Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

Download Full-text

Genome Sequence of Cotton Leafroll Dwarf Virus Infecting Cotton in Georgia, USA

Microbiology Resource Announcements ◽

10.1128/mra.00812-20 ◽

2020 ◽

Vol 9 (34) ◽

Author(s):

Afsha Tabassum ◽

Phillip M. Roberts ◽

Sudeep Bag

Keyword(s):

United States ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

The United States ◽

Dwarf Virus ◽

Dwarf Disease ◽

Cotton Leafroll Dwarf Virus

ABSTRACT Cotton leafroll dwarf disease (CLRDD), caused by the aphid-borne Cotton leafroll dwarf virus (CLRDV; genus, Polerovirus; family, Luteoviridae), has been recently reported from the major cotton-growing regions of the United States. Here, we present the nearly complete genome sequence of a CLRDV isolate from cotton in Georgia.

Download Full-text

Illumina Sequencing Reveals the First Near-Complete Genome Sequence of Ugandan Passiflora Virus

Microbiology Resource Announcements ◽

10.1128/mra.00358-19 ◽

2019 ◽

Vol 8 (20) ◽

Cited By ~ 1

Author(s):

E. K. Mbeyagala ◽

S. Maina ◽

M. W. Macharia ◽

S. B. Mukasa ◽

T. Holton

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Amino Acid Identity ◽

Passion Fruit ◽

Passiflora Edulis ◽

Content Type ◽

Acid Identity ◽

Symptomatic Sample

Here, we present the first near-complete genome of Ugandan Passiflora virus (UPV) sequenced from a symptomatic sample of KH7 passion fruit (Passiflora edulis Sims) variety. UPV had limited amino acid identity with other potyviruses known to cause passion fruit woodiness disease (PWD).

Download Full-text

Complete Genome Sequence of Sulfurospirillum Strain ACSTCE, a Tetrachloroethene-Respiring Anaerobe Isolated from Contaminated Soil

Microbiology Resource Announcements ◽

10.1128/mra.00941-20 ◽

2020 ◽

Vol 9 (40) ◽

Author(s):

Leitao Huo ◽

Yi Yang ◽

Yan Lv ◽

Xiuying Li ◽

Frank E. Löffler ◽

...

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Contaminated Soil ◽

Complete Genome Sequence ◽

Complete Genome ◽

Amino Acid Identity ◽

Circular Chromosome ◽

Content Type ◽

Acid Identity ◽

Circular Plasmid

ABSTRACT Here, we report the complete genome sequence of the tetrachloroethene-to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACSTCE. The genome consists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which encodes 3 identical reductive dehalogenases with 91.47% amino acid identity to the PceA of Sulfurospirillum multivorans strain DSM 12446.

Download Full-text

Complete Genome Sequence of the First Isolate of Hibiscus Latent Singapore Virus Detected in Japan

Genome Announcements ◽

10.1128/genomea.00054-18 ◽

2018 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Tetsuya Yoshida ◽

Yugo Kitazawa ◽

Yutaro Neriya ◽

Naoi Hosoe ◽

Yuji Fujimoto ◽

...

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Nucleotide Identity ◽

Japanese Isolate ◽

Encoded Proteins

ABSTRACT The complete genome sequence of the first Japanese isolate of hibiscus latent Singapore virus (HLSV-J) was determined. The genomes of HLSV-J and a reported isolate from Singapore had only 86.7% nucleotide identity, while the encoded proteins shared amino acid identities of more than 95%.

Download Full-text

Molecular Characterization of the Porcine Group A Rotavirus NSP2 and NSP5/6 Genes from São Paulo State, Brazil, in 2011/12

The Scientific World JOURNAL ◽

10.1155/2013/241686 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Bruna Rocha Passos Barbosa ◽

Nara Thiers Cacciatori Galleti Bernardes ◽

Laila Andreia Rodrigues Beserra ◽

Fábio Gregori

Keyword(s):

Amino Acid ◽

Amino Acid Identity ◽

Sao Paulo ◽

Nucleotide Identity ◽

Nucleotide Sequencing ◽

São Paulo ◽

Acid Identity ◽

Paulo State ◽

Pig Farms ◽

São Paulo State

Rotaviruses are responsible for the acute diarrhea in various mammalian and avian species. The nonstructural proteins NSP2 and NSP5 are involved in the rotavirus replication and the formation of viroplasm, cytoplasmic inclusion bodies within which new viral particles morphogenesis and viral RNA replication occur. There are few studies on the genetic diversity of those proteins; thus this study aims at characterizing the diversity of rotavirus based on NSP2 and NSP5 genes in rotaviruses circulating in Brazilian pig farms. For this purpose, 63 fecal samples from pig farms located in six different cities in the São Paulo State, Brazil, were screened by nested RT-PCR. Seven strains had the partial nucleotide sequencing for NSP2, whereas in six, the total sequencing for NSP5. All were characterized as genotype H1 and N1. The nucleotide identity of NSP2 genes ranged from 100% to 86.4% and the amino acid identity from 100% to 91.5%. For NSP5, the nucleotide identity was from 100% to 95.1% and the amino acid identity from 100% to 97.4%. It is concluded that the genotypes of the strains circulating in the region of study are in agreement with those reported in the literature for swine and that there is the possibility of interaction between human and animal rotaviruses.

Download Full-text

Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee ( Poecile atricapillus ) Gastrointestinal Tract Sample

Genome Announcements ◽

10.1128/genomea.01081-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 7

Author(s):

Zachary R. Hanna ◽

Charles Runckel ◽

Jérôme Fuchs ◽

Joseph L. DeRisi ◽

David P. Mindell ◽

...

Keyword(s):

Amino Acid ◽

Gastrointestinal Tract ◽

Genome Sequence ◽

Amino Acid Identity ◽

Virus Genome ◽

Genome Sequences ◽

Poecile Atricapillus ◽

Single Stranded Dna ◽

Acid Identity

We report here the genome sequence of a circular virus isolated from samples of an Alaskan black-capped chickadee ( Poecile atricapillus ) gastrointestinal tract. The genome is 2,152 bp in length and is most similar (30 to 44.5% amino acid identity) to the genome sequences of other single-stranded DNA (ssDNA) circular viruses belonging to the gemycircularvirus group.

Download Full-text

Avian Pneumovirus (APV) RNA from Wild and Sentinel Birds in the United States Has Genetic Homology with RNA from APV Isolates from Domestic Turkeys

Journal of Clinical Microbiology ◽

10.1128/jcm.38.11.4282-4284.2000 ◽

2000 ◽

Vol 38 (11) ◽

pp. 4282-4284 ◽

Cited By ~ 37

Author(s):

Hyun-Jin Shin ◽

M. Kariuki Njenga ◽

Brian McComb ◽

David A. Halvorson ◽

Kakambi V. Nagaraja

Keyword(s):

United States ◽

Amino Acid ◽

Respiratory Illness ◽

The United States ◽

Amino Acid Identity ◽

Wild Birds ◽

M Gene ◽

Acid Identity ◽

Genetic Homology ◽

Avian Pneumovirus

Nasal turbinates or swabs were collected from wild ducks, geese, owls, sparrows, swallows, and starlings and from sentinel ducks placed next to turkey farms experiencing avian pneumovirus (APV) infections and were analyzed for APV genome and infectious particles. APV RNA was detected in samples examined from geese, sparrows, and starlings. APV RNA and antibodies were also detected in two different groups of sentinel ducks. Infectious APV was recovered from sentinel duck samples. The APV M gene isolated from the wild birds had over 96% predicted amino acid identity with APV/Minnesota 2A, which was isolated earlier from domestic turkeys showing respiratory illness, suggesting that wild birds may be involved in spreading APV infection.

Download Full-text

Complete Genome Sequence of Cotton Leafroll Dwarf Virus Isolated from Cotton in Texas, USA

Microbiology Resource Announcements ◽

10.1128/mra.01587-19 ◽

2020 ◽

Vol 9 (16) ◽

Cited By ~ 1

Author(s):

Akhtar Ali ◽

Samira Mokhtari

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Growing Season ◽

Dwarf Virus ◽

Cotton Leafroll Dwarf Virus

Cotton leafroll dwarf virus (CLRDV; genus, Polerovirus; family, Luteoviridae) was first described in Alabama. In this study, we present the complete genome (5,865 nucleotides) sequence of a CLRDV isolate (CS4) that was collected from cotton during the 2019 growing season in Texas.

Download Full-text

Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi province, Southern China

10.21203/rs.3.rs-17589/v1 ◽

2020 ◽

Author(s):

Kaichuang Shi ◽

Shou-yu Xie ◽

Jing Zhao ◽

Hui-xin Liu ◽

Yan-wen Yin ◽

...

Keyword(s):

Genetic Diversity ◽

Amino Acid ◽

Complete Genome ◽

Southern China ◽

Amino Acid Identity ◽

Genomic Sequences ◽

Guangxi Province ◽

Acid Identity ◽

Congenital Tremor ◽

Complete Genomic

Abstract Background: Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A-II in new born piglets and has been reported in many countries around the world since 2015. In China, the first APPV infection in swine herds was reported in Guangdong province in 2016. To investigate the genetic characteristics of APPV from Guangxi province seated in Southern China, the full-length sequences of APPV strains were amplified and analyzed. Results: Tissue samples from neonatal piglets with CT from Guangxi province were detected by reverse transcription-polymerase chain reaction (RT-PCR). APPV positive samples were amplified, cloned and sequenced, and the complete genomic sequences of five APPV strains were obtained. Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from other researchers, shared 83.3%-97.5% nucleotide identity of complete genome and 91.7%-99.1% amino acid identity of open reading frame (ORF) with one another, and shared 77.7%-97.7% nucleotide identity of complete genome and 90.6%-99.3% amino acid identity of ORF with other reference strains available in Genbank. Phylogenetic analysis indicated that the APPV strains from Guangxi province belonged to four different subgroups in the phylogenetic tree based on the complete genomic sequences, and similar topology was observed in the phylogenetic trees based on N pro , E rns and E2 gene sequences, respectively. No sign of recombination was observed for strains from Guangxi province by using Recombination Detection Program 4 (RDP4) and Simplot analysis. Evolution analysis performed on the complete genome of 58 APPV strains available in Genbank showed that APPV strains from America, Europe and Asia during 2006-2019 evolved at a mean rate of 1.37×10 -4 substitutions/site/year, and the most recent common ancestor ( tMRCA ) of them was estimated as 1700.5 years ago. Conclusions: The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.

Download Full-text

First Report of Grapevine leafroll-associated virus 5 in Spain

Plant Disease ◽

10.1094/pdis-07-10-0508 ◽

2010 ◽

Vol 94 (12) ◽

pp. 1507-1507 ◽

Cited By ~ 4

Author(s):

C. V. Padilla ◽

E. Cretazzo ◽

I. Hita ◽

N. López ◽

V. Padilla ◽

...

Keyword(s):

United States ◽

Amino Acid ◽

The United States ◽

Amino Acid Identity ◽

Wine Industry ◽

Rt Pcr ◽

Acid Identity ◽

First Report ◽

Virus Indexing ◽

Homologous Genes

Grapevine leafroll-associated viruses (GLRaVs) cause significant reductions in yield and quality in the wine industry worldwide. At least nine different GLRaVs have been found in different regions of the world. In the process of virus indexing of candidate grapevine clones for certification, which includes grafting of scions onto rootstocks, we observed strong leafroll symptoms 1 year after grafting with one vine of cv. Estaladina in Castilla y León, Spain and one vine of cv. Tempranillo in La Rioja, Spain, collected in 2008 and 2007, respectively. Both vines tested positive by real-time reverse transcription (RT)-PCR with TaqMan probes specific for Grapevine leafroll-associated virus 5 and double-antibody sandwich (DAS)-ELISA with a mix of monoclonal antibodies that recognizes GLRaV-4, 5, 6, 7, and 9 (Bioreba, Reinach, Switzerland). RNA extracts of both GLRaV-5 positive vines were analyzed by conventional RT-PCR with a pair of consensus degenerated primers derived from GLRaV-5 hsp70 sequences available in GenBank: LR5HYF (5′-TGGGATGAAYAARTTCAATGC-3′) and LR5HYR (5′-TGAAATTCCTCATRTARGAGC-3′) that amplified a 250-bp fragment. Amplicons were cloned and the comparison of the amino acid sequences (Estaladina isolate, Est110: Accession No. HM208622; Tempranillo isolate, Tem020: Accession No. HM208618) showed in the case of the Est110 isolate, 100 and 82.6% identity, respectively, with the homologous genes of one GLRaV-5 isolate from the United States (AF233934 [3]) and Argentina (EU815935 [2]). For isolate Tem020, the hsp70 gene showed 97.1 and 81.2% amino acid identity with the homologous hsp70 genes of the United States and Argentina isolates. The coat protein (cp) genes of both isolates were also amplified and cloned using the specific GLRaV-5 primers, LR53413 (5′-CGTGATACAAGGTAGGACAACCGT-3′) and LR53843 (5′-CTTGCACTATCGCTGCCGTGAAT-3′), designed according to the sequence of AF233934. Fragments were of the expected size (430 bp) and the nucleotide sequences were obtained (Est110: Accession No. HM363522; Tem020: Accession No. HM363523) and used for pairwise nucleotide comparisons. The Est110 isolate showed 96.7 and 97.5% amino acid identity with the isolates from the United States and Argentina, respectively, while the Tem020 isolate showed 94.8 and 95.6% identity, respectively. Amino acid identity of Est110 and Tem020 cp genes was 100% when compared with the homologous genes of isolates AF233934 and EU815935. To our knowledge this is the first report of GRLaV-5 in Spain. Since 2008, we have detected eight additional vines positive for this virus in 200 clones analyzed for certification, suggesting that the incidence of GLRaV-5 in Spain could be widespread. This research indicates that virus indexing for GLRaV should be included in certification schemes for grapevine candidate clones (1) in Spain. References: (1) Anonymous. OEPP/EPPO Bull. 38:422, 2008. (2) S. Gomez Talquenca et al. Virus Genes 38:184, 2009. (3) F. Osman et al. J. Virol. Methods 141:22, 2007.

Download Full-text