| ObjectiveDengue fever(DF)is a mosquito-borne viral disease caused by dengue viruses(DENV)of the genus Flavivirus of the family Flavivirus(including the four serotypes DENV-1、DENV-2、DENV-3 and DENV-4),which are mainly transmitted by two insect vectors,Aedes albopictus and Aedes aegypti.It occurs in tropical and subtropical climates and occurs frequently in summer and autumn in China.According to the severity of clinical symptoms,dengue fever is classified as dengue fever,dengue hemorrhagic fever(DHF)and dengue shock syndrome(DSS).According to the 2021 China Health Development Statistics Bulletin,there were 41 cases of dengue fever in China that year,an increase from the previous year,and mainly imported infections from Southeast Asian countries,African countries and South American countries.This shows that DF remains a potential public health threat in the country.Previous studies showed that the phylogeny,recombination variation,and evolutionary correlation of the recombinant strains of DENY strains result in the annual variation of the epidemic and evolutionary trends of different branches,which brings great difficulties for epidemic surveillance and control.Considering the above reasons,we used bioinformatics to screen DENV mutant and recombinant strains in mainland China to predict the DENV epidemic trend,and explored the recombinant breakpoints and positive selection sites of DF,which is of great significance for monitoring and preventing the epidemic.MethodA total of 266 complete genome sequences of DENV in mainland China from 2015 to 2020 were downloaded from the NCBI nucleotide sequence database and the Virus Pathogen Database,together with 4 reference sequences and 21 full-length sequences from dengue endemic countries during the decade.And then,We selected the 291 aligned sequences,and analyzed recombination analysis according to seven methods RDP,GENCONV,BOOTSCAN,MaxChi,CHIMAERA,SiScan,and 3SEQ.Because Recombinant strains are not suitable for selective pressure analysis,sequences with recombination signals detected by the method of RDP4 were excluded.The remaining 212 sequences were divided into four separate datasets according to serotype.At last,the cryptographic ratio was carried out using mega x,and the selective pressure analysis was finally analyzed after the recombinant signal was eliminated,ResultIn this study,those variants with recombination and adaptive evolutionary sites of circulating DENV strains were identified during 2015-2020.Phylogenetic analysis showed that the DENV-2 was the dominant epidemic serotype,and the dengue epidemic in China was closely related to the imported virus from Southeast Asian countries.The results of recombination analysis experiments showed that two or three recombination regions in a single dengue isolate.In particular,two recombinant strains and with extremely large exchange fragments were detected.For example,this large-scale gene fragment exchange(eight genomic regions)of strain DENV-4/China/YN/15DGR394(2015)with substitutions a both the 5’ and 3’ends of the genome,had never been described before.Moreover,selection pressure analyses revealed seven positive selection sites located in regions encoding the NS1,NS3 and NS5 proteins.ConclusionWe established a phylogenetic tree of the whole genome from 2015 to 2020 and reaffirmed the important influence of Southeast Asian countries on the dengue epidemic in China and the possibility of endemicity in Guangdong.However,the little is known about recombinants and positively selected mutants of circulating DENV strains in mainland China.Our results of recombination and selective pressure shed light on the formation of DENV genomic diversity and the difficulties in vaccine and drug development from an evolutionary standpoint.Overall,this study is the first to report ten specific intra-serotype recombinants and seven positive selection sites of Chinese epidemic strains of DENV,which highlight their significance for DENV surveillance and effective control. |
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