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Wang X, Cheng J, Jiang Y, Ou J, Cai S, Xu L, Zhong L, Xiao Y, Hu X, Lu G, Yuan L. Natural recombination of the torque teno canis virus within the ORF1, -2, and -3 genes and the untranslated region. Virus Res 2023; 338:199227. [PMID: 37793437 PMCID: PMC10582477 DOI: 10.1016/j.virusres.2023.199227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
The torque teno canis virus (TTCaV) was first reported in 2001 and it shares similarities with the known Torque teno virus (TTV) in terms of genomic organization and putative transcriptional features. It is a single-stranded DNA virus characterized by high rates of recombination and nucleotide substitution, like RNA viruses. Studies reported recombination events in torque teno virus; however, there is limited reporting of TTCaV reorganization events. This study screened fecal samples from domestic dogs in Henan Province. There was a positivity rate of 16.5% (19/115) for TTCaV. Four nearly complete TTCaV genomes, namely Canine/HeNan/4, 5, 6, and 13/2019, were obtained from the 19 positive fecal samples, whose genome sequence was obtained using gap-filling PCR. Sequence analysis revealed two unique amino acid mutation sites in the TTCaV strains, K278Q (compared with the first isolate Cf-TTV10 in Japan) and V/L268I (compared with the TTCaV strain from southern China). Subsequently, 17 near full-length TTCaV genome sequences were subjected to phylogenetic and recombination detection program analyzes. We obtained evidence supporting recombination events in the Chinese TTCaV strains. These findings suggest that mutation and recombination occurred in the three individual gene segments (ORF1, ORF2, ORF3) and the untranslated region, an area of major recombination in the Chinese TTCaV strain GX265 genome. Interestingly, the TTCaV strain (Canine/HeNan/6/2019) was a major parent involved in the genetic recombination of the GX265 strain. This study provides insights into the genetic variability and evolution of TTCaV.
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Affiliation(s)
- Xuyang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Jiaojiao Cheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Yujie Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Jiajun Ou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Siqi Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Liang Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Lintao Zhong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Yuqing Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Xuerui Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China.
| | - Liguo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China.
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Miyata R, Miyabe C, Oki H, Motooka D, Nakamura S, Miyabe Y, Takenaka Y, Fukuya Y, Yudo K, Ishiguro N. Alteration of microbial composition in the skin and blood in vasculitis. Sci Rep 2023; 13:15317. [PMID: 37714908 PMCID: PMC10504252 DOI: 10.1038/s41598-023-42307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023] Open
Abstract
Vasculitis is a systemic autoimmune disease characterized by leukocyte infiltration into blood vessels. Various microorganisms have been associated with the pathogenesis of vasculitis; however, the causal microbial agents and underlying mechanisms are not fully understood, possibly because of the technical limitations of pathogen detection. In the present study, we characterized the microbiome profile of patients with cutaneous vasculitis using comprehensive metagenome shotgun sequencing. We found that the abundance of the SEN virus was increased in the affected skin and serum of patients with vasculitis compared to healthy donors. In particular, the abundance of SEN virus reads was increased in the sera of patients with cutaneous arteritis. Among the bacteria identified, Corynebacteriales was the most differentially associated with vasculitis. Linear discriminant analysis effect size also indicated differences in the microbial taxa between patients with vasculitis and healthy donors. These findings demonstrate that vasculitis is associated with considerable alteration of the microbiome in the blood and skin and suggest a role for the infectious trigger in vasculitis.
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Affiliation(s)
- Ryujin Miyata
- Division of Dermatology, Department of Dermatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Chie Miyabe
- Division of Dermatology, Department of Dermatology, Tokyo Women's Medical University, Tokyo, Japan.
- Department of Frontier Medicine, Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1 Sugao, Kawasaki City, Kanagawa, Japan.
| | - Hiroya Oki
- Department of Infection Metagenomics, Genome Information Research Center, Osaka University Research Institute for Microbial Diseases, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Osaka University Research Institute for Microbial Diseases, Suita, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Osaka University Research Institute for Microbial Diseases, Suita, Japan
| | - Yoshishige Miyabe
- Department of Immunology and Parasitology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yuko Takenaka
- Division of Dermatology, Department of Dermatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yasuko Fukuya
- Division of Dermatology, Department of Dermatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Kazuo Yudo
- Department of Frontier Medicine, Institute of Medical Science, St. Marianna University School of Medicine, 2-16-1 Sugao, Kawasaki City, Kanagawa, Japan
| | - Naoko Ishiguro
- Division of Dermatology, Department of Dermatology, Tokyo Women's Medical University, Tokyo, Japan
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Bezerra RDS, Ximenez JPB, Giovanetti M, Zucherato VS, Bitencourt HT, Zimmermann A, Alcantara LCJ, Covas DT, Kashima S, Slavov SN. METAVIROME COMPOSITION OF BRAZILIAN BLOOD DONORS POSITIVE FOR THE ROUTINELY TESTED BLOOD-BORNE INFECTIONS. Virus Res 2022; 311:198689. [PMID: 35090996 DOI: 10.1016/j.virusres.2022.198689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022]
Abstract
Viral metagenomics is widely applied to characterize emerging viral pathogens but it can also reveal the virome composition in health and disease. The evaluation of the virome in healthy blood donors can provide important knowledge on possible transfusion threats. Currently, there is still a paucity of information regarding the virome of blood donors who test positive for routinely tested blood-borne infections. Such analysis may reveal co-infections which in turn appear to be crucial for transfusion medicine and for patient management. The aim of this study was to evaluate the metavirome in blood donors who tested positive for routinely tested blood-borne infections, the information for which is important for transfusion medicine and blood donor management. For this purpose, we analyzed 18 blood donations obtained from HIV and HBV-infected blood donors from the Brazilian Amazon (Amapa state) and 11 HIV, HBV, HCV, syphilis and Chagas disease - positive blood donations obtained from blood donors sampled in South Brazil (Rio Grande do Sul state). We additionally included a control group of 20 blood donors obtained from Southeast Brazil (State of São Paulo). Samples were assembled in pools and sequenced by the Illumina NovaSeq 6000 platform. To link a given virus with geographic region or type of blood donor, we performed supervised machine learning classification (fingerprint analysis). The virome of both locations was predominantly composed of commensal viruses. However, in HBV-infected blood donors from the Brazilian Amazon, the Human Pegivirus-1 (HPgV-1) reads were prevailing, while in HIV-infected donors from the same location, the torque teno virus (TTV) reads expressive abundance. In blood donors from South Brazil, the most abundant reads were classified as Human endogenous retrovirus K (HERV-K). Putative emerging viruses like the Human gemykibivirus-2 (HuGkV-2) were exclusively identified in samples from the Brazilian Amazon. The fingerprint analysis demonstrated that the HERV-K, TTV-7, 13, and 15 were statistically important for the infected blood donors, while TTV-5, 12 and 20 were linked to geographic localization. Our study revealed differences in the viral composition among blood donors who tested positive for routinely tested blood-borne infections from two different Brazilian regions and indicated the presence of putative emerging viruses in samples obtained from the Amazon. Together our results show that the presence of specific commensal viruses may be related donor infection status but additional investigations including larger study groups and samples from other Brazilian regions are needed to confirm this hypothesis.
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Affiliation(s)
- Rafael Dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Paulo Bianchi Ximenez
- Department of Clinical Analysis, Toxicology and Food Science, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marta Giovanetti
- Laboratory of Flaviviruses, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil;; Laboratory of Molecular and Cellular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Victoria Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Ana Zimmermann
- Hematology and Hemotherapy Service of Santa Maria, Hospital "Astrogildo de Azevedo" Santa Maria, Rio Grande do Sul, Brazil
| | - Luiz Carlos Júnior Alcantara
- Laboratory of Flaviviruses, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil;; Laboratory of Molecular and Cellular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil;; Biotechnology Unit (NUCEL), Butantan Institute, São Paulo, São Paulo, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil;; Biotechnology Unit (NUCEL), Butantan Institute, São Paulo, São Paulo, Brazil.
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Mujahid Al-Shuwaikh A, Abbas khudair E, Basil Hanna D. Phylogenetic and molecular evolutionary analysis of SENV DNA isolated from Iraqi Hepatitis Patients. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.04.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
SEN Virus (SENV) is a newly discovered group of transmissible, hepatotropic, single-stranded, circular, non-enveloped DNA viruses that are distantly linked to the widely distributed Torque Teno Virus (TTV) family. This research aimed to use nucleotide sequencing to identify the genetic alterations of SEN-V and to investigate the similarities between isolates. Seven DNA samples of SENV, which were previously extracted from blood of post transfusion hepatitis, were used to identify the genetic variation of SEN-V by nucleotide sequencing. According to the current analysis results, specific primer pairs were used to detect SENV DNA sequences isolated from Iraqi patients with hepatitis; however, those specific primers can also detect two new variants of SENV that are closely related to the Torque Teno Virus. In addition, four SENV isolates showed several substitution mutations, and one of them revealed the replacement of Proline (P) at position 11 with Serine (S). Only one local isolate of SENV was 100% identical to the Iranian isolate (GenBank acc. no. GQ452051.1) from thalassemia.
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Affiliation(s)
| | - Ealaf Abbas khudair
- Microbiology Department, College of Medicine, Al-Nahrain University, Baghdad – Iraq
| | - Dalya Basil Hanna
- Department of Clinical Laboratory Sciences, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
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Elnagi EA, AL-Maqati TN, Alnaam Y, Adam AA, Rabaan AA, Mohamed ZS, Amer A, Almarfoi HL. The prevalence of SEN virus among blood donors in the Eastern Province of KSA. Saudi J Biol Sci 2021; 28:3922-3925. [PMID: 34220248 PMCID: PMC8241597 DOI: 10.1016/j.sjbs.2021.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Elmoeiz A. Elnagi
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
| | - Thekra N. AL-Maqati
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
| | - Yaser Alnaam
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
| | - Ahmed A. Adam
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopklins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Zeinab S. Mohamed
- Faculty of Clinical Laboratory Sciences, Alzaiem Alazhari University, Khartoum, Sudan
| | - Anisah Amer
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
| | - Hussa L. Almarfoi
- Clinical Laboratory Sciences Department, Prince Sultan Military College of Health Sciences, Dammam, Saudi Arabia
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He W, Gao Y, Wen Y, Ke X, Ou Z, Li Y, He H, Chen Q. Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats. Front Microbiol 2021; 12:653873. [PMID: 34177835 PMCID: PMC8221242 DOI: 10.3389/fmicb.2021.653873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Hepatitis is a major global health concern. However, the etiology of 10-20% hepatitis cases remains unclear. Some hepatitis-associated viruses, like the hepatitis E virus, are zoonotic pathogens. Rats, shrews, and bats are reservoirs for many zoonotic pathogens. Therefore, understanding the virome in the liver of these animals is important for the investigation of the etiologies of hepatitis and monitoring the emerging zoonotic viruses. In this study, viral metagenomics and PCR methods were used to investigate viral communities in rats, mice, house shrews, and bats livers. Viral metagenomic analysis showed a diverse set of sequences in liver samples, comprising: sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses. Using PCR methods, we first detected hepatovirus sequences in Hipposideros larvatus (3.85%). We also reported the first detection of Zika virus-related sequences in rats and house shrews. Sequences related to influenza A virus and herpesviruses were detected in liver. Higher detection rates of pegivirus sequences were found in liver tissue and serum samples from rats (7.85% and 15.79%, respectively) than from house shrews. Torque teno virus sequences had higher detection rates in the serum samples of rats and house shrews (52.72% and 5.26%, respectively) than in the liver. Near-full length genomes of pegivirus and torque teno virus were amplified. This study is the first to compare the viral communities in the liver of bats, rats, mice, and house shrews. Its findings expand our understanding of the virome in the liver of these animals and provide an insight into hepatitis-related viruses.
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Affiliation(s)
- Wenqiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuhan Gao
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yuqi Wen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Xuemei Ke
- Xiamen Center for Disease Control and Prevention, Xiamen, China
| | - Zejin Ou
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Yongzhi Li
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Huan He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
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Maev IV, Karlovich TI, Burmistrov AI, Chekmazov IA, Andreev DN, Reshetnyak VI. Current Views of Torque Teno Virus (TTV) in Liver Diseases. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2020; 30:7-22. [DOI: 10.22416/1382-4376-2020-30-4-7-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Affiliation(s)
- I. V. Maev
- Moscow State University of Medicine and Dentistry
| | - T. I. Karlovich
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
| | | | - I. A. Chekmazov
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
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Reshetnyak VI, Maev IV, Burmistrov AI, Chekmazov IA, Karlovich TI. Torque teno virus in liver diseases: On the way towards unity of view. World J Gastroenterol 2020; 26:1691-1707. [PMID: 32351287 PMCID: PMC7183866 DOI: 10.3748/wjg.v26.i15.1691] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023] Open
Abstract
The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology, diagnostic methods, possible replication sites, and pathogenicity factors are described. TTV is a virus that is frequently detectable in patients with different viral hepatitides, in cases of hepatitis without an obvious viral agent, as well as in a healthy population. There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection. There are sufficient histological signs of liver damage, which confirm that the virus can undergo a replicative cycle in hepatocytes. Along with this, cytological hybridization in TTV-infected cells has shown no substantial cytopathic (cell-damaging) effects that are characteristic of pathogenic hepatotropic viruses. Studying TTV has led to the evolution of views on its role in the development of human pathology. The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses, including the viruses of the known types of hepatitides. The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a non-pathogenic virus. It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status. The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses. Fortunately, the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties. The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.
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Affiliation(s)
- Vasiliy I Reshetnyak
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor V Maev
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Alexandr I Burmistrov
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor A Chekmazov
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
| | - Tatiana I Karlovich
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
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Elesinnla AR, Adeleye IA, Ayolabi CI, Bessong PO. Prevalence of torque viruses in HIV-infected and non-HIV-infected Nigerian subjects: analysis of near-full-length genome sequences. Arch Virol 2020; 165:571-582. [PMID: 32030535 DOI: 10.1007/s00705-020-04538-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/30/2019] [Indexed: 12/22/2022]
Abstract
Torque teno virus (TTV), torque teno mini virus (TTMV) and torque teno midi virus (TTMDV) are members of the family Anelloviridae that are known to infect humans. Although no pathogenic roles have been associated with anelloviruses, their high prevalence and perceived ubiquitousness have provoked scientific interest in understanding their molecular and biological characteristics. We used nested PCR to determine the prevalence of anelloviruses among 130 human immunodeficiency virus (HIV)-infected patients and 130 healthy blood donors, and analyzed three near-full-length genome sequences of TTV isolates from HIV-infected and non-HIV infected Nigerians. Statistical analysis showed that the rate of TTV infection was significantly higher in the HIV-infected group (65%) than in the blood donor group (26%) (p < 0.05, χ2 = 40.3). TTMV and TTMDV infections were very high in both groups, ranging between 88 and 95%. No significant association was found between TTV infection and age, sex, CD4+ cell count, HIV viral load or alanine aminotransferase (ALT) level. Near-full-length genome sequences of TTV isolates FL100, FL08 and BD67 determined by next-generation sequencing were 3.6 kb, 3.2 kb and 2.9 kb, respectively, in size. Their GenBank accession numbers are MK820644, MK820645, MK820646, respectively. These isolates shared 59% sequence identity across the whole genome and clustered in two different phylogenetic groups. Our study established for the first time the circulation of TTV, TTMV and TTMDV in the Nigerian population, with a disproportionately higher prevalence of TTV in HIV-infected patients. The near-complete TTV genome sequences from Nigeria are similar to the sequences KT163879 and KT163916 (3748 and 3190 respectively), obtained from the plasma of HIV-infected subjects from the United States, and EU305675 (2919), identified in human plasma samples from France.
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Affiliation(s)
| | | | | | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, University of Venda, Thohoyandou, 0950, South Africa
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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.
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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.)
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Surveillance and impact of occult hepatitis B virus, SEN virus, and torque teno virus in Egyptian hemodialysis patients with chronic hepatitis C virus infection. Int J Infect Dis 2019; 92:13-18. [PMID: 31863879 DOI: 10.1016/j.ijid.2019.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/12/2019] [Accepted: 12/08/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Egypt ranks first regarding the prevalence of hepatitis C virus (HCV) infection. Many patients have concomitant diseases like kidney disorders requiring hemodialysis, a procedure carrying the hazard of transmitting other hepatitis viruses. The purpose of this study was to investigate for occult hepatitis B virus (HBV), SEN virus (SENV), and torque teno virus (TTV) among chronic HCV patients on maintenance hemodialysis to identify their impacts. METHODS A total of 325 hemodialysis patients were enrolled and divided into two groups based on HCV RNA testing results. Blood samples were collected before hemodialysis. Sera were tested for hepatitis B core antibodies (anti-HBc) and hepatitis B surface antibodies (anti-HBs) using ELISA. HBV, SENV, and TTV DNA were detected by PCR. The serum alanine aminotransferase (ALT) level was measured. RESULTS Anti-HBc and HBV DNA were detected in 73.1% and 50.8% of group 1 versus 36.4% and 22.6% of group 2. The serum ALT level was higher in group 1 than group 2. SENV was detected in 11.5% of group 1 versus 8.2% of group 2. TTV was detected in 29% of group 1 versus 27% of group 2. CONCLUSIONS There is an increased prevalence of occult HBV in our locality among chronic HCV patients undergoing hemodialysis. The existence of SENV and TTV viremia has no clinical impact.
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Rezahosseini O, Drabe CH, Sørensen SS, Rasmussen A, Perch M, Ostrowski SR, Nielsen SD. Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation. Transplant Rev (Orlando) 2019; 33:137-144. [PMID: 30981537 DOI: 10.1016/j.trre.2019.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 12/27/2022]
Abstract
Solid organ transplantation (SOT) recipients receive immunosuppressive therapy to avoid rejection of the transplanted organ. Immunosuppressive therapy increases the risk of infections. However, no existing marker reliably reveals the status of the immune function in SOT recipients. Torque-Teno virus or Transfusion-transmitted virus (TTV) has gained attention as a possible endogenous marker of the immune function. TTV is a non-enveloped, circular single strand DNA virus, and it may be considered a part of the human virome. In a bidirectional relationship, the immune system detects TTV and TTV may also modulate the activity of immune system. These characteristics have made the virus a possible candidate indicator of immune function. In this systematic review, we describe the role and potential function of TTV viral load as an endogenous marker of the immune function and consequently the level of immune suppression in SOT recipients.
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Affiliation(s)
- Omid Rezahosseini
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Heldbjerg Drabe
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Allan Rasmussen
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Michael Perch
- Department of Cardiology, Section for Lung Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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Najafimemar Z, Tabarraei A, Talei G, Moradi A. Prevalence and Genotyping of Torque Teno Virus in HBV/HIV and Chronic HBV Patients in Iran. IRANIAN BIOMEDICAL JOURNAL 2017; 22:338-44. [PMID: 29253922 PMCID: PMC6058187 DOI: 10.29252/ibj.22.5.338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Torque teno virus (TTV) was the first human Anelloviridae detected in a Japanese patient with an unknown type of hepatitis in 1997. TTV is by far the first known single-stranded circular DNA virus infecting human. In spite of its widespread nature in human population, its pathogenesis is still unclear. In addition, information regarding TTV infection in Iranian population is limited. Therefore, we attempted to determine the prevalence and genotype of TTV in three groups: HIV/HBV patients, chronic hepatitis B patients, and healthy individuals. Methods: The presence of TTV DNA in sera was investigated using PCR. The primer sets encompassing two 5’-UTR and N22 regions were used, and the positive products were collected for sequencing. Phylogenetic tree was generated based on N22 region and using the MEGA 7 software. Results: TTV DNA was detected in 452 patients with HIV/HBV and chronic hepatitis B, as well as in healthy control groups. The results from PCR indicated positive rates for these three groups 48%, 54%, and 49.3% using 5’-UTR primer and 15.1%, 12%, and 8% using N22 primer, respectively. Conclusion: Five genogroups were observed, which the second group was found to be the most frequent. The results of 5’-UTR primer showed more prevalence of TTV DNA comparing to N22 primer in patients and healthy control.
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Affiliation(s)
- Zahra Najafimemar
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabarraei
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran
| | - Gholamreza Talei
- Department of Microbiology, Faculty of Medicine, Lorestan University of Medical Sciences, Lorestan, Iran
| | - Abdolvahab Moradi
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Golestan, Iran
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Higher Frequency of Transfusion-Transmitted Virus (TTV) in HIV Patients in Comparison with Healthy Blood Donors. INTERNATIONAL JOURNAL OF HIGH RISK BEHAVIORS & ADDICTION 2017. [DOI: 10.5812/ijhrba.59363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bhattacharya PK, Mukherjee S. Natural history of liver fibrosis progression in patients confected with hepatitis c virus and human immunodeficiency virus type 1. Rev Soc Bras Med Trop 2016; 49:803-805. [DOI: 10.1590/0037-8682-0402-2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 11/03/2016] [Indexed: 11/22/2022] Open
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Prasetyo AA, Dharmawan R, Raharjo I, Hudiyono. Human Leukocyte Antigen-E Alleles are Associated with Hepatitis C Virus, Torque Teno Virus, and Toxoplasma Co-infections but are not Associated with Hepatitis B Virus, Hepatitis D Virus, and GB Virus C Co-infections in Human Immunodeficiency Virus Patients. J Glob Infect Dis 2016; 8:75-81. [PMID: 27293362 PMCID: PMC4879794 DOI: 10.4103/0974-777x.182121] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Context: Data regarding the distribution of Human Leukocyte Antigen (HLA)-E alleles and their association with blood-borne pathogen infections/co-infections are limited for many populations, including Indonesia. Aims: The aim of this study was to analyze the association between HLA-E allelic variants and infection with blood-borne pathogens such as hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), torque teno virus (TTV), GB virus C (GBV-C), and Toxoplasma gondii (T. gondii) in Indonesian Javanese human immunodeficiency virus (HIV) patients. Settings and Design: A total of 320 anti-HIV-positive blood samples were analyzed for HBV, HCV, HDV, TTV, GBV-C, and T. gondii infection status and its association with HLA-E allelic variants. Materials and Methods: Nucleic acid was extracted from plasma samples and used for the molecular detection of HBV DNA, HCV RNA, HDV RNA, TTV DNA, and GBV-C RNA, whereas hepatitis B surface antigen, anti-HCV, immunoglobulin M and G (IgM and IgG) anti-T. gondii were detected through serological testing. The blood samples were genotyped for HLA-E loci using a sequence-specific primer-polymerase chain reaction. Statistical Analysis Used: Either the Chi-square or Fisher's exact test was performed to analyze the frequency of HLA-E alleles and blood-borne pathogen infections in the population. Odds ratios (ORs) were calculated to measure the association between the antibodies found and the participants’ possible risk behaviors. A logistic regression analysis was used to assess the associations. Results: HLA-E*101/0101 was associated with HCV/TTV co-infection (adjusted OR [aOR]: 3.5; 95% confidence interval [CI]: 1.156-10.734; P = 0.027) and IgM/IgG anti-Toxo positivity (aOR: 27.0; 95% CI: 3.626-200.472; P = 0.001). HLA-E*103/0103 was associated with TTV co-infection (aOR: 2.7; 95% CI: 1.509-4.796; P = 0.001). Conclusions: HLA-E alleles in Indonesian Javanese HIV patients were found to be associated with HCV, TTV, and toxoplasma co-infections.
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Affiliation(s)
- Afiono Agung Prasetyo
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Microbiology, Faculty of Medicine, Sutami 36A, Surakarta, Indonesia; Center of Biotechnology and Biodiversity Research and Development, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Ruben Dharmawan
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Parasitology, Faculty of Medicine, Surakarta, Indonesia
| | - Irvan Raharjo
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia
| | - Hudiyono
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Microbiology, Faculty of Medicine, Sutami 36A, Surakarta, Indonesia; Center of Biotechnology and Biodiversity Research and Development, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
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Li L, Deng X, Da Costa AC, Bruhn R, Deeks SG, Delwart E. Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels. J Clin Virol 2015; 72:106-13. [PMID: 26479202 DOI: 10.1016/j.jcv.2015.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/01/2015] [Accepted: 09/16/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND Abnormally high levels of T-cell activation can persist in HIV-infected subjects despite effective anti-retroviral therapy (ART) and has been associated with negative health outcomes. The nature of the antigenic drivers or other causes of this residual T-cell activation remain uncertain. Anelloviruses are universally acquired soon after birth, resulting in persistent viremia, and considered part of the commensal human virome. Reduced immunocompetence results in increased anellovirus levels. OBJECTIVES To test whether increased levels of anelloviruses or other viruses in plasma are associated with higher levels of persistent T-cell activation during ART. STUDY DESIGN Two amplification methods combined with next generation sequencing were used to detect all viruses and estimate relative anellovirus levels in plasma from 19 adults on effective ART who exhibited a wide range of T-cell activation levels. RESULTS Nucleic acids from HBV and HCV were detected in one patient each while pegivirus A (GBV-C) was found in three patients. Anellovirus DNA was detected in all patients with some individuals carrying up to eight different genotypes. Specific anellovirus genotypes or higher level of co-infections were not detected in subjects with higher levels of T-cell activation. No association was detected between relative plasma anellovirus DNA levels and the percentage of activated CD4 or CD8 T cells. CONCLUSIONS Human anelloviruses were detected in all HIV suppressed subjects, exhibited a wide range of viremia levels, and were genetically highly diverse. The level of persistent T-cell activation was not correlated with the level of viremia or genotypes present indicating that anellovirus antigens are unlikely to be a dominant source of antigens driving chronic T-cell activation.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Antonio Charlys Da Costa
- Blood Systems Research Institute, San Francisco, CA, USA; Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Roberta Bruhn
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Steven G Deeks
- Positive Health Program, San Francisco General Hospital, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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