Complete Genome Sequence of a Putative Novel Ilarvirus Isolated From Eleocharis Dulcis

Abstract The complete genomic sequence of a novel ilarvirus from Eleocharis dulcis, tentatively named water chestnut virus A (WCVA), was determined using next generation sequencing (NGS) combined with reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The three genomic RNA components of WCVA were 3578 (RNA1), 2873 (RNA2) and 2073 (RNA3) nucleotides long, with four predicted open reading frames containing conserved domains and motifs typical of ilarviruses. Phylogenetic analyses of each predicted protein consistently placed WCVA in subgroup 4 of the genus Ilarvirus, together with prune dwarf virus, viola white distortion associated virus, fragaria chiloensis latent virus and potato yellowing virus. The genetic distances and lack of serological reaction to antisera of other ilarviruses suggest that WCVA is a novel member of the genus.

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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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Prevalence of GII.4 Sydney Norovirus Strains and Associated Factors of Acute Gastroenteritis in Children: 2019/2020 Season in Guangzhou, China

Food and Environmental Virology ◽

10.1007/s12560-021-09482-0 ◽

2021 ◽

Author(s):

Lei Duan ◽

Xiaohan Yang ◽

Jia Xie ◽

Wenli Zhan ◽

Changbin Zhang ◽

...

Keyword(s):

Acute Gastroenteritis ◽

Continuous Monitoring ◽

Gene Sequence ◽

Phylogenetic Analyses ◽

Open Reading Frames ◽

Severe Diarrhoea ◽

Chain Reaction ◽

Women And Children ◽

Polymerase Chain ◽

Reading Frames

AbstractNorovirus, the leading cause of non-bacterial acute gastroenteritis (AGE) worldwide, is constantly mutating. Continuous monitoring of the evolution of epidemic genotypes and emergence of novel genotypes is, therefore, necessary. This study determined the prevalence and clinical characteristics of norovirus strains in AGE in Guangzhou, China in 2019/2020 season. This study included children aged 2–60 months diagnosed with AGE in Guangzhou Women and Children Hospital, from August 2019 to January 2020. Norovirus was detected by real-time polymerase chain reaction and clinical data were obtained. Genotyping and phylogenetic analyses were performed with partial gene sequence fragments located within the open reading frames 1 and 2. During the study period, 168 children (61.3% males) were confirmed as norovirus infectious AGE. The main symptoms were diarrhoea and vomiting and 38 patients (22.6%) had seizures. Norovirus was mainly prevalent in October and November, and GII.4 Sydney[P31] was the major genotype circulating in Guangzhou. The phylogenetic tree showed that the Guangzhou strains had high homology with the strains circulating in 2017–2019 worldwide. GII.4 Sydney was the main prevalent norovirus genotype in Guangzhou from August 2019 to January 2020, which had more severe diarrhoea than those of other genotypes. These findings provide a valuable reference for the prevention, control, and treatment of norovirus in the future.

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Pax3 Gene Regulated Melanin Synthesis by Tyrosinase Pathway in Pteria penguin

International Journal of Molecular Sciences ◽

10.3390/ijms19123700 ◽

2018 ◽

Vol 19 (12) ◽

pp. 3700 ◽

Cited By ~ 3

Author(s):

Feifei Yu ◽

Bingliang Qu ◽

Dandan Lin ◽

Yuewen Deng ◽

Ronglian Huang ◽

...

Keyword(s):

Total Content ◽

Tissue Expression ◽

Melanin Synthesis ◽

Mizuhopecten Yessoensis ◽

Pax3 Gene ◽

Pteria Penguin ◽

Tissue Expression Profile ◽

Polymerase Chain ◽

Rapid Amplification ◽

Race Pcr

The paired-box 3 (Pax3) is a transcription factor and it plays an important part in melanin synthesis. In this study, a new Pax3 gene was identified from Pteria penguin (Röding, 1798) (P. penguin) by RACE-PCR (rapid-amplification of cDNA ends-polymerase chain reaction) and its effect on melanin synthesis was deliberated by RNA interference (RNAi). The cDNA of PpPax3 was 2250 bp long, containing an open reading fragment of 1365 bp encoding 455 amino acids. Amino acid alignment and phylogenetic tree showed PpPax3 shared the highest (69.2%) identity with Pax3 of Mizuhopecten yessoensis. Tissue expression profile showed that PpPax3 had the highest expression in mantle, a nacre-formation related tissue. The PpPax3 silencing significantly inhibited the expression of PpPax3, PpMitf, PpTyr and PpCdk2, genes involved in Tyr-mediated melanin synthesis, but had no effect on PpCreb2 and an increase effect on PpBcl2. Furthermore, the PpPax3 knockdown obviously decreased the tyrosinase activity, the total content of eumelanin and the proportion of PDCA (pyrrole-2,3-dicarboxylic acid) in eumelanin, consistent with influence of tyrosinase (Tyr) knockdown. These data indicated that PpPax3 played an important regulating role in melanin synthesis by Tyr pathway in P. penguin.

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Sequencing, Improved Detection, and a Novel Form of Kalanchoë top-spotting virus

Plant Disease ◽

10.1094/pd-89-0298 ◽

2005 ◽

Vol 89 (3) ◽

pp. 298-302 ◽

Cited By ~ 8

Author(s):

Zihong Yang ◽

Mogens Nicolaisen ◽

Neil E. Olszewski ◽

B. E. L. Lockhart

Keyword(s):

Genomic Sequence ◽

Pcr Amplification ◽

Leaf Tissue ◽

Open Reading Frames ◽

Oligonucleotide Primer ◽

Infected Leaf ◽

Breeding Lines ◽

Double Stranded Dna ◽

Extraction Step ◽

Polymerase Chain

Virions of Kalanchoë top-spotting virus (KTSV) were purified from infected leaf tissue of Kalanchoë blossfeldiana using a procedure that prevented loss of virus in the initial extraction step. The double-stranded DNA viral genome was cloned and sequenced. The KTSV genome was 7,591 bp in size and contained three open reading frames capable of encoding proteins of 21, 14, and 223 kDa, respectively. The size and organization of the KTSV genome were similar to those of other mealybug-transmitted badnaviruses. Several oligonucleotide primer pairs, based on the KTSV genomic sequence, were used to efficiently detect the virus in plants, thereby removing a major constraint to reliable screening of kalanchoë propagating stock and breeding lines for KTSV infection. Two KTSV sequences, one symptom-inducing and the other not, were identified and differentiated by polymerase chain reaction (PCR) amplification and digestion of the resulting amplicon with restriction endonucleases. Preliminary results from graft-transmission tests and PCR indexing suggest that the nonsymptomatic form of KTSV may represent an integrated viral element. The occurrence of such integrated pararetroviral elements poses practical problems for routine PCR indexing of breeding and propagating stock, and also raises the possibility of symptomatic episomal infections arising from these viral integrants.

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Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6

Journal of General Virology ◽

10.1099/vir.0.83460-0 ◽

2008 ◽

Vol 89 (2) ◽

pp. 444-452 ◽

Cited By ~ 20

Author(s):

Ling Lu ◽

Donald Murphy ◽

Chunhua Li ◽

Shuanghu Liu ◽

Xueshan Xia ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Genomic Sequence ◽

Phylogenetic Analyses ◽

Genetic Distances ◽

Reading Frame ◽

Novel Variants ◽

Reference Sequences ◽

Complete Genomic

In this study, the complete genomic sequence was determined for three hepatitis C virus variants (VT21, TV241 and TV249) of genotype 6 that do not classify within the established subtypes. All three genomes were isolated from patients in Vietnam and sequenced using 100 μl of serum. They showed 91.4–93.6 % nucleotide similarities to each other but only 71.7–79.4 % similarities to 17 reference sequences representing subtypes 6a–6q and to isolates km41 and gz52557. VT21, TV241 and TV249 displayed genome lengths of 9407, 9460 and 9445 nt, respectively. All three isolates contained a single open reading frame of 9051 nt while the 5′UTRs and 3′UTRs were 324–338 nt and 32–71 nt, respectively. They shared common sizes with QC227/6o and QC216/6p isolates in all ten protein regions. Phylogenetic analyses demonstrated that VT21, TV241 and TV249 clustered independently and were assigned subtype 6t, following the recent designations of 6r and 6s. Analysis of partial genomic sequences available for genotype 6 variants revealed five additional subtype 6t isolates, all originating from Vietnam. This analysis revealed two additional groups of isolates, and at least seven novel variants analogous to km41 and gz52557 that group independently and do not classify within the subtypes 6a–6t. This suggests the existence of at least 11 additional subtypes for genotype 6. In addition, the existence of isolates showing genetic distances greater than those within subtypes, but lesser than those between subtypes, raises interesting questions regarding the classification of HCV.

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Early-Transmitted Variants and Their Evolution in a HIV-1 Positive Couple: NGS and Phylogenetic Analyses

Viruses ◽

10.3390/v13030513 ◽

2021 ◽

Vol 13 (3) ◽

pp. 513

Author(s):

Alessia Lai ◽

Vania Giacomet ◽

Annalisa Bergna ◽

Gian Vincenzo Zuccotti ◽

Gianguglielmo Zehender ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Phylogenetic Analyses ◽

Viral Evolution ◽

Genetic Distances ◽

Viral Recombination ◽

Combined Antiretroviral Therapy ◽

Initiation Of Therapy ◽

Inference Methods ◽

Next Generation Sequencing Ngs ◽

Hiv 1

We had access to both components of a couple who became infected with human immunodeficiency virus (HIV)-1 through sexual behavior during the early initial phase of infection and before initiation of therapy. We analyzed blood samples obtained at the time of diagnosis and after six months of combined antiretroviral therapy. Next-generation sequencing (NGS) and phylogenetic analyses were used to investigate the transmission and evolution of HIV-1 quasispecies. Phylogenetic analyses were conducted using Bayesian inference methods. Both partners were infected with an HIV-1 B subtype. No evidence of viral recombination was observed. The lowest intrapersonal genetic distances were observed at baseline, before initiation of therapy, and in particular in the V1V2 fragment (distances ranging from 0.102 to 0.148). One HIV-1 single variant was concluded to be dominant in all of the HIV-1 regions analyzed, although some minor variants could be observed. The same tree structure was observed both at baseline and after six months of therapy. These are the first extended phylogenetic analyses performed on both members of a therapy-naïve couple within a few weeks of infection, and in which the effect of antiretroviral therapy on viral evolution was analyzed. Understanding which HIV-1 variants are most likely to be transmitted would allow a better understanding of viral evolution, possibly playing a role in vaccine design and prevention strategies.

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Molecular Identification of Trypanosoma evansi Isolated from Arabian Camels (Camelus dromedarius) in Riyadh and Al-Qassim, Saudi Arabia

Animals ◽

10.3390/ani11041149 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1149

Author(s):

Dina M. Metwally ◽

Isra M. Al-Turaiki ◽

Najwa Altwaijry ◽

Samia Q. Alghamdi ◽

Abdullah D. Alanazi

Keyword(s):

Saudi Arabia ◽

Infection Rate ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Trypanosoma Evansi ◽

Camelus Dromedarius ◽

18S Ribosomal Rna ◽

18S Ribosomal Rna Gene ◽

Polymerase Chain ◽

Pcr Targeting

We analyzed the blood from 400 one-humped camels, Camelus dromedarius (C. dromedarius), in Riyadh and Al-Qassim, Saudi Arabia to determine if they were infected with the parasite Trypanosoma spp. Polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) gene was used to detect the prevalence of Trypanosoma spp. in the camels. Trypanosoma evansi (T. evansi) was detected in 79 of 200 camels in Riyadh, an infection rate of 39.5%, and in 92 of 200 camels in Al-Qassim, an infection rate of 46%. Sequence and phylogenetic analyses revealed that the isolated T. evansi was closely related to the T. evansi that was detected in C. dromedarius in Egypt and the T. evansi strain B15.1 18S ribosomal RNA gene identified from buffalo in Thailand. A BLAST search revealed that the sequences are also similar to those of T. evansi from beef cattle in Thailand and to T. brucei B8/18 18S ribosomal RNA from pigs in Nigeria.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India

Scientific Reports ◽

10.1038/s41598-021-88859-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Manokaran Kamalakannan ◽

Chandrakasan Sivaperuman ◽

Shantanu Kundu ◽

Govindarasu Gokulakrishnan ◽

Chinnadurai Venkatraman ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Genetic Distances ◽

Medium Size ◽

Mitochondrial Cytochrome ◽

Volcanic Island ◽

Mammal Species ◽

Molecular Approaches ◽

Mitochondrial Cytochrome B ◽

Mitochondrial Cytochrome B Gene

AbstractWe discovered a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is of medium size (head and body lengths) and has a distinct external morphology (darker grey dense fur with a thick, darker tail) and craniodental characters (braincase is rounded and elevated with weak lambdoidal ridges) in comparison to other close congeners. This is the first discovery of a shrew from this volcanic island and increases the total number of Crocidura species catalogued in the Indian checklist of mammals to 12. The newly discovered species shows substantial genetic distances (12.02% to 16.61%) to other Crocidura species known from the Indian mainland, the Andaman and Nicobar Archipelago, Myanmar, and from Sumatra. Both Maximum-Likelihood and Bayesian phylogenetic inferences, based on mitochondrial (cytochrome b) gene sequences showed distinct clustering of all included soricid species and exhibit congruence with the previous evolutionary hypothesis on this mammalian group. The present phylogenetic analyses also furnished the evolutionary placement of the newly discovered species within the genus Crocidura.

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Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

Journal of International Medical Research ◽

10.1177/0300060520967778 ◽

2020 ◽

Vol 48 (12) ◽

pp. 030006052096777

Author(s):

Peisong Chen ◽

Xuegao Yu ◽

Hao Huang ◽

Wentao Zeng ◽

Xiaohong He ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ion Torrent ◽

Next Generation ◽

Large Deletions ◽

Different Types ◽

Variant Detection ◽

Polymerase Chain ◽

Next Generation Sequencing Ngs ◽

Accuracy And Repeatability ◽

Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

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