A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015.Based on the genetic and phylogenetic analyses,the viruses possess a stable gene con...A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015.Based on the genetic and phylogenetic analyses,the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA,a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin.The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain(A/Alberta/01/2014).Further analysis showed that similar viruses have been circulating in wild birds in China,Russia,Dubai(Western Asia),Bulgaria and Romania(Europe),as well as domestic poultry in some regions of Africa.The affected areas include the Central Asian,East Asian-Australasian,West Asian-East African,and Black Sea/Mediterranean flyways.These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds,thus posing a serious threat to wild birds and potentially humans.展开更多
The highly pathogenic influenza A virus subtype H5N1 spread throughout Asia since 2003, reached to Europe in 2005, and the Middle East, as well as Africa and caused a global concern for a potential pandemic threat las...The highly pathogenic influenza A virus subtype H5N1 spread throughout Asia since 2003, reached to Europe in 2005, and the Middle East, as well as Africa and caused a global concern for a potential pandemic threat last decade. A Clade 2.3.2 H5N1 virus became dominate in the Qinghai Lake region in 2009 with sporadic mammal cases of infection and transferred to Russia and Europe through wild migratory birds. Currently, HPAI H5N1 of clades 2.3.4, 2.3.2, and 7 are the dominant co-circulating H5N1 viruses in poultry in Asia. 2.3.2 Clade is dominant in wild birds through the world whereas there is no evident data about Clade 7 circulation in wild birds. We detected HPAI H5N1 virus of Clade 7.1 in Qinghai Lake, that closely related to Shanxi-like and Vietnam viruses co-circulating in poultry. This is the first report of Clade 7.1 H5N1 in wild birds. Based on phylogenetic analyses, the virus can be originated from Clade 7.1 virus gene pool that spread in Vietnam and Chinese poultry and could spread with migratory birds to Qinghai Lake. The Qinghai Lake continues to be significant hotspot for H5N1 surveillance since the regular outbreaks occurred there in wild birds and mammals. Based on these facts and findings, the related researchers should pay more attention to the Qinghai Lake basin as significant hotspot for H5N1 avian influenza surveillance since the regular H5N1 outbreaks occurred there in wild birds with sporadic mammal cases of infection.展开更多
Dinoflagellates in the genus Symbiodinium, including nine clades(A–I), mainly form mutualistic symbioses with corals. More than 100 Symbiodinium molecular types have been identified by the ITS2-based genotype method ...Dinoflagellates in the genus Symbiodinium, including nine clades(A–I), mainly form mutualistic symbioses with corals. More than 100 Symbiodinium molecular types have been identified by the ITS2-based genotype method within any given clade, and specifically within Symbiodinium clade C. However, the genotype identification method using the ITS2 sequence is likely to lead to high diversity estimates due to the intra-genomic variations in the ITS2 space; thus, further validation is essential for a correct identification. In this study, the molecular diversity of Symbiodinium ITS2 sequences cloned from two stone corals, Acropora sp. SY-01 and Pocillopora sp. SY-05, and one soft coral, Sarcophyton sp. SY-07, living in the northern part of South China Sea(SCS), were analyzed and compared using the ITS2-based genotype identification method, coupled with ITS2-based secondary structural and phylogenetic analyses. As the result, 12 Symbiodinium ITS2 genotypes were identified, while only six and three Symbiodinium ITS2 genotypes were supported by ITS2-based secondary structural and phylogenetic analyses, respectively. In addition, no shared Symbiodinium ITS2 genotypes were observed among the three coral species, suggesting coral species-dependent Symbiodinium genotypes were within clade C. In summary, the present study provides a theoretical basis for validating the molecular diversity of Symbiodinium ITS2 genotypes in corals.展开更多
Background The rapid increase in the number of monkeypox cases poses a considerable threat to the international community,necessitating sensitive,fast,and available diagnostic methods.Therefore,the objective of this s...Background The rapid increase in the number of monkeypox cases poses a considerable threat to the international community,necessitating sensitive,fast,and available diagnostic methods.Therefore,the objective of this study was to develop a rapid,sensitive and simple method with high clinical applicability.Methods We developed a simple,rapid point-of-care assay to detect monkeypox virus(MPXV)using multienzyme isothermal rapid amplification(MIRA)coupled with the clustered regularly interspaced short palindromic repeats(CRISPR)-Cas13a system.The detection system was optimized by synthesizing plasmids,and the detection sensitivity was explored by the continuous dilution of the plasmid.We validated the accuracy of this assay on 202 clinical MPXV samples and 104 interference samples through the kappa test.The visual interpretation of the results was realized by combining the assay with lateral flow strips.In addition,we developed a PCR-based method to identify MPXV Clades Ⅰ and Ⅱ,and the accuracy was tested through a kappa test on 202 clinical monkeypox samples and 104 interference samples.Results Our assay achieved an analytical sensitivity of 14.4 copies/ml and high selectivity,as it differentiated MPXV from three other Orthopoxvirus species.The clinical testing results for 202 monkeypox samples and 104 interference samples demonstrated 100%sensitivity and specificity.Compared with quantitative PCR(qPCR),three samples tested as positive using our assay,which showed that the performance of this assay was superior to that of the qPCR assay.Combined with lateral flow strips,its availability and simplicity provide an alternative point-of-care diagnostic method for MPXV testing in remote settings and resource-poor areas.The results of 32 clinical samples showed that lateral flow strips had a high detection sensitivity and could identify samples with Ct value of 39 as positive.The clade identification assay detected as few as 200 copies/ml within 40 min and no cross-reaction was observed between Clades Ⅰ and Ⅱ.The clinical samples tested were all Clade II,which was consistent with the circulating clade in the Chinese mainland.Conclusions The MIRA-CRISPR-Cas13a-MPXV system offers a rapid,sensitive and specific approach for monkeypox diagnosis,with significance for monitoring monkeypox epidemics.The clade identification assay based on PCR could accurately distinguish Clade Ⅰ from Clade Ⅱ within 40 min and can be implemented for high-throughput operation.展开更多
基金supported by grants from the National Natural Science Foundation of China (31311120063,81470096,31570026,31471253)the Ministry of Education and Science of the Russian Federation (Chinese-Russian project:RFMEFI61315X0045)+3 种基金the intramural special grant for influenza virus research from the Chinese Academy of Sciences (KJZD-EW-L09)the IDRCAPEIR program (106915-001)Special Project of Ministry of Science and Technology (2013FY113500)supported by the “Taishan Scholar” project of Shandong Province
文摘A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015.Based on the genetic and phylogenetic analyses,the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA,a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin.The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain(A/Alberta/01/2014).Further analysis showed that similar viruses have been circulating in wild birds in China,Russia,Dubai(Western Asia),Bulgaria and Romania(Europe),as well as domestic poultry in some regions of Africa.The affected areas include the Central Asian,East Asian-Australasian,West Asian-East African,and Black Sea/Mediterranean flyways.These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds,thus posing a serious threat to wild birds and potentially humans.
文摘The highly pathogenic influenza A virus subtype H5N1 spread throughout Asia since 2003, reached to Europe in 2005, and the Middle East, as well as Africa and caused a global concern for a potential pandemic threat last decade. A Clade 2.3.2 H5N1 virus became dominate in the Qinghai Lake region in 2009 with sporadic mammal cases of infection and transferred to Russia and Europe through wild migratory birds. Currently, HPAI H5N1 of clades 2.3.4, 2.3.2, and 7 are the dominant co-circulating H5N1 viruses in poultry in Asia. 2.3.2 Clade is dominant in wild birds through the world whereas there is no evident data about Clade 7 circulation in wild birds. We detected HPAI H5N1 virus of Clade 7.1 in Qinghai Lake, that closely related to Shanxi-like and Vietnam viruses co-circulating in poultry. This is the first report of Clade 7.1 H5N1 in wild birds. Based on phylogenetic analyses, the virus can be originated from Clade 7.1 virus gene pool that spread in Vietnam and Chinese poultry and could spread with migratory birds to Qinghai Lake. The Qinghai Lake continues to be significant hotspot for H5N1 surveillance since the regular outbreaks occurred there in wild birds and mammals. Based on these facts and findings, the related researchers should pay more attention to the Qinghai Lake basin as significant hotspot for H5N1 avian influenza surveillance since the regular H5N1 outbreaks occurred there in wild birds with sporadic mammal cases of infection.
基金supported by the Major National Scientific Research Project, China (No. 2013CB956103)the Minhang Leading Talent Project
文摘Dinoflagellates in the genus Symbiodinium, including nine clades(A–I), mainly form mutualistic symbioses with corals. More than 100 Symbiodinium molecular types have been identified by the ITS2-based genotype method within any given clade, and specifically within Symbiodinium clade C. However, the genotype identification method using the ITS2 sequence is likely to lead to high diversity estimates due to the intra-genomic variations in the ITS2 space; thus, further validation is essential for a correct identification. In this study, the molecular diversity of Symbiodinium ITS2 sequences cloned from two stone corals, Acropora sp. SY-01 and Pocillopora sp. SY-05, and one soft coral, Sarcophyton sp. SY-07, living in the northern part of South China Sea(SCS), were analyzed and compared using the ITS2-based genotype identification method, coupled with ITS2-based secondary structural and phylogenetic analyses. As the result, 12 Symbiodinium ITS2 genotypes were identified, while only six and three Symbiodinium ITS2 genotypes were supported by ITS2-based secondary structural and phylogenetic analyses, respectively. In addition, no shared Symbiodinium ITS2 genotypes were observed among the three coral species, suggesting coral species-dependent Symbiodinium genotypes were within clade C. In summary, the present study provides a theoretical basis for validating the molecular diversity of Symbiodinium ITS2 genotypes in corals.
基金supported by the Nanjing Science and Technology Plan Project(202308003)the Social Development Project of Jiangsu Provincial Science and Technology Department(BE2022669)+1 种基金the Graduate Research and Innovation Projects of Jiangsu Province(SJCX23_0855)the Talent Lift Program of The Second Hospital of Nanjing(RCMS24008).
文摘Background The rapid increase in the number of monkeypox cases poses a considerable threat to the international community,necessitating sensitive,fast,and available diagnostic methods.Therefore,the objective of this study was to develop a rapid,sensitive and simple method with high clinical applicability.Methods We developed a simple,rapid point-of-care assay to detect monkeypox virus(MPXV)using multienzyme isothermal rapid amplification(MIRA)coupled with the clustered regularly interspaced short palindromic repeats(CRISPR)-Cas13a system.The detection system was optimized by synthesizing plasmids,and the detection sensitivity was explored by the continuous dilution of the plasmid.We validated the accuracy of this assay on 202 clinical MPXV samples and 104 interference samples through the kappa test.The visual interpretation of the results was realized by combining the assay with lateral flow strips.In addition,we developed a PCR-based method to identify MPXV Clades Ⅰ and Ⅱ,and the accuracy was tested through a kappa test on 202 clinical monkeypox samples and 104 interference samples.Results Our assay achieved an analytical sensitivity of 14.4 copies/ml and high selectivity,as it differentiated MPXV from three other Orthopoxvirus species.The clinical testing results for 202 monkeypox samples and 104 interference samples demonstrated 100%sensitivity and specificity.Compared with quantitative PCR(qPCR),three samples tested as positive using our assay,which showed that the performance of this assay was superior to that of the qPCR assay.Combined with lateral flow strips,its availability and simplicity provide an alternative point-of-care diagnostic method for MPXV testing in remote settings and resource-poor areas.The results of 32 clinical samples showed that lateral flow strips had a high detection sensitivity and could identify samples with Ct value of 39 as positive.The clade identification assay detected as few as 200 copies/ml within 40 min and no cross-reaction was observed between Clades Ⅰ and Ⅱ.The clinical samples tested were all Clade II,which was consistent with the circulating clade in the Chinese mainland.Conclusions The MIRA-CRISPR-Cas13a-MPXV system offers a rapid,sensitive and specific approach for monkeypox diagnosis,with significance for monitoring monkeypox epidemics.The clade identification assay based on PCR could accurately distinguish Clade Ⅰ from Clade Ⅱ within 40 min and can be implemented for high-throughput operation.
