Emergence of a novel recombinant of CV-A5 in HFMD epidemics in Xiangyang, China

Abstract Background Hand, foot and mouth disease (HFMD) is caused by a variety of enterovirus serotypes and the etiological spectrum worldwide has changed since a large scale of outbreaks occurred in 1997. Methods A large number of clinical specimens of HFMD patients were collected in Xiangyang and genotyping was performed by qRT-PCR, conventional PCR amplification and sequencing. Among the 146 CV-A5 detected cases, the complete genome sequences of representative strains were determined for genotyping and for recombination analysis. Results It was found that CV-A5 was one of the six major serotypes that caused the epidemic from October 2016 to December 2017. Phylogenetic analyses based on the VP1 sequences showed that these CV-A5 belonged to the genotype D which dominantly circulated in China. Recombination occurred between the CV-A5 and CV-A2 strains with a breakpoint in the 2A region at the nucleotide 3791. Conclusions The result may explain the emergence of CV-A5 as one of the major pathogens of HFMD. A multivalent vaccine against HFMD is urgently needed to control the disease and to prevent emerging and spreading of new recombinants.

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Emergence of a Novel Recombinant of CV-A5 in HFMD Epidemics in Xiangyang, China

10.21203/rs.3.rs-191606/v1 ◽

2021 ◽

Author(s):

Yuting Yu ◽

Zhiyu Luo ◽

Weiping Jin ◽

Jianyi Mai ◽

Jia Lu ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Pcr Amplification ◽

Foot And Mouth Disease ◽

Conventional Pcr ◽

Genome Sequences ◽

Qrt Pcr ◽

Etiological Spectrum ◽

Major Pathogens ◽

Enterovirus Serotypes

Abstract Hand, foot and mouth disease (HFMD) is caused by a variety of enterovirus serotypes and the etiological spectrum worldwide has been changing since a large scale of outbreaks occurred in 1997. A large number of clinical specimens of HFMD patients were collected in Xiangyang and genotyping was performed by qRT-PCR, conventional PCR amplification and sequencing. Among the146 CV-A5 cases detected, the complete genome sequences of representative strains were determined for genotyping and for recombination analysis. It was found that CV-A5 was one of the six major serotypes that caused the epidemic from October 2016 to December 2017. Phylogenetic analyses based on the VP1 sequences showed that these CV-A5 belong to the genotype D which dominantly circulates in China. Recombination occurred between the CV-A5 and CV-A2 strains with a breakpoint at the nt position 3,791 in the 2A region. The result may explain the emergence of CV-A5 as one of the major pathogens of HFMD.

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The Previously Unidentified, Divergent Badnavirus Species Cacao red vein-banding virus is Associated with Cacao Swollen Shoot Disease in Nigeria

Plant Disease ◽

10.1094/pdis-09-18-1561-re ◽

2019 ◽

Vol 103 (6) ◽

pp. 1302-1308 ◽

Cited By ~ 2

Author(s):

Nomatter Chingandu ◽

Lelia Dongo ◽

Osman A. Gutierrez ◽

Judith K. Brown

Keyword(s):

Phylogenetic Analyses ◽

Pcr Amplification ◽

West African ◽

Open Reading Frames ◽

Nucleotide Identity ◽

Genome Sequences ◽

Foliar Symptoms ◽

Field Samples ◽

Polymerase Chain ◽

Reading Frames

Cacao swollen shoot disease (CSSD) of Theobroma cacao was reported in Nigeria in 1944; however, no badnaviral genome sequences have been found associated with the symptomatic trees. In 2017, leaf samples (n = 18) were collected from cacao trees from Osun and Oyo, Nigeria showing foliar symptoms that included red vein-banding and shoot swelling, and variable secondary mosaic, mottling, and fern-like pattern symptoms. Abutting primers designed around previously determined 500-bp intergenic region sequences were used for polymerase chain reaction (PCR) amplification. Of the 18 samples, 9 yielded an approximately 7,000-bp, apparently genome-size product. The nine genomes were sequenced and found to encode four open reading frames, and to share 86 to 99% nucleotide identity. Pairwise analysis of the Nigerian genomes with 21 previously reported CSSD badnaviruses, at the complete genome and reverse-transcription ribonuclease H (1,230 bp) sequence levels, indicated 71 to 75 and 72 to 76% nucleotide identity, respectively. Phylogenetic analysis of the nine complete genomes indicated that the closest relatives of the divergent Nigerian isolates were previously described West African CSSD badnaviruses. Based on pairwise comparisons and phylogenetic analyses, the Nigerian CSSD isolates constitute a previously unrecognized Badnavirus sp., herein named Cacao red vein-banding virus (CRVBV). Primers designed based on the CRVBV genome sequences amplified a 1,068-bp fragment from 16 of 18 field samples tested by PCR, suggesting the possible existence of additional CRVBV variants.

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Epidemical and etiological study on hand, foot and mouth disease following EV-A71 vaccination in Xiangyang, China

Scientific Reports ◽

10.1038/s41598-020-77768-7 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Xiao-Dan Meng ◽

Yeqing Tong ◽

Zhen-Ni Wei ◽

Lei Wang ◽

Jian-Yi Mai ◽

...

Keyword(s):

Foot And Mouth Disease ◽

Mouth Disease ◽

Conventional Pcr ◽

Coxsackievirus A16 ◽

Enterovirus A71 ◽

Coxsackievirus A6 ◽

Foot And Mouth ◽

Etiological Spectrum ◽

Etiological Study ◽

Infants And Young Children

AbstractCoxsackievirus A6 (CV-A6) and Coxsackievirus A10 (CV-A10) have been emerging as the prevailing serotypes and overtaking Enterovirus A71 (EV-A71) and Coxsackievirus A16 (CV-A16) in most areas as main pathogens of hand, foot and mouth disease (HFMD) in China since 2013. To investigate whole etiological spectrum following EV-A71 vaccination of approximate 40,000 infants and young children in Xiangyang, enteroviruses were serotyped in 4415 HFMD cases from October 2016 to December 2017 using Real Time and conventional PCR and cell cultures. Of the typeable 3201 specimen, CV-A6 was the predominant serotype followed by CV-A16, CV-A10, CV-A5, CV-A2 and EV-A71 with proportions of 59.54%, 15.31%, 11.56%, 4.56%, 3.78% and 3.03%, respectively. Other 12 minor serotypes were also detected. The results demonstrated that six major serotypes of enteroviruses were co-circulating, including newly emerged CV-A2 and CV-A5. A dramatic decrease of EV-A71 cases was observed, whereas the total cases remained high. Multivalent vaccines against major serotypes are urgently needed for control of HFMD.

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Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽

10.3390/v13061017 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1017

Author(s):

Hirohisa Mekata ◽

Tomohiro Okagawa ◽

Satoru Konnai ◽

Takayuki Miyazawa

Keyword(s):

Phylogenetic Analyses ◽

Foamy Virus ◽

Pcr Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Whole Genome Analysis ◽

Virus Family ◽

Bovine Foamy Virus ◽

Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽

10.1126/science.abf2946 ◽

2021 ◽

pp. eabf2946

Author(s):

Louis du Plessis ◽

John T. McCrone ◽

Alexander E. Zarebski ◽

Verity Hill ◽

Christopher Ruis ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Transmission Dynamics ◽

Genetic Lineage ◽

Size Dependent ◽

Spatio Temporal ◽

The Uk ◽

Lineage Structure ◽

And Control ◽

Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

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Intercistronic heterogeneity of the 16S–23S rRNA spacer region among Pseudomonas strains isolated from subterranean seeds of hog peanut (Amphicarpa bracteata)

Microbiology ◽

10.1099/mic.0.028274-0 ◽

2009 ◽

Vol 155 (8) ◽

pp. 2630-2640 ◽

Cited By ~ 7

Author(s):

J. T. Tambong ◽

R. Xu ◽

E. S. P. Bromfield

Keyword(s):

Root Zone ◽

Phylogenetic Analyses ◽

Melting Curve ◽

Pcr Amplification ◽

23S Rrna ◽

Melting Curve Analysis ◽

Its1 Region ◽

A Genome ◽

Pure Cultures ◽

Intercalating Dye

Intercistronic heterogeneity of the 16S–23S rRNA internal transcribed spacer regions (ITS1) was investigated in 29 strains of fluorescent pseudomonads isolated from subterranean seeds of Amphicarpa bracteata (hog peanut). PCR amplification of the ITS1 region generated one or two products from the strains. Sequence analysis of the amplified fragments revealed an ITS1 fragment of about 517 bp that contained genes for tRNAIle and tRNAAla in all 29 strains; an additional smaller ITS1 of 279 bp without tRNA features was detected in 15 of the strains. The length difference appeared to be due to deletions of several nucleotide blocks between the 70 bp and 359 bp positions of the alignment. The end of the deletions in the variant ITS1 type coincided with the start of antiterminator box A, which is homologous to box A of other bacteria. Phylogenetic analyses using the neighbour-joining algorithm revealed two major phylogenetic clusters, one for each of the ITS1 types. Using a single specific primer set and the DNA-intercalating dye SYBR Green I for real-time PCR and melting-curve analysis produced highly informative curves with one or two recognizable melting peaks that readily distinguished between the two ITS1 types in pure cultures. The assay was used to confirm the presence of the variant ITS1 type in the Pseudomonas community in total DNA from root-zone soil and seed coats of hog peanut. Heterogeneity of the ITS1 region between species has potential for studying molecular systematics and population genetics of the genus Pseudomonas, but the presence of non-identical rRNA operons within a genome may pose problems.

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Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

ICES Journal of Marine Science ◽

10.1093/icesjms/fsw255 ◽

2017 ◽

Vol 74 (7) ◽

pp. 1875-1884 ◽

Cited By ~ 2

Author(s):

Dmitry N. Kulagin ◽

Tatiana V. Neretina

Keyword(s):

Atlantic Ocean ◽

Large Scale ◽

Phylogenetic Analyses ◽

Morphological Diversity ◽

Maturity Stage ◽

Congeneric Species ◽

Morphological Examination ◽

Posterior Teeth ◽

Biogeographic Patterns ◽

True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

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Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering

Scientific Reports ◽

10.1038/s41598-021-87491-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Smritikana Dutta ◽

Anwesha Deb ◽

Prasun Biswas ◽

Sukanya Chakraborty ◽

Suman Guha ◽

...

Keyword(s):

Large Scale ◽

Forest Ecology ◽

Phylogenetic Analyses ◽

Functional Characterization ◽

Constitutive Expression ◽

Transcript Level ◽

In Planta ◽

Mobility Shift ◽

Vegetative Development ◽

Sequence Comparisons

AbstractBamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.

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A global phylogenetic analysis of Japanese tonsil-derived Epstein–Barr virus strains using viral whole-genome cloning and long-read sequencing

Journal of General Virology ◽

10.1099/jgv.0.001549 ◽

2021 ◽

Author(s):

Misako Yajima ◽

Risako Kakuta ◽

Yutaro Saito ◽

Shiori Kitaya ◽

Atsushi Toyoda ◽

...

Keyword(s):

Viral Genome ◽

Epstein Barr Virus ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Regional Distribution ◽

Genome Sequences ◽

Barr Virus ◽

Endemic Areas ◽

Epstein Barr ◽

Genome Heterogeneity

Epstein–Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.

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