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Objective:To retrospectively analyze the molecular epidemiological features and genetic recombination of coxsackievirus A4 (CVA4) strains isolated in Jiangsu from 2015 to 2022.Methods:Throat or anal swab samples were collected from patients with herpangina or hand, foot and mouth disease (HFMD). Real-time PCR was used to detect CVA4. A comprehensive and systematic phylogenetic analysis was conducted based on 72 whole genomes and 99 VP1 sequences of CVA4 strains. Several bioinformatics software including DNAStar, MEGA7.0 and Similarity plots3.5.1 was used for analysis of homology, genetic recombination and amino acid variation sites.Results:Four genotypes (A, B, C and D) and five sub-genotypes (C1-C5) of CVA4 were identified based on the VP1 nucleotide sequences. C2 was the predominant sub-genotype causing HFMD. The Jiangsu strains showed high homology with the CVA4 prototype in the P1 region, and higher identity with other strains of enterovirus group A (EV-A) in the P2 and P3 regions. Genetic recombination analysis revealed that the Jiangsu strains had three genetic recombination patterns with other EV-A epidemic strains in the P2, P3 and 3′-UTR regions. These recombination patterns took place during the sustained and widespread circulation of CVA4 in people and increased the transmissibility of CVA4.Conclusions:This study analyzes the phylogenetic and molecular features of 28 whole genomes of Jiangsu CVA4 strains, which helps to better understand the genomic diversity of CVA4. By analyzing the genetic recombination and amino acid mutations in the VP1 region, this study elucidates the evolution and transmission of CVA4, which is conducive to the control and prevention of CVA4 infection.
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ObjectiveTo analyze the epidemic characteristics of measles and rubella in Pudong New Area of Shanghai from 2013 to 2022, and to provide data support for the elimination of measles and rubella. MethodsEnzyme linked immunosorbent assay was used to detect IgM antibodies in serum samples. The sequence of 630 nucleotides at the C-terminal of N gene of measles virus was amplified by reverse transcription-polymerase chain reaction and the phylogenic tree was constructed. ResultsA total of 1 529 suspected cases of measles were detected from 2013 to 2022, among which the positive rate of measles IgM antibody was 33.55% (513/1 529). The highest positive rate (20.73%) was from March to May , and the positive rate of rubella IgM antibody was 6.80% (104/1 529). The positive rate of both IgM was higher in males than that in females (P<0.05). The IgM against measles was mainly detected in 0‒ years old (63.16%, 96/152) and 20‒ years old (45.61%, 161/353). The IgM against rubella was mainly detected in 10‒20 years old (27.27%, 18/66). The IgM antibody could be detected more easily from 4 to 28 days after eruption, and the IgM antibody positive rate of measles/rubella from 2020 to 2022 was significantly lower than previous years (2013‒2019). There were 2 D8 genotype strains, and the rest were H1a gene subtypes. ConclusionThe positive rate of IgM antibodies against measles/rubella in Pudong New Area of Shanghai decreased significantly. People aged 0‒ years and 20‒ years old are more susceptible to measles, and rubella is concentrated in 10‒ years old. It is necessary to strengthen the vaccination of school-age children, in order to achieve the goal of eliminating measles. The age group with high risk of exposure should be checked for vaccination status to ensure the enhanced immunization, and the surveillance of imported measles cases should be strengthened.
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ObjectiveTo investigate the infection and genotypes of Wolbachia in Aedes albopictus. MethodsAdult and larval samples of Aedes albopictus were collected from different residential and wild areas from 2020 to 2021, Wolbachia surface protein (wsp) gene was amplified and genotyped for wAlbA and wAlbB by PCR, and sequenced for phylogenetic analysis. The difference of detection rate among different habitats, male and female adult mosquitoes, adult and larvae was compared by χ2 analysis. ResultsThe detection rate of Wolbachia in adult and larvae of Aedes albopictus were 43.5% (77/177) and 70.4% (190/270), respectively, with a statistically significant difference (χ2=32.086,P<0.001), and wAlbA and wAlbB were mainly detected together. The detection rate of Wolbachia in female and male Aedes albopictus were 50.7% (76/150) and 3.7% (1/27), respectively, with a statistically significant difference(χ2=20.533,P<0.001). The detection rate of adult Aedes albopictus in Songjiang wild area, residential area and Hongkou residential area were 91.7% (55/60), 18.8% (22/117) and 41.7% (30/72), respectively, with a statistically significant difference (χ2=54.322,P<0.001). Genotyping and phylogenetic analysis showed that adult and larvae of Aedes albopictus infected with Wolbachia were mainly wAlb A and wAlb B. In addition, some sequences formed clades independently, and the genetic distance from other sequences was relatively large. ConclusionInfection of Wolbachia in Aedes albopictus is relatively common in Songjiang District. The main genotypes are wAlb A and wAlb B and there may be other subtypes, which are worthy of further exploration and research.
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In this study, the chloroplast genome of Camellia insularis Orel & Curry was sequenced using high-throughput sequencing technology. The results showed that the chloroplast genome of C. insularis was 156 882 bp in length with a typical tetrad structure, encoding 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Codon preference analysis revealed that the highest number of codons coded for leucine, with a high A/U preference in the third codon position. Additionally, 67 simple sequence repeats (SSR) loci were identified, with a preference for A and T bases. The inverted repeat (IR) boundary regions of the chloroplast genome of C. insularis were relatively conserved, except for a few variable regions. Phylogenetic analysis indicated that C. insularis was most closely related to C. fascicularis. Yellow camellia is a valuable material for genetic engineering breeding. This study provides fundamental genetic information on chloroplast engineering and offers valuable resources for conducting in-depth research on the evolution, species identification, and genomic breeding of yellow Camellia.
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Genoma de Cloroplastos/genética , Filogenia , Melhoramento Vegetal , Camellia/genética , Cloroplastos/genéticaRESUMO
This study investigated the choroplast genome sequence of wild Atractylodes lancea from Yuexi in Anhui province by high-throughput sequencing, followed by characterization of the genome structure, which laid a foundation for the species identification, analysis of genetic diversity, and resource conservation of A. lancea. To be specific, the total genomic DNA was extracted from the leaves of A. lancea with the improved CTAB method. The chloroplast genome of A. lancea was sequenced by the high-throughput sequencing technology, followed by assembling by metaSPAdes and annotation by CPGAVAS2. Bioiformatics methods were employed for the analysis of simple sequence repeats(SSRs), inverted repeat(IR) border, codon bias, and phylogeny. The results showed that the whole chloroplast genome of A. lancea was 153 178 bp, with an 84 226 bp large single copy(LSC) and a 18 658 bp small single copy(SSC) separated by a pair of IRs(25 147 bp). The genome had the GC content of 37.7% and 124 genes: 87 protein-coding genes, 8 rRNA genes, and 29 tRNA genes. It had 26 287 codons and encoded 20 amino acids. Phylogenetic analysis showed that Atractylodes species clustered into one clade and that A. lancea had close genetic relationship with A. koreana. This study established a method for sequencing the chloroplast genome of A. lancea and enriched the genetic resources of Compositae. The findings are expected to lay a foundation for species identification, analysis of genetic diversity, and resource conservation of A. lancea.
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Filogenia , Atractylodes/genética , Genoma de Cloroplastos , Sequenciamento Completo do Genoma , Repetições de Microssatélites , LamialesRESUMO
This study determined the whole genome sequence and phylogenetic characteristics of a rat coronavirus.Nucleic acids were extracted from rat intestinal tissues collected in Inner Mongolia,and high-throughput sequencing was performed.A novel alphacoronavirus was present in the samples.The complete genome was amplified with PCR and RACE.Multiple se-quence alignment and a phylogenetic tree were constructed in MEGA.The whole genome of the rat coronavirus,denoted NMR-13,was 27 674 bp and included two non-coding regions and eight open reading frames,successively 5'UTR-ORF1ab-S-ORF3-E-M-ORF6-N-ORF8-3'UTR.Sequence identity analysis indicated that NMR-13 was most closely related to alphacoronavirus,which shared 91.3%nt identity with strain FiCoV/UMN2020.NMR-13h shared the next highest-sequence identitywiththe strains Lucheng/Lijiang-170,Lucheng/Ruian-83 and Lucheng/Lijiang-71 found in Zhejiang Province,China(79.49%,80.6%and 81.0%,respectively).Phylogeneticanalysis indicated that NMR-13 clustered with FiCoV/UMN2020.Recombination analy-sis indicated no recombination phenomenon.A rat coronavirus was isolated in this study,thus enriching the diversity of known alphacoronaviruses,and providing a reference for understanding the molecular genetic characteristics and molecular evolution of mouse coronaviruses in China.
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Objective:To analyze the whole-genome sequences of coxsackievirus A10 (CVA10) strains isolated in Jiangsu Province from 2015 to 2022 and their molecular epidemiological characteristics.Methods:Forty-five CVA10 isolates circulating in Jiangsu Province during 2015 to 2022 were selected for whole-genome sequencing. Phylogenetic trees were constructed based on the whole genome, VP1, P1, P2 and P3 sequences of CVA10 strains. Bioinformatics software, including DNAStar, MEGA7.0 and Similarity plots3.5.1, was used for analysis of homology, genetic recombination and major amino acid variation sites.Results:The nucleotide and amino acid sequence homology of the whole-genome sequences of 45 CVA10 strains was 90.3%-99.1% and 97.9%-99.8%, respectively. The nucleotide sequence homology of P1 region was the highest (92.1%-100.0%), while the nucleotide sequence homology of P3 region ranged from 84.7% to 100.0%. In contrast to the diversity of nucleotide sequences, the amino acid sequences of each region were conserved. A phylogenetic analysis based on the complete VP1 sequences of CVA10 strains revealed eight genotypes: A-H. The CVA10 isolates in Jiangsu Province and other prevalent strains in China mainly belonged to genogroup C. Results of the phylogenetic analysis based on the whole-genome sequences and complete VP1 sequences were consistent. Phylogenetic analysis bases on different gene segments and Simplot recombination analysis revealed that Jiangsu isolates GD07/Lianyungang/2017 and N180/Suqian/2016 showed high homology with the CVA10 prototype in the P1 region, but had recombination sites with other strains of enterovirus group A in the P2, P3, 5′-UTR and 3′-UTR regions. Compared with the prototype strain AY421767/Kowalik/2004, the Jiangsu isolates showed frequent variations in the VP1 region and many other major amino acid sites, which might result in some imperceptible changes in capsid structure and potential receptor-binding sites.Conclusions:By analyzing the evolution and genetic recombination features of CVA10 strains at the genome level in Jiangsu Province, this study elucidated the influence of genetic recombination and amino acid site mutation on CVA10 infection, providing basic data for the prevention and control of hand-foot-mouth disease in Jiangsu Province.
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OBJECTIVE@#To investigate the infection and genotypes of Wolbachia in common mosquito species in Henan Province, so as to provide insights into management of mosquito-borne diseases.@*METHODS@#Aedes, Culex and Anopheles samples were collected from cowsheds, sheepfolds and human houses in Puyang, Nanyang City and Xuchang cities of Henan Province from July to September, 2022, and the infection of Wolbachia was detected. The 16S rDNA and wsp genes of Wolbachia were amplified and sequenced. Sequence alignment was performed using the BLAST software, and the obtained 16S rDNA gene sequence was compared with the sequence of the 16S rDNA gene in GenBank database. In addition, the phylogenetic trees were created based on 16S rDNA and wsp gene sequences using the software MEGA 11.0.@*RESULTS@#A total 506 female adult mosquitoes were collected from three sampling sites in Nanyang, Xuchang City and Puyang cities from July to September, 2022. The overall detection of Wolbachia was 45.1% (228/506) in mosquitoes, with a higher detection rate in A. albopictus than in Cx. pipiens pallens [97.9% (143/146) vs. 50.6% (85/168); χ2 = 88.064, P < 0.01]. The detection of Wolbachia in Cx. pipiens pallens was higher in Xuchang City (96.8%, 62/64) than in Nanyang (15.6%, 7/45) and Puyang cities (27.1%, 16/59) (χ2 = 89.950, P < 0.01). The homologies of obtained Wolbachia 16S rDNA and wsp gene sequences were 95.3% to 100.0% and 81.7% to 99.8%. Phylogenetic analysis based on wsp gene sequences showed Wolbachia supergroups A and B in mosquito samples, with wAlbA and wMors strains in supergroup A and wPip and wAlbB strains in supergroup B. Wolbachia strain wAlbB infection was detected in A. albopictus in Puyang and Nanyang Cities, while Wolbachia strain wPip infection was identified in A. albopictus in Xuchang City. Wolbachia strain wAlbA infection was detected in Cx. pipiens pallens sampled from three cities, and one Cx. pipiens pallens was found to be infected with Wolbachia strain wMors in Nanyang City.@*CONCLUSIONS@#Wolbachia infection is commonly prevalent in Ae. albopictus and Cx. pipiens pallens from Henan Province, and Wolbachia strains wAlbB and wAlbA are predominant in Ae. albopictus, while wPip strain is predominant in Cx. pipiens pallens. This is the first report to present Wolbachia wMors strain infection in Cx. pipiens pallens in Henan Province.
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Animais , Humanos , Filogenia , Wolbachia/genética , Culex/genética , Aedes/genética , DNA RibossômicoRESUMO
Aims@#Rice (Oryza sativa) is one of Malaysia’s most significant crops. Rice blast caused by Pyricularia oryzae is one of the most serious diseases of Oryza sativa, causing significant damage to the Malaysian rice crop and impacting productivity. This study was carried out to isolate and characterize phytopathogenic fungal isolates associated with rice blast collected in a paddy field in Alor Setar, Kedah, Malaysia.@*Methodology and results@#Morphological characterization of seven fungal isolates obtained showed thin, white, and grayish green mycelia and the reverse colony was light yellow to brown. The fungal isolates produced two-septate pyriform (pear-shaped) conidia with solitary, unbranched and light brown conidiophores. Pathogenicity tests of all isolates on rice leaves revealed diamond-shaped symptoms with a grayish center and brown edge. All isolates showed similar morphological and pathogenicity characteristics; thus, a representative isolate was further identified through DNA sequencing and phylogenetic analysis of the internal transcribed spacer (ITS) region for species confirmation. Based on DNA sequences of ITS and phylogenetic analysis, the representative isolate was confirmed as P. oryzae.@*Conclusion, significance and impact of study @#Seven isolates morphologically identified as Pyricularia sp. were tested as pathogenic by causing rice blast disease. Representative isolate P2 (USM-PD1) was confirmed to be P. oryzae by DNA sequencing and phylogenetic analysis of the ITS region. This study provides information on the etiology and symptomatology of rice blast disease caused by P. oryzae USM-PD1 that can be applied to diagnose and mitigate the threat posed by this plant pathogen for the disease management.
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Objective:To analyze the non-enterovirus A71 (non-EVA71) and non-coxsackievirus A16 (non-CVA16) enteroviruses causing hand, foot and mouth disease (HFMD) in Kunming and Qujing of Yunnan Province in 2021 by sequencing the VP4/VP2 and VP1 genes and to analyze the phylogenetic characteristics of the VP1 gene of CVA2, aiming to provide reference for the prevention and control of CVA2.Methods:The samples were made and extracted strictly according to the Laboratory Manual for Hand, Foot and Mouth Disease (China Center for Disease Control and Prevention, 2018 Edition). VP4/VP2 junction regions were firstly amplified and sequenced by MD91/OL68-1 primers. These sequences were firstly edited and then "blasted" on the GenBank to determine the virus serotype. To analyze the phylogenetic characteristics of CVA2, the entire VP1 gene sequences were amplified in two segments using enterovirus species A primers. Virus serotype was again confirmed online by "Enterovirus Genotyping Tool Version 0.1". The sequences of the reference virus genotypes/sub-genotypes were downloaded according to the reference. The phylogenetic trees were constructed by Mega5.2 software and the genetic characteristics were analyzed.Results:A total of 749 non-EVA71 and non-CVA16 enteroviruses were detected in the two areas in 2021. Group A enteroviruses were the main pathogens, with CVA16 as the predominant virus, and a small number of group B enteroviruses were reported. Only five strains of CVA2 were detected with a detection rate of 0.67% (5/749), indicating that CVA2 was a rare pathogen for HFMD in the two areas. The sequencing and serotyping results were consistent using the two genomic regions of VP4/VP2 junction region and VP1 region. Phylogenetic analysis showed that three Kunming strains belonged to genotype A, while two Qujing strains belonged to genotype D.Conclusions:The detection rate of CVA2 in Kunming and Qujing was 0.67% in 2021. CVA2 was a rare pathogen for HFMD in the two regions. Phylogenetic analysis showed genotypes A and D spread in Kunming and Qujing, respectively, but had not caused epidemics. To our knowledge, this was the first report of genotype A of CVA2 in China. Strengthening the laboratory surveillance especially molecular epidemiological surveillance is valuable for the monitor and analysis of transmission source for CVA2.
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Objective:To identify and characterize one Spiroplasma strain (designated as DGKH1) isolated from the blood of a patient with sepsis. Methods:The traditional bacterial culture, staining, morphological observation, physiological and biochemical identification, 16S rRNA gene sequencing, phylogenetic analysis, genome sequencing, and the genome-related index analysis were performed to accurately determine the taxonomic status of the strain DGKH1. Antibiotic susceptibility testing was performed using a specific kit for culturing and testing Ureaplasma urealyticum/ Metamycoplasma hominis. Results:The strain DGKH1 could weakly grow on Columbia blood agar, chocolate agar, and Haemophilus chocolate 2 agar. However, it did not grow in liquid culture medium containing tetracycline (4 μg/ml), doxycycline (1 μg/ml), minocycline (1 μg/ml), josamycin (2 μg/ml), roxithromycin (1 μg/ml), clarithromycin (1 μg/ml), or telithromycin (1 μg/ml). DGKH1 resembling Metamycoplasma hominis formed "fried egg-like colonies" on Mycoplasma solid culture medium. DGKH1 could not be stained by Gram staining. When observed under transmission electron microscopy (TEM) using phosphate buffer as the matrix, the bacteria were spiral-shaped. Results of 16S rRNA gene sequence alignment showed that DGKH1 was highly similar (99.85%) to Spiroplasma eriocheiris CCTCC M 207170 T. However, the urea decomposition test was positive, which was different from all of the known Spiroplasma species. The phylogenetic analysis based on whole genome showed that DGKH1 was clustered in a small branch along with Spiroplasma eriocheiris CCTCC M 207170 T. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 94.14% and 56.00%, respectively, both below the threshold for prokaryotic species identification. Conclusions:DGKH1 represented a potential new species of genus Spiroplasma, closely related to Spiroplasma eriocheiris. Some microbiological characteristics of DGKH1 were similar to Mycoplasmas. However, the natural host and epidemiological data of DGKH1 need to be further studied.
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@#Objective: Human respiratory syncytial virus (RSV) is a primary cause of paediatric severe acute respiratory infection (SARI) worldwide, especially in developing countries. We investigated the genetic characteristics of RSV in northern Viet Nam to determine the prevalence and distribution of subtypes as well as the diversity and transmission patterns of genotypes. Methods: In two facilities, from January 2017 to December 2020, 1563 clinical specimens were collected from paediatric patients hospitalized with SARI and tested for RSV. Selected positive samples underwent sequencing analysis targeting the second hypervariable region of the G gene using next-generation sequencing. Results: The RSV positivity rate was 28.02% (438/1563 samples), and prevalence was highest in children aged <1 year (43.84%; 192/438). Subtype RSV-A accounted for 53.42% (234/438) of cases, RSV-B for 45.89% (201/438), and there was coinfection in 0.68% (3/438). Both subtypes cocirculated and peaked during August–September in each year of the study. Phylogenetic analysis showed that RSV-A samples belonged to the ON1 genotype, which has three subgenotypes: ON1.1, ON1.2 and ON1.3. However, we did not find the 72-nucleotide duplication in the second hypervariable region of the G gene, a characteristic of genotype ON1, in any RSV-A samples. RSV-B samples belonged to genotype BA9. Discussion: Our results provide additional molecular characterization of RSV infections in Viet Nam. Specially, our study is the first to report the absence of the 72-nucleotide duplication in the G gene of RSV-A genotype ON1 in Viet Nam, which may help in understanding the genetic evolution of RSV and be useful for vaccine development in the future.
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Objective To investigate the HIV-1 genotype and distribution of newly diagnosed HIV-1 cases in Fujian Province in 2020, so as to provide insights into formulation of the precise AIDS control strategy in the province. Methods Newly diagnosed HIV-1 cases without antiretroviral therapy (excluding AIDS patients) were randomly sampled from each city of Fujian Province in 2020 at a proportion of 50% of the mean number of HIV-infected cases reported across 9 cities of Fujian Province during the past three years. Subjects’ demographic and epidemiological data were collected and blood samples were collected. The HIV-1 pol gene was amplified using nested reverse-transcription PCR assay, and the gene sequences were used for HIV-1 genotyping and phylogenetic analysis. The gene sequences were uploaded to the HIV Drug Resistance Database (http://hivdb.stanford.edu) for genotypic drug resistance assays, and the scores and level of HIV drug resistance were estimated using the HIVDB Algorithm version 9.5. Results A total of 1 043 newly diagnosed HIV-1 cases were reported in Fujian Province in 2020, and 936 gene sequences were successfully obtained following sequencing of blood samples. There were 9 HIV-1 genotypes characterized in blood samples from 936 newly diagnosed HIV-1 cases, with CRF07_BC (52.1%) and CRF01_AE (30.4%) as predominant subtypes, followed by CRF08_BC (4.9%), CRF55_01B (3.0%), subtype C (2.5%), subtype B (2.1%), CRF85_BC (1.7%), CRF59_01B (0.3%) and CRF65_CPX (0.1%), and unidentified subtypes were found in 26 blood samples. HIV-1 drug resistance was detected in 43 out of the 936 newly diagnosed HIV-1 cases, with 4.6% prevalence of HIV-1 drug resistance prior to therapy, and the highest drug resistance was found in the HIV CRF59_01B subtype, followed by in CRF08_BC, B, C, CRF01_AE, CRF07_BC and other subtypes, with a significant difference in the genotype-specific prevalence of HIV-1 drug resistance (χ2 = 45.002, P < 0.05). Conclusions There was a HIV-1 genotype diversity in Fujian Province in 2020, and emerging recombinant and drug-resistant HIV-1 strains were detected and spread across patients and regions. Monitoring of HIV-1 genotypes is recommended to be reinforced for timely understanding of the transmission and spread of novel recombinant and drug-resistant HIV-1 strains.
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The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.
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Filogenia , Rubus/genética , Genoma de Cloroplastos , Frutas/genética , Códon/genéticaRESUMO
"Tangjie" leaves of cultivated Qinan agarwood were used to obtain the complete chloroplast genome using high-throughput sequencing technology. Combined with 12 chloroplast genomes of Aquilaria species downloaded from NCBI, bioinformatics method was employed to determine the chloroplast genome characteristics and phylogenetic relationships. The results showed that the chloroplast genome sequence length of cultivated Qinan agarwood "Tangjie" leaves was 174 909 bp with a GC content of 36.7%. A total of 136 genes were annotated, including 90 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Sequence repeat analysis detected 80 simple sequence repeats(SSRs) and 124 long sequence repeats, with most SSRs composed of A and T bases. Codon preference analysis revealed that AUU was the most frequently used codon, and codons with A and U endings were preferred. Comparative analysis of Aquilaria chloroplast genomes showed relative conservation of the IR region boundaries and identified five highly variable regions: trnD-trnY, trnT-trnL, trnF-ndhJ, petA-cemA, and rpl32, which could serve as potential DNA barcodes specific to the Aquilaria genus. Selection pressure analysis indicated positive selection in the rbcL, rps11, and rpl32 genes. Phylogenetic analysis revealed that cultivated Qinan agarwood "Tangjie" and Aquilaria agallocha clustered together(100% support), supporting the Chinese origin of Qinan agarwood from Aquilaria agallocha. The chloroplast genome data obtained in this study provide a foundation for studying the genetic diversity of cultivated Qinan agarwood and molecular identification of the Aquilaria genus.
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Filogenia , Genoma de Cloroplastos , Códon , Anotação de Sequência Molecular , Thymelaeaceae/genéticaRESUMO
Introducción. El síndrome respiratorio agudo grave causado por el nuevo coronavirus SARS-CoV-2 es causa de la emergencia sanitaria por la pandemia de COVID-19. Si bien el humano es el principal huésped vulnerable, en estudios experimentales y reportes de infección natural, se han encontrado casos de zoonosis inversa de SARS-CoV-2 en animales. Objetivo. Evaluar la infección natural por SARS-CoV-2 en gatos y perros de propietarios con diagnóstico de COVID-19 en el Valle de Aburrá, Antioquia, Colombia. Materiales y métodos. La circulación del SARS-CoV-2 se evaluó por RT-qPCR y RT-PCR en muestras de frotis nasofaríngeos y orofaríngeos de gatos y perros cuyos propietarios se encontraban dentro del periodo de los 14 días de aislamiento. Los casos positivos se verificaron amplificando fragmentos de los genes RdRp, N y E; se secuenció el gen RdRp y se analizó filogenéticamente. Resultados. De 80 animales evaluados, seis gatos y tres perros fueron casos confirmados de infección natural por SARS-CoV-2. Los animales no presentaron signos clínicos y sus propietarios, que padecían la infección, reportaron únicamente signos leves de la enfermedad sin complicaciones clínicas. En el análisis de una de las secuencias, se encontró un polimorfismo de un solo nucleótido (SNP) con un cambio en la posición 647, con sustitución del aminoácido serina (S) por una isoleucina (I). Los casos se presentaron en los municipios de Caldas, Medellín y Envigado. Conclusiones. Se infiere que la infección natural en los gatos y perros se asocia al contacto directo con un paciente con COVID-19. No obstante, no es posible determinar la virulencia del virus en este huésped, ni su capacidad de transmisión zoonótica o entre especie.
Introduction: The severe acute respiratory syndrome caused by the new coronavirus SARS-CoV-2 is the cause of the health emergency due to the COVID-19 pandemic. Although humans are the main susceptible host, experimental studies and reported cases of natural infection have evidenced scenarios of SARS-CoV-2 reverse zoonosis in animals. Objective: To evaluate the natural infection of SARS-CoV-2 in cats and dogs with owners diagnosed with COVID-19 in the Valle de Aburrá subregion in Antioquia, Colombia. Materials and methods. The circulation of SARS-CoV-2 was evaluated by RT-qPCR and RT-PCR in samples of nasopharyngeal and oropharyngeal smears from cats and dogs whose owners presented latent COVID-19 infection. Positive cases were verified through amplification of N, E and RdRp gene fragments; with the latter being sequenced and the phylogenetically analyzed. Results. From 80 tested animals, 6 cats and 3 dogs resulted positive for natural SARS-CoV-2 infection. These animals did not show any clinical signs; and their infected owners only reported mild signs of COVID-19, without clinical complications. Regarding analysis of one of the sequences, a single nucleotide polymorphism (SNP) was found, with a substitution in position 647, resulting in the change of the amino acid serine (S) for isoleucine (I). The cases occurred in the municipalities of Caldas, Medellín and Envigado. Conclusions. It is inferred that natural infection in cats and dogs is associated with direct contact with a positive COVID-19 patient.
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Zoonoses , Infecções por Coronavirus , Filogenia , Síndrome Respiratória Aguda Grave , Interações entre Hospedeiro e MicrorganismosRESUMO
Objective:To investigate the predominant types of enteroviruses and the characteristics of the VP1 gene of coxsackievirus A4 (CVA4) causing hand, foot and mouth disease (HFMD) in Yunnan Province from 2018 to 2020.Methods:Throat swab and stool samples were collected from HFMD cases and tested by real-time quantitative PCR for nucleic acid detection. The samples positive for enterovirus nucleic acids were used for viral isolation and sent to the National Center for Disease Control and Prevention. The VP1 gene of the isolated strains was sequenced and analyzed.Results:From 2018 to 2020, a total of 21 757 HFMD samples were collected, 16 457 (75.64%) of which were positive for enteroviruses. Altogether 533 strains were isolated from 4 114 positive samples that were selected for viral isolation, including 89 strains of enterovirus 71 (EVA71, 16.70%), 180 strains of coxsackievirus A16 (CVA16, 33.77%), 76 strains of CVA10 (14.26%), 118 strains of CVA6 (22.14%), 26 strains of CVA4 (4.88%) and 44 strains of other types (8.26%). HFMD occurred mainly in children under five years old with higher incidence in males than in females (1.35∶1). The incidence of HFMD reached the peak in the second and third quarters. In Yunnan Province, CVA4 mainly circulated in Qujing and Kunming, and was sporadically detected in Wenshan and Honghe. The VP1 gene was 915 bp in length. Twenty-six CVA4 strains belonged to C2 subtype, which were genetically far from the prototype strain AY421762-HighPoint. Mutations in the VP1 gene were found at multiple sites including 18, 23, 34, 102, 148, 164, 200, 262, 174, 275, 285 and 303. These strains showed 80.4%-99.0% homology in nucleotide sequence and 95.6%-99.0% in amino acid sequence. Nucleotide mutations were mostly synonymous mutations.Conclusions:CVA16, CVA6, EVA71 and CVA10 were the predominant enteroviruses causing HFMD in Yunnan Province from 2018 to 2020. The prevalence of CVA4 was also worthy of attention. CVA4 isolates in Yunnan Province belonged to C2 subtype, mainly circulating in the east and southeast of Yunnan Province and gradually becoming a cocirculating predominant strain. Long-term dynamic monitoring would be of great public health significance for improving the sensitivity of HFMD early warning.
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ObjectiveTo analyze the genetic characteristics of the hemagglutinin (H) gene of measles virus (MeV) in Shanghai, 2001‒2018. MethodsNasopharyngeal swab specimens were collected from suspected measles cases reported in Shanghai from 2001 to 2018, and the isolation of measles virus was conducted with Vero/hSLAM cell line. RT-PCR amplification and sequencing were conducted after RNA extraction to analyze the genetic characteristics of the complete H gene. ResultsIn total, 5 665 nasopharyngeal swab samples were collected by suspected measles case surveillance from 2001 to 2018, and 1 394 measles virus strains were isolated. The homology of nucleotide acid and amino acid among 349 representative measles virus isolates was 87.4%‒100.0% and 85.1%‒100.0%, respectively. The homology of nucleotide acid and amino acid between representative measles virus isolates and China vaccine strain (S191) was 85.7%‒100.0% and 84.1%‒100.0%, respectively. All the sub-genotype H1a MeV isolates had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. ConclusionMost of the MeV isolates are sub-genotype H1a analyzed based on H gene, which are identical to those of the N gene. The predicted amino acid sequences of the H protein are relatively conserved at most of the functionally significant amino acid positions.
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Docynia longiunguis is a plant uniquely present in China and is of high edible and medicinal value. The analysis of its chloroplast genome will help clarify the phylogenetic relationship among Docynia and facilitate the development and utilization of D. longiunguis resources. Based on the alignment of chloroplast genome sequences of related species, the phylogeny and codon preference were analyzed. The total length of D. longiunguis chloroplast genome sequence was 158 914 bp (GenBank accession number is MW367027), with an average GC content of 36.7%. The length of the large single-copy (LSC), the small single-copy (SSC), and inverted repeats (IRs) are 87 020 bp, 19 156 bp, and 26 369 bp, respectively. A total of 102 functional genes were annotated, including 72 protein-coding genes, 26 tRNA genes, and 4 rRNA genes. The best model for constructing phylogenetic tree was TVM+F+R2. D. longiunguis and Docynia indica were clustered into a single group, while Docynia and Malus were clustered into a single group. Comparison of the chloroplast genome sequences of D. longiunguis and its five related species revealed that trnY (GUA)-psbD, ndhC-trnV (UAC), accD-psaI, psbZ-trnfM (CAU), ndhF-trnL gene regions varied greatly. The nucleic acid diversity analysis showed that there were 11 high variation areas with nucleotide variability > 0.01, all were located in the LSC and SSC regions. Except for D. longiunguis, the trnH genes in other sequences were located at the IRs/LSC junction and did not cross the boundary. Codon preference analysis showed that D. longiunguis chloroplast genome has the largest number of isoleucine (Ile) codons, up to 1 205. D. longiunguis has the closest genetic relationship with Malus baccata, Malus sieboldii, Malus hupehensis and Chaenomeles sinensis. Its chloroplast genome codon prefers to end with A/T. The chloroplast genome of D. longiunguis and other Rosaceae chloroplast genomes showed great differences in gene distribution in four boundary regions, while relatively small differences from the chloroplast genomes of Docynia delavayi and D. indica of the same genus were observed. The genome annotation, phylogenetic analysis and sequence alignment of chloroplast genome of D. longiunguis may facilitate the identification, development and utilization of this species.
Assuntos
Uso do Códon , Genoma de Cloroplastos , Genômica , Filogenia , RosaceaeRESUMO
Soybean mosaic virus (SMV) is a critical pathogen that reduces the soybean yield and seed quality worldwide, and SMV has a restricted natural host range. In this study, we used sequence-independent amplification (SIA) methods to identify the viruses that may cause the Atractylodes macrocephala Koidz disease. Results revealed that there is SMV in diseased Atractylodes macrocephala leaves, and we named this isolate as SMV-Am. To further characterize the genomic structural and phylogenetic relationships of SMV-Am, genomic dsRNA was extracted, and the genomic sequence was amplified by RT-PCR and RACE. The results of bioinformatics analysis showed that the genomic RNA of SMV-Am is 9587 nucleotides in length, which conforms to the typical characteristics of Potyvirus. According to the sequence alignment of complete nucleotide sequences, SMV-Am showed the highest level of nucleotide homology and amino acid sequences to SMV-Liaoning, 96. 57% and 98. 86%, respectively. In addition, phylogenetic analysis based on the nucleotide sequences of other SMV isolates of SMV-Am revealed that SMV-Am was most closely related to SMV-Liaoning. Then, the SMV-Am protein was further analyzed by I-TASSER and PyMOL software, revealing that the key amino acid mutations led to the structural changes of P1, HC-Pro, P3, 6K2, NIa-pro and NIb proteins, with P1 the most obvious. Finally, recombination has been detected at the position of 6560-8950 nucleotides, the main parent is the isolate SMV-XFQ012 (accession number KP710875. 1), and the secondary parent is isolate SMV-pCB301-SC15 (accession number MH919386. 1). This study is the first report of SMV in Atractylodes macrocephala Koidz, and these results are expected to provide a scientific basis for the prevention and control of SMV infection on Atractylodes macrocephala Koidz.