),Crimean-Congo hemorrhagic fever virus(CCHFV),Tamdy virus(TAMV),and Karshi virus(KSIV)based on a newly established luciferase immunoprecipitation system(LIPS)assays,and Zika virus(ZIKV)by enzyme-linked immunosorbent assays(ELISA).Neutralizing activities against these arboviruses were further examined from the antibody positive samples.The results showed that the seroprevalence of SFTSV,CCHFV,TAMV,KSIV,and ZIKV was 17.37%,7.58%,4.41%,1.10%,and 6.48%,respectively,and neutralizing to SFTSV(1.79%),CCHFV(2.62%),and ZIKV(0.69%)were identified,as well as to the SFTSV-related Guertu virus(GTV,0.83%).Risk factors associated with the incidence of exposure and levels of antibody response were analyzed.Moreover,co-exposure to different arboviruses was demonstrated,as thirty-seven individuals were having antibodies against multiple viruses and thirteen showed neutralizing activity.Males,individuals aged40 years,and outdoor workers had a high risk of exposure to arboviruses.All these results reveal the substantial risks of infection with arboviruses in Pakistan,and indicate the threat from co-exposure to multiple arboviruses.The findings raise the need for further epidemiologic investigation in expanded regions and populations and the necessity to improve health surveillance in Pakistan.
基金supported by the International Cooperation on Key Technologies of Biosafety along the China-Pakistan Economic Corridor(153B42KYSB20170004)by the External Cooperation Program of CAS(153211KYSB20160001)
文摘Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic pathogen capable of causing severe respiratory disease in humans. Although dromedary camels are considered as a major reservoir host, the MERS-CoV infection dynamics in camels are not fully understood. Through surveillance in Pakistan, nasal (n = 776) and serum (n = 1050)samples were collected from camels between November 2015 and February 2018. Samples were collected from animal markets, free-roaming herds and abattoirs. An in-house ELISA was developed to detect IgG against MERS-CoV. A total of 794 camels were found seropositive for MERS-CoV. Prevalence increased with the age and the highest seroprevalence was recorded in camels aged [ 10 years (81.37%) followed by those aged 3.1–10 years (78.65%) and B 3 years (58.19%).Higher prevalence was observed in female (78.13%) as compared to male (70.70%). Of the camel nasal swabs, 22 were found to be positive by RT-qPCR though with high Ct values. Moreover, 2,409 human serum samples were also collected from four provinces of Pakistan during 2016–2017. Among the sampled population, 840 humans were camel herders.Although we found a high rate of MERS-CoV antibody positive dromedaries (75.62%) in Pakistan, no neutralizing antibodies were detected in humans with and without contact to camels.
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This work was supported by the National Project for Prevention and Control of Transboundary Animal Diseases(Grant No.2017YFD0501800)the National Key R&D Program for the 13th Five-Year Plan,the Ministry of Science and Technology,China.
文摘Globally,arboviruses are public health problems.Pakistan has seen a fast-paced increase in mosquito-borne Flavivirus diseases such as dengue because of deforestation,climate change,urbanization,poor sanitation and natural disasters.The magnitude and distribution of these diseases are poorly understood due to the lack of a competitive nationwide surveillance system.In dengue-endemic countries,the recent epidemics of chikungunya(CHIKV)and human West Nile virus(WNV)have created panic among the public and are thought to provoke an outbreak of Zika virus(ZIKV)in Pakistan.Recently,hospital-based surveillance has indicated the presence of Japanese encephalitis virus(JEV),which is deeply concerned by developing countries such as Pakistan.The situation could become more devastating because of poorly developed diagnostic infrastructure.To date,no licensed vaccine has been used in Pakistan,and preventive measures are mainly based on vector control.This review provides comprehensive information concerning the association of risk factors with disease occurrence,epidemiological trends,and prediction of the spread of mosquito-borne diseases,attention to new threats of ZIKV,and future perspectives by benchmarking global health policies.
文摘Background:Coronavirus disease 2019(COVID-19)linked with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)cause severe illness and life-threatening pneumonia in humans.The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection.Therefore,the present study was aimed to design a multiepitope-based subunit vaccine(MESV)against COVID-19.Methods:Structural proteins(Surface glycoprotein,Envelope protein,and Membrane glycoprotein)of SARS-CoV-2 are responsible for its prime functions.Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B-and T-cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV.Results:Predicted epitopes suggested high antigenicity,conserveness,substantial interactions with the human leukocyte antigen(HLA)binding alleles,and collective global population coverage of 88.40%.Taken together,276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes(CTL),6 helper T lymphocyte(HTL)and 4 B-cell epitopes with suitable adjuvant and linkers.The MESV construct was non-allergenic,stable,and highly antigenic.Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3(TLR3).Furthermore,in silico immune simulation revealed significant immunogenic response of MESV.Finally,MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system,to ensure its increased expression.Conclusion:The MESV developed in this study is capable of generating immune response against COVID-19.Therefore,if designed MESV further investigated experimentally,it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.
文摘Background The ongoing coronavirus disease 2019(COVID-19)pandemic caused by the severe acute respiratory syndrome-coronavirus 2(SARS-CoV-2)and the Omicron variant presents a formidable challenge for control and prevention worldwide,especially for low-and middle-income countries(LMICs).Hence,taking Kazakhstan and Pakistan as examples,this study aims to explore COVID-19 transmission with the Omicron variant at different contact,quarantine and test rates.Methods A disease dynamic model was applied,the population was segmented,and three time stages for Omicron transmission were established:the initial outbreak,a period of stabilization,and a second outbreak.The impact of population contact,quarantine and testing on the disease are analyzed in five scenarios to analysis their impacts on the disease.Four statistical metrics are employed to quantify the model’s performance,including the correlation coefficient(CC),normalized absolute error,normalized root mean square error and distance between indices of simulation and observation(DISO).Results Our model has high performance in simulating COVID-19 transmission in Kazakhstan and Pakistan with high CC values greater than 0.9 and DISO values less than 0.5.Compared with the present measures(baseline),decreasing(increasing)the contact rates or increasing(decreasing)the quarantined rates can reduce(increase)the peak values of daily new cases and forward(delay)the peak value times(decreasing 842 and forward 2 days for Kazakhstan).The impact of the test rates on the disease are weak.When the start time of stage Ⅱ is 6 days,the daily new cases are more than 8 and 5 times the rate for Kazakhstan and Pakistan,respectively(29,573 vs.3259;7398 vs.1108).The impact of the start times of stageⅢon the disease are contradictory to those of stageⅡ.Conclusions For the two LMICs,Kazakhstan and Pakistan,stronger control and prevention measures can be more effective in combating COVID-19.Therefore,to reduce Omicron transmission,strict management of population movement should be employed.Moreover,the timely application of these strategies also plays a key role in disease control.
