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1. An isolate of sweet potato chlorotic stunt virus from Brazil with a distinct genome organization

Author:
Rossato, Maurício; Souza, Caroline Amaral; Melo, Fernando Lucas; Orilio, Anelise Franco; Resende, Renato Oliveira; Ribeiro, Simone Graça; Naito, Fernanda Yuri Borges; Ribeiro, Gilvan Pio; Andrade, Genira Pereira; Pereira-Carvalho, Rita Cássia
Source:
Archives of virology 2019 v.164 no.8 pp. 2175-2178
ISSN:
0304-8608
Subject:
Ipomoea; RNA; Sweet potato chlorotic stunt virus; coat proteins; genes; genetic distance; genomics; grafting (plants); open reading frames; pathogens; phylogeny; sequence analysis; sweet potatoes; Brazil
Abstract:
... Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae), is an economically important pathogen of sweet potato. In the present work, the nucleotide sequences of two RNA segments of SPCSV (isolate SPCSV-UNB-01) were determined by MiSeq Illumina sequencing of samples of sweet potato plants grafted onto Ipomoea setosa. A comparative analysis of the genome organization of ...
DOI:
10.1007/s00705-019-04281-2

2. A novel bat-associated circovirus identified in northern Hokkaido, Japan

Author:
Matsumoto, Takashi; Sato, Masahiko; Nishizono, Akira; Ahmed, Kamruddin
Source:
Archives of virology 2019 v.164 no.8 pp. 2179-2182
ISSN:
0304-8608
Subject:
Chiroptera; Circovirus; genome; nucleotide sequences; nucleotides; sequence analysis; viruses; Japan
Abstract:
... We identified two novel circoviruses, HK02976 and HK00220, in oral swabs from bats. The size of their full genome was 2,010 nucleotides (nt). The full-genome sequence of our strains shared 96.1% nucleotide sequence identity with each other, and 39.9%–69.5% identity with bat-associated circoviruses (BatACVs)1–9. Based on the species demarcation threshold for viruses of the family Circoviridae, whic ...
DOI:
10.1007/s00705-019-04286-x

3. Characterization of Iranian canarypox and pigeonpox virus strains

Author:
Zarifi, Fatemeh; Nakhaei, Peyman; Nourani, Hossein; Mirshokraei, Pezhman; Razmyar, Jamshid
Source:
Archives of virology 2019 v.164 no.8 pp. 2049-2059
ISSN:
0304-8608
Subject:
Canarypox virus; Pigeonpox virus; chick embryos; chorioallantoic membrane; cross infection; electron microscopy; fibroblasts; genes; genetic variation; histopathology; host specificity; inclusion bodies; nucleotide sequences; phylogeny; pigeons; polymerase chain reaction; sequence analysis; viral growth; virion; virus replication; viruses; Iran
Abstract:
... Avipoxviruses (APVs) are large DNA viruses that are detected widely in many species of birds. Little information is available regarding genetic variations in these host-specific viruses. In the present study, nine canarypox virus and five pigeonpox virus isolates were collected from northeastern Iran and isolated via the chorioallantoic membrane of chicken embryos. Further investigations were cond ...
DOI:
10.1007/s00705-019-04277-y

4. Characterization of the endonuclease activity of the replication-associated protein of beak and feather disease virus

Author:
Chen, Jui-Kai; Hsiao, Chiaolong; Wu, Jian-Shin; Lin, Shin-Yi; Wang, Chi-Young
Source:
Archives of virology 2019 v.164 no.8 pp. 2091-2106
ISSN:
0304-8608
Subject:
Beak and feather disease virus; DNA; DNA fragmentation; adenosinetriphosphatase; divalent metals; enzyme activity; enzyme inhibitors; genes; guanosinetriphosphatase; magnesium; manganese; metal ions; mutants; oligonucleotides; proteins; replication origin; site-directed mutagenesis
Abstract:
... Beak and feather disease virus (BFDV) belongs to the family Circoviridae. A rolling-circle replication strategy based on a replication-associated protein (Rep) has been proposed for BFDV. The Rep gene of BFDV was expressed and purified, and it was shown to cleave short oligonucleotides containing the conserved nonanucleotide sequence found in the replication origin of circoviruses. This endonuclea ...
DOI:
10.1007/s00705-019-04292-z

5. Characterization of vB_ApiM_fHyAci03, a novel lytic bacteriophage that infects clinical Acinetobacter strains

Author:
Pulkkinen, Elsi; Wicklund, Anu; Oduor, Joseph M. O.; Skurnik, Mikael; Kiljunen, Saija
Source:
Archives of virology 2019 v.164 no.8 pp. 2197-2199
ISSN:
0304-8608
Subject:
Acinetobacter baumannii; Myoviridae; amino acid sequences; bacteriophages; genes; host range; hosts; phage therapy; phylogeny
Abstract:
... We present here the isolation and characterization of Acinetobacter pittii phage vB_ApiM_fHyAci03 (fHyAci03), which belongs to the family Myoviridae. The fHyAci03 genome was found to be 165,975 bp in length and predicted to contain 255 genes. While the whole genome was 92.4% identical to Acinetobacter baumannii phage KARL-1, phylogenetic analysis based on phage long distal tail fiber amino acid se ...
DOI:
10.1007/s00705-019-04284-z
PubMed:
31123962
PubMed Central:
PMC6591195

6. Complete genome characterization of three enterovirus C96 isolates in China

Author:
Wang, Qian; Ji, Feng; Wang, Suting; Lin, Xiaojuan; Tao, Zexin; Xu, Aiqiang
Source:
Archives of virology 2019 v.164 no.8 pp. 2183-2186
ISSN:
0304-8608
Subject:
Enterovirus C; genetic variation; genome; monitoring; nucleotide sequences; paralysis; phylogeny; serotypes; sewage; China
Abstract:
... Enterovirus C96 (EV-C96) is a newer member of the species Enterovirus C. In this study, we determined the complete genome sequences of three EV-C96 isolates, one recovered from domestic sewage in 2013 and the other two isolated during surveillance of acute flaccid paralysis cases in 1991 and 2009, respectively. The complete genome sequences of these isolates were 75.6–84.2% identical to each other ...
DOI:
10.1007/s00705-019-04291-0

7. Complete genomic sequence and organization of a novel mycovirus from Phoma matteuccicola strain LG915

Author:
Zheng, Fan; Xu, Gang; Zhou, Jia; Xie, Changping; Cui, Hongguang; Miao, Weiguo; Kang, Zhensheng; Zheng, Li
Source:
Archives of virology 2019 v.164 no.8 pp. 2209-2213
ISSN:
0304-8608
Subject:
Colletotrichum acutatum; Curcuma wenyujin; Gammapartitivirus; Phoma; RNA-directed RNA polymerase; Ustilaginoidea virens; coat proteins; double-stranded RNA; genome; leaf blight; mycoviruses; open reading frames; phylogeny; polypeptides; sequence homology; virion
Abstract:
... The complete genome of a double-stranded RNA (dsRNA) mycovirus, Phoma matteuccicola partitivirus 1 (PmPV1) was sequenced. It consists of two dsRNA segments, 1664 bp (dsRNA-1) and 1383 bp (dsRNA-2) in length, each containing a single open reading frame (ORF) potentially encoding a 46.78-kDa protein and a 40.92-kDa protein, respectively. dsRNA-1 encodes a putative polypeptide with a conserved RNA-de ...
DOI:
10.1007/s00705-019-04314-w

8. Detection and genome characterization of a novel member of the genus Polerovirus from zucchini (Cucurbita pepo) in China

Author:
Peng, Bin; Kang, Baoshan; Wu, Huijie; Liu, Lifeng; Liu, Liming; Fei, Zhangjun; Hong, Ni; Gu, Qinsheng
Source:
Archives of virology 2019 v.164 no.8 pp. 2187-2191
ISSN:
0304-8608
Subject:
Chickpea chlorotic stunt virus; Cucurbita pepo; genome; nucleotides; open reading frames; phylogeny; sequence alignment; viruses; zucchini; China
Abstract:
... Here, we report a novel member of the genus Polerovirus, zucchini aphid-borne yellows virus (ZABYV), which was identified in zucchini grown for seed production in the Xinjiang Uygur Autonomous Region, China. The complete nucleotide sequence of the ZABYV genome was determined and found to be 5,792 nucleotides in length, and like those of other poleroviruses, to contain seven open reading frames (OR ...
DOI:
10.1007/s00705-019-04217-w

9. Emergence of G12P[6] rotavirus strains among hospitalised children with acute gastroenteritis in Belém, Northern Brazil, following introduction of a rotavirus vaccine

Author:
Guerra, Sylvia F. S.; Fecury, Priscylla C. M. S.; Bezerra, Delana A. M.; Lobo, Patricia S.; Penha Júnior, Edvaldo T.; Sousa Júnior, Edivaldo C.; Mascarenhas, Joana D’Arc P.; Soares, Luana S.; Justino, Maria Cleonice A.; Linhares, Alexandre C.
Source:
Archives of virology 2019 v.164 no.8 pp. 2107-2117
ISSN:
0304-8608
Subject:
RNA; Rotavirus; children; feces; gastroenteritis; genotype; infants; monitoring; reverse transcriptase polymerase chain reaction; sequence analysis; vaccines; Brazil
Abstract:
... Species A rotavirus still remains a major cause of acute gastroenteritis in infants and young children. Globally, six genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) account for >90% of circulating strains; however, genotype G12 in combination with P[6] or P[9] has been detected at increasing rates. We sought to broaden our knowledge about the rotavirus strains circulating during th ...
DOI:
10.1007/s00705-019-04295-w

10. Epidemiology of blood-borne viral infections in Afghanistan

Author:
Husseini, Abbas Ali; Saeed, Khwaja Mir Islam; Yurdcu, Esra; Sertoz, Rüçhan; Bozdayi, A. Mithat
Source:
Archives of virology 2019 v.164 no.8 pp. 2083-2090
ISSN:
0304-8608
Subject:
Hepatitis B virus; Hepatitis C virus; Hepatitis delta virus; Human immunodeficiency virus 1; T-lymphocytes; antibodies; automation; chemiluminescence; hepatitis B antigens; humans; immunoassays; leukemia; screening; seroprevalence; viral load; viruses; Afghanistan; Mediterranean region
Abstract:
... Although a few studies have been done on transmissible blood-borne viral infections in high-risk groups, little attention has been given to assessing the infection status of the general population in Afghanistan. To investigate the epidemiological status in the general population, we tested the serological markers of hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis delta virus (HDV), hu ...
DOI:
10.1007/s00705-019-04285-y

11. Epidemiology of respiratory viruses in Saudi Arabia: toward a complete picture

Author:
Farrag, Mohamed A.; Hamed, Maaweya E.; Amer, Haitham M.; Almajhdi, Fahad N.
Source:
Archives of virology 2019 v.164 no.8 pp. 1981-1996
ISSN:
0304-8608
Subject:
Coronavirinae; Muslims; epidemiological studies; evolution; respiratory tract diseases; viruses; Middle East; Saudi Arabia
Abstract:
... Acute lower respiratory tract infection is a major health problem that affects more than 15% of the total population of Saudi Arabia each year. Epidemiological studies conducted over the last three decades have indicated that viruses are responsible for the majority of these infections. The epidemiology of respiratory viruses in Saudi Arabia is proposed to be affected mainly by the presence and mo ...
DOI:
10.1007/s00705-019-04300-2
PubMed:
31139937
PubMed Central:
PMC7087236

12. Expression of autophagy-modulating genes in peripheral blood mononuclear cells from familial clustering patients with chronic hepatitis B virus infection

Author:
Tian, Zhen; Wang, Meifang; Yao, Naijuan; Yang, Shujuan; Liu, Jinfeng; Yang, Yuan; Chen, Tianyan; Zhao, Yingren; He, Yingli
Source:
Archives of virology 2019 v.164 no.8 pp. 2005-2013
ISSN:
0304-8608
Subject:
DNA microarrays; Hepatitis B virus; Western blotting; autophagy; chronic hepatitis B; gene expression regulation; genes; genetic factors; hepatoma; liver cirrhosis; lysosomes; messenger RNA; mononuclear leukocytes; patients; spouses
Abstract:
... We previously found that genetic factors are associated with a familial predisposition for developing liver cirrhosis and hepatocellular carcinoma during chronic hepatitis B virus (HBV) infection. Autophagy has been shown to play a role in HBV replication and the course of disease. More than 190 host genes have been identified that modify the process of autophagy, but which of these genes are invo ...
DOI:
10.1007/s00705-019-04248-3

13. Full genome sequence of a new polymycovirus infecting Fusarium redolens

Author:
Mahillon, Mathieu; Decroës, Alain; Liénard, Charlotte; Bragard, Claude; Legrève, Anne
Source:
Archives of virology 2019 v.164 no.8 pp. 2215-2219
ISSN:
0304-8608
Subject:
Fusarium redolens; agar gel electrophoresis; amino acid sequences; bioinformatics; databases; double-stranded RNA; genome; high-throughput nucleotide sequencing; mycoviruses; open reading frames; proteins; screening; sequence homology
Abstract:
... By screening a collection of Fusarium spp. for the presence of dsRNA, the Fusarium redolens strain A63-1 was found harboring a pattern of multiple dsRNA bands when analyzed by agarose gel electrophoresis. Using NextSeq Illumina sequencing, the full sequences of eight dsRNA molecules were determined, compared to databases, and gathered into a new viral genome. This novel virus shares similarities w ...
DOI:
10.1007/s00705-019-04301-1

14. Full genome sequence of a novel potexvirus from Euonymus bungeanus Maxim based on RNA-Seq analysis

Author:
Yang, Caixia; Li, Liang; Hou, Qiushi; Wang, Junzhu; Yu, Meichun; Gang, Shuang; Zhang, Song; Cao, Mengji
Source:
Archives of virology 2019 v.164 no.8 pp. 2201-2204
ISSN:
0304-8608
Subject:
Cymbidium mosaic virus; Euonymus hamiltonianus var. maackii; amino acid sequences; coat proteins; foliar diseases; genes; leaves; nucleotides; open reading frames; phylogeny; sequence homology; transcriptomics; viruses; China
Abstract:
... In July 2018, a yellow mottle leaf disease was observed on the leaves of Euonymus bungeanus Maxim plants in Liaoning Province of China. Typical flexuous filaments (diameter, 13 nm; length, ca. 500 nm) were observed in extracts on the symptomatic leaves. Transcriptome sequencing indicated the presence of a potexvirus in the infected samples. The complete viral genome, determined to be 6,784 nucleot ...
DOI:
10.1007/s00705-019-04293-y

15. Genomic characterization of four novel Staphylococcus myoviruses

Author:
Oduor, Joseph Michael Ochieng’; Kiljunen, Saija; Kadija, Ermir; Mureithi, Marianne W.; Nyachieo, Atunga; Skurnik, Mikael
Source:
Archives of virology 2019 v.164 no.8 pp. 2171-2173
ISSN:
0304-8608
Subject:
DNA; Myoviridae; Staphylococcus; bacteriophages; genome; genomics; sequence analysis
Abstract:
... We report here the annotation of the complete genomes of four novel lytic Staphylococcus phages; Stab20, Stab21, Stab22 and Stab23. These phages have double-stranded DNA genomes ranging between 153,338 and 155,962 bp in size with terminal repeats of 10,814–12,304 bp. The genome analysis suggests that they represent new phage species within the genus Kayvirus in the subfamily Twortvirinae of the fa ...
DOI:
10.1007/s00705-019-04267-0

16. Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds

Author:
Welch, Catharine N.; Shittu, Ismaila; Abolnik, Celia; Solomon, Ponman; Dimitrov, Kiril M.; Taylor, Tonya L.; Williams-Coplin, Dawn; Goraichuk, Iryna V.; Meseko, Clement A.; Ibu, John O.; Gado, Dorcas A.; Joannis, Tony M.; Afonso, Claudio L.
Source:
Archives of virology 2019 v.164 no.8 pp. 2031-2047
ISSN:
0304-8608
Subject:
Avian orthoavulavirus 1; Newcastle disease; epidemiology; genetic variation; genomics; host range; indigenous species; monitoring; nucleotide sequences; phylogeny; poultry; poultry health; subgenotype; vaccines; virulent strains; viruses; wild birds; Nigeria
Abstract:
... Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still larg ...
Handle:
10113/6480143
DOI:
10.1007/s00705-019-04288-9
CHORUS:
10.1007/s00705-019-04288-9

17. Global distribution of white spot syndrome virus genotypes determined using a novel genotyping assay

Author:
Oakey, J.; Smith, C.; Underwood, D.; Afsharnasab, M.; Alday-Sanz, V.; Dhar, A.; Sivakumar, S.; Sahul Hameed, A. S.; Beattie, K.; Crook, A.
Source:
Archives of virology 2019 v.164 no.8 pp. 2061-2082
ISSN:
0304-8608
Subject:
White spot syndrome virus; genome; genotype; genotyping; geographical distribution; microsatellite repeats; shrimp culture; strain differences; Queensland
Abstract:
... White spot disease, caused by infection with white spot syndrome virus (WSSV), is a serious panzootic affecting prawn aquaculture. The disease has spread rapidly around the prawn-culturing regions of the world through a number of previously identified mechanisms. The ability to distinguish and trace strains of WSSV is of great benefit to identify, and then limit, the translocation routes of the di ...
DOI:
10.1007/s00705-019-04265-2
PubMed:
31131427
PubMed Central:
PMC6591196

18. High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago

Author:
Scussel, Sarah; Candresse, Thierry; Marais, Armelle; Claverie, Sohini; Hoareau, Murielle; Azali, Hamza A.; Verdin, Eric; Tepfer, Mark; Filloux, Denis; Fernandez, Emmanuel; Roumagnac, Philippe; Robène, Isabelle; Lefeuvre, Pierre; Jourda, Cyril; Roux-Cuvelier, Michel; Lett, Jean-Michel
Source:
Archives of virology 2019 v.164 no.8 pp. 2193-2196
ISSN:
0304-8608
Subject:
Cassava brown streak virus; Ugandan cassava brown streak virus; double-stranded RNA; genome; high-throughput nucleotide sequencing; open reading frames; phylogeny; small interfering RNA; viruses; Comoros
Abstract:
... Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large OR ...
DOI:
10.1007/s00705-019-04228-7

19. Isolation and complete genome sequence analysis of a novel ovine adenovirus type representing a possible new mastadenovirus species

Author:
Vidovszky, Márton Z.; Szeredi, Levente; Doszpoly, Andor; Harrach, Balázs; Hornyák, Ákos
Source:
Archives of virology 2019 v.164 no.8 pp. 2205-2207
ISSN:
0304-8608
Subject:
Mastadenovirus; genes; high-throughput nucleotide sequencing; immunohistochemistry; lungs; males; nucleotide sequences; polymerase chain reaction; proteins; suckling; superinfection; viral pneumonia; viruses
Abstract:
... Pathological examination of a suckling male lamb showed severe viral pneumonia with suspected bacterial superinfection. Adenovirus was detected by immunohistochemical examination of the affected lung samples. Detection of the suspected adenovirus by PCR and subsequent isolation of the virus were successful. Using next-generation sequencing, the full genome of this ovine adenovirus was sequenced an ...
DOI:
10.1007/s00705-019-04299-6
PubMed:
31152248
PubMed Central:
PMC6591194

20. Isolation and sequence analysis of the complete H gene of canine distemper virus from domestic dogs in Henan Province, China

Author:
Liu, Yuxiu; Liu, Caihong; Liu, Wujie; Wu, Hongchao; Ding, Hangtian; Cao, Yujiao; Spibey, Norman; Wang, Linxiao; He, Wenxi; Hao, Liying; Li, Xiangdong; Tian, Kegong
Source:
Archives of virology 2019 v.164 no.8 pp. 2153-2158
ISSN:
0304-8608
Subject:
Canine morbillivirus; amino acids; antibody specificity; dogs; genes; genotype; glycosylation; hemagglutinins; monoclonal antibodies; nucleotide sequences; phylogeny; sequence analysis; vaccines; viruses; China
Abstract:
... Eighteen canine distemper virus (CDV) isolates were obtained from clinical samples in Henan province, China, between 2012 and 2016. These viruses could not be recognized by 1A4, a monoclonal antibody specific for the H protein of CDV vaccine strains. The complete haemagglutinin (H) genes of all 18 isolates were sequenced, and phylogenetic analysis showed that they segregated into two clusters with ...
DOI:
10.1007/s00705-019-04298-7
PubMed:
31134355
PubMed Central:
PMC7086856