1
|
Li X, Liu Q, Chen X, Xiao Y, Yang S, Zhang W, Chen J. The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin. Future Virol 2022. [DOI: 10.2217/fvl-2020-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.
Collapse
Affiliation(s)
- Xinlin Li
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Qi Liu
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
| |
Collapse
|
2
|
A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft. Viruses 2021; 13:v13060964. [PMID: 34067378 PMCID: PMC8224587 DOI: 10.3390/v13060964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems.
Collapse
|
3
|
Agnihotri K, Smith C, Oakey J, Storie G. Pigeon adenovirus and pigeon torque teno virus associated with acute multifocal hepatic necrosis in pigeons in Queensland, Australia. Arch Virol 2021; 166:1469-1475. [PMID: 33721100 DOI: 10.1007/s00705-021-05033-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/23/2021] [Indexed: 01/04/2023]
Abstract
In 2018, an outbreak resulting in deaths of 28 breeding pigeons was reported north of Brisbane, Australia. The affected birds had runny nasal discharge and poor body condition. Two birds were submitted to Biosecurity Sciences Laboratory, Brisbane, for investigation. A range of diagnostic tests excluded a number of known pathogens, and no virus was isolated in cell culture. Histopathological examination revealed severe acute multifocal necrosis in the liver with eosinophilic intranuclear inclusions in hepatocytes and Kupffer cells. High-throughput sequencing (HTS) revealed full-length sequences for pigeon adenovirus 1 (PiAd-A) and pigeon torque teno virus (PTTV). This report indicates concomitant PiAd-1and PTTV infections in Australian pigeons.
Collapse
Affiliation(s)
- Kalpana Agnihotri
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Department of Agriculture and Fisheries, Queensland Government, Health and Food Sciences Precinct, 39, Coopers Plains, QLD, 4108, Australia.
| | - Craig Smith
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Department of Agriculture and Fisheries, Queensland Government, Health and Food Sciences Precinct, 39, Coopers Plains, QLD, 4108, Australia
| | - Jane Oakey
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Department of Agriculture and Fisheries, Queensland Government, Health and Food Sciences Precinct, 39, Coopers Plains, QLD, 4108, Australia
| | - Greg Storie
- Biosecurity Sciences Laboratory, Biosecurity Queensland, Department of Agriculture and Fisheries, Queensland Government, Health and Food Sciences Precinct, 39, Coopers Plains, QLD, 4108, Australia
| |
Collapse
|
4
|
Sarairah H, Bdour S, Gharaibeh W. The Molecular Epidemiology and Phylogeny of Torque Teno Virus (TTV) in Jordan. Viruses 2020; 12:v12020165. [PMID: 32023916 PMCID: PMC7077251 DOI: 10.3390/v12020165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
Torque teno virus (TTV) is the most common component of the human blood virobiota. Little is known, however, about the prevalence of TTV in humans and the most common farm domesticates in Jordan, or the history and modality of TTV transmission across species lines. We therefore tested sera from 396 Jordanians and 171 farm animals for the presence of TTV DNA using nested 5'-UTR-PCR. We then performed phylogenetic, ordination and evolutionary diversity analyses on detected DNA sequences. We detected a very high prevalence of TTV in Jordanians (~96%); much higher than in farm animal domesticates (~29% pooled over species). TTV prevalence in the human participants is not associated with geography, demography or physical attributes. Phylogenetic, ordination and evolutionary diversity analyses indicated that TTV is transmitted readily between humans across the geography of the country and between various species of animal domesticates. However, the majority of animal TTV isolates seem to derive from a single human-to-animal transmission event in the past, and current human-animal transmission in either direction is relatively rare. In conclusion, animal TTV in Jordan is historically derived from human variants; however, ongoing human-animal TTV exchange is minimal and zoonotic infection seems to be of limited importance.
Collapse
Affiliation(s)
- Haneen Sarairah
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
| | - Salwa Bdour
- Department of the Clinical Laboratory Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (W.G.); Tel.: +962-6-5355000 (ext. 22233) (S.B.); +962-6-5355000 (ext. 22205) (W.G.)
| | - Waleed Gharaibeh
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (W.G.); Tel.: +962-6-5355000 (ext. 22233) (S.B.); +962-6-5355000 (ext. 22205) (W.G.)
| |
Collapse
|
5
|
Nishizawa T, Sugimoto Y, Takeda T, Kodera Y, Hatano Y, Takahashi M, Okamoto H. Identification and whole genome characterization of novel anelloviruses in masked palm civets (Paguma larvata): Segregation into four distinct clades. Virus Res 2018; 256:183-191. [PMID: 30149046 DOI: 10.1016/j.virusres.2018.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
The members of the family Anelloviridae are small and single-stranded DNA viruses with marked diversity in sequence and length, which ubiquitously infect many vertebrates, including mammals, birds and reptiles. The anelloviruses isolated from mammals are currently classified into 11 assigned and four proposed genera; some anelloviruses remain unassigned. The present study was conducted to identify anelloviruses in wild-caught masked palm civets (Paguma larvata) in Japan using a rolling-circle amplification method. Thirteen novel anellovirus strains were identified from 8 of 10 masked palm civets and their entire genomic sequences (2039-2535 nucleotides) were determined; they were classifiable into four distinct clades. Comparative analyses of all reported anelloviruses for which the entire or near-entire genomic sequences have been determined, including the 13 strains obtained in the present study, revealed that anelloviruses can provisionally be classified into 20 clades, which may correspond to 20 genera (including 11 assigned and four proposed genera) by a >70% amino acid sequence difference in open reading frame 1 (ORF1). This study suggested that novel anelloviruses of marked diversity are circulating in animals worldwide, and that the rolling-circle amplification method would be useful for identifying novel anelloviruses and other viruses with a circular DNA genome.
Collapse
Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yuji Sugimoto
- Nikko Branch, Tochigi Hunter Association, Nikko, Tochigi, 321-2522, Japan
| | - Tsutomu Takeda
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuuji Kodera
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yumi Hatano
- Sakakibara Heart Institute Clinic, Shinjuku-ku, Tokyo, 163-0804, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan.
| |
Collapse
|
6
|
Wan C, Chen C, Cheng L, Fu G, Shi S, Fu Q, Liu R, Chen H, Huang Y. Development of a TaqMan-based real-time PCR assay for the rapid and specific detection of pigeon torque teno virus. Mol Cell Probes 2018; 39:53-56. [DOI: 10.1016/j.mcp.2018.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
|