Design and development of a quantitative real time PCR assay for monitoring of HTLV-1 provirus in whole blood

Naderi, Mahmood; Paryan, Mahdi; Azadmanesh, Kayhan; Rafatpanah, Houshang; Rezvan, H; Samiee, Siamak Mirab

doi:10.1016/j.jcv.2011.12.033

Cited by 26 publications

(18 citation statements)

References 36 publications

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“…Amplification and analysis were performed with the Applied Biosystems 7500 real-time PCR system using an initial denaturation step at 95°C for 2 minutes, followed by 40 cycles of 95°C for 10 seconds and 57°C for 45 seconds. A fragment of the RNase P gene from humans [29] was used as an internal control. A negative, no-template control (H 2 O control) was run with every assay.…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology

Pessôa¹,

Watanabe²,

Nukui

et al. 2014

PLoS ONE

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BackgroundHere, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol.MethodsBlood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis.ResultsA high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil.ConclusionsThis study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the evolutionary history of this medically important virus.

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Section: Methodsmentioning

confidence: 99%

Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology

Pessôa¹,

Watanabe²,

Nukui

et al. 2014

PLoS ONE

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“…Although, the distribution of HTLV‐1 is worldwide, southern western Japan, the Caribbean islands, South America, West Africa, the Melanesian Islands, and Middle East are the main endemic areas for the virus [Tabei, ; Naderi et al, ; Yamashiro et al, ]. HTLV‐2 is endemic amongst some American and African populations and also intravenous drug users in Europe and North America [Pouliquen et al, ; Souza et al, ; Treviño et al, ].…”

Section: Introductionmentioning

confidence: 99%

Prevalence and phylogenetic analysis of HTLV‐1 in a segregated population in Iran

Rafatpanah

Torkamani

Valizadeh

et al. 2016

Journal of Medical Virology

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Human T-lymphotropic virus type 1 (HTLV-1) infection is an important health issue that affects a variety of endemic areas. The Khorasan province, mainly its capital Mashhad in northeastern Iran, was reported to be as one of these endemic regions. Torbat-e Heydarieh, a large city Southwest border to Mashhad with a segregated population was investigated for the prevalence and associated risk factors of HTLV-1 infection in 400 randomly selected individuals. Blood samples were tested for the presence of HTLV-1 antibodies via the ELISA method and then were confirmed by an Immunoblot test. For the presence of HTLV-1 in lymphocytes of infected subjects, PCR was performed on LTR and TAX regions. DNA sequencing of LTR fragment was also carried out to determine the phylogenetic of HTLV-1, using the Maximum likelihood method. HTLV-1 sero-reactivity (sero-prevalence) among the study population was 2% (8/400), of which 1.25% had HTLV-1 provirus in lymphocytes (actual prevalence). HTLV-1 infection was significantly associated with the age, marital status, and history of blood transfusion (P < 0.05). However, there were no statistical differences between HTLV-1 infection, and gender, surgery, and hospitalization. In regression analysis, age showed the most significant correlation with the infection (P = 0.006, OR = 4.33). Based on our phylogenetic study, the HTLV-1 prevalent sequence type of Torbat-e Heydarieh belongs to the cosmopolitan subtype A. HTLV-1 prevalence in Torbat-e Heydarieh (1.25%) is low comparing to those of both Mashhad (2-3%) and Neishabour (3.5-5%) in the province of Khorasan. Thus, traveling mobility and population mixing such as marriage, bureaucratic affairs, occupation, and economic activities could be the usual routs of HTLV-1 new wave of spreading in this segregated city.

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“…have been identified globally (Naderi et al, 2012). Although there are usually no symptoms initially in most infected people, there is a relationship between HTLV-1 and severe diseases, such as ATL and HAM/TSP (Takatsuki, 2005).…”

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confidence: 99%

Current approaches for detection of human T‐lymphotropic virus Type 1: A systematic review

Fani

Rezayi

Meshkat

et al. 2019

Journal Cellular Physiology

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Background Human T‐lymphotropic virus Type 1 (HTLV‐1) is a retrovirus that is endemic in some regions of the world. It is known to cause several diseases like adult T‐cell leukemia (ATL) and HTLV‐1‐associated myelopathy/tropical spastic paraparesis (HAM/TSP). Serology and molecular methods have been used to detect this virus. Of these, enzyme‐linked immunosorbent assay (ELISA) is used as a primary screening method and this is usually followed by western blotting (WB) and polymerase chain reaction (PCR) methods as confirmatory tests. We conducted a systematic review of the different techniques used in the diagnosis of HTLV‐1 infection. Materials and Methods Our search was limited to original papers in the English language from 2010 to 2018 using several databases including Pubmed, Scopus, Google Scholar, Iranmedex, and Scientific Information Database. A manual search of references provided in the included papers was also performed. Results Of 101 electronically searched citations, 43 met the inclusion criteria. ELISA is commonly used for qualitative and screening detection, and WB and PCR techniques are used to confirm infection. Conclusion Among all the reported methods for detection of HTLV‐1, only serological and molecular tests are used as the most common technical assays for HTLV‐1. The ELISA assay, without a confirmatory test, has several limitations and affect the accuracy of the results. Owing to the prevalence of HTLV‐1 and limitations of the current detection methods, further evaluation of the accuracy of these methods is needed. There are new opportunities for applying novel technological advances in microfluidics, biosensors, and lab‐on‐a‐chip systems to perform HTLV‐1 diagnostics.

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Design and development of a quantitative real time PCR assay for monitoring of HTLV-1 provirus in whole blood

Cited by 26 publications

References 36 publications

Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology

Molecular Characterization of Human T-Cell Lymphotropic Virus Type 1 Full and Partial Genomes by Illumina Massively Parallel Sequencing Technology

Prevalence and phylogenetic analysis of HTLV‐1 in a segregated population in Iran

Current approaches for detection of human T‐lymphotropic virus Type 1: A systematic review

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