The Nature of HTLV-1 Provirus in Naturally Infected Individuals Analyzed by Viral DNA-Capture-Seq Approach

Katsuya, Hiroo; Islam, Saiful; Tan, Benjy J.Y.; Ito, Jumpei; Miyazato, Paola; Matsuo, Misaki; Inada, Yuki; Iwase, Saori C.; Uchiyama, Yoshikazu; Hata, Hiroyuki; Sato, Tomoo; Yagishita, Naoko; Araya, Natsumi; Ueno, Takaharu; Nosaka, Kisato; Tokunaga, Masahito; Yamagishi, Masaaki; Watanabe, Toshiki; Uchimaru, Kaoru; Fujisawa, Jun–ichi; Utsunomiya, Atae; Yamano, Yoshihisa; Satou, Yorifumi

doi:10.2139/ssrn.3354888

Cited by 11 publications

(26 citation statements)

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“…Another important detail that emerged from this study was the high rate of defective provirus particles (around 30%) detected in HIV/HTLV-1- and HIV/HTLV-2-coinfected individuals, which is similar to the overall rates described in ATL individuals infected with HTLV-1 ( 20 – 22 ). However, the percentages differ depending on the type of defective provirus (type 1 or type 2).…”

Section: Discussionsupporting

confidence: 72%

“…However, the percentages differ depending on the type of defective provirus (type 1 or type 2). While in HTLV-1-infected individuals the majority of cases are defective provirus type 2 instead of type 1 (26.7% versus 2.2% in ATL, 14.5% versus 2.9% in asymptomatic carriers, and 13.1% versus 2.0% in HAM/TSP, respectively) ( 22 ), in the present study we detected more defective type 1 particles in HIV/HTLV-1 coinfection (20.4% versus 11.4%) and the same rates of type 1 and type 2 in HIV/HTLV-2-coinfected individuals (16.0%).…”

Section: Discussionmentioning

confidence: 99%

“…Concerning the limitations of the present study, we take into account that we used a conventional DNA sequencing methodology (Sanger sequencing), which generates provirus DNA fragments (not the complete provirus) present only in the major clones. Although we consider that the best way to search for defective proviruses is using a high-throughput sequencing-by-synthesis instrument (Illumina massively parallel sequencing technology) ( 32 ) or a recent viral DNA sequencing capture approach, which amplifies the full-length proviruses and provides information about the proviral structure and the viral integration sites ( 22 ), we tried to avert this lack of amplifying large fragments of the 5′LTR, env , and tax regions used in HTLV subtyping. We employed degenerate primers and protocols optimized previously for detecting all Brazilian sequences described in the literature ( 29 , 35 , 50 , 53 , 54 ); indeed, we increased the DNA input and repeated the reaction several times, and, to ascertain that the 5′LTR and not the 3′LTR of HTLV-1 was amplified, we employed primers pairs that cover the entire LTR region plus a close fragment of the gag gene of 66 bp (nucleotides 756 to 821).…”

Section: Discussionmentioning

confidence: 99%

“…Two types of defective HTLV-1 provirus were described in the 1990s: type 1, which retains both LTRs and lacks internal sequences, and type 2, which lacks the 5′LTR region ( 20 , 21 ). Interestingly, infected cells with HTLV-1-defective proviruses proliferate more than those with intact ones ( 22 ) and were detected at high frequencies in ATL cells and in aggressive forms of ATL ( 20 , 21 , 23 ). These defective sequences were also identified in asymptomatic carriers and HAM/TSP patients, albeit at low frequencies ( 22 , 24 ).…”

Section: Introductionmentioning

confidence: 99%

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Provirus Mutations of Human T-Lymphotropic Virus 1 and 2 (HTLV-1 and HTLV-2) in HIV-1-Coinfected Individuals

Campos

Caterino–de–Araujo

2020

mSphere

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Provirus mutations of human T-lymphotropic virus 1 (HTLV-1), mostly the lack of the 5′ long terminal repeat (LTR) genomic region, have been described and associated with severe adult T cell leukemia/lymphoma (ATLL), non-sense point mutations with low proviral load, and Western blotting indeterminate results. Until now, no information concerning provirus mutations of HTLV-2 and its consequences, as well as those of HTLV-1/2 in HIV-coinfected individuals, had been described. Therefore, we searched for these mutations in provirus samples of 44 HIV/HTLV-1- and 25 HIV/HTLV-2-coinfected individuals. Using protocols well established for amplification and sequencing of segments of the LTR, env, and tax regions, we searched for defective type 1 particles that retain LTRs and lack internal sequences and type 2 particles that lack the 5′LTR region. In addition, using as references the prototypes ATK (HTLV-1) and Mo (HTLV-2), we searched for point mutations in the LTR and synonyms and nonsynonymous mutations and non-sense mutations in env and tax regions. Defective HTLV-1 and HTLV-2 provirus type 1 or 2 was detected in 31.8% of HIV/HTLV-1- and 32.0% of HIV/HTLV-2-coinfected individuals. Synonymous and nonsynonymous mutations were identified mostly in HTLV-2 and associated with lower levels of specific antibodies. No non-sense mutations that resulted in premature termination of Env and Tax proteins were detected. On the contrary, mutation in the stop codon of Tax2a produced a long protein characteristic of the HTLV-2c subtype. The clinical significance of these mutations in coinfected individuals remains to be defined, but they confirmed the lower sensitivity of serological and molecular diagnostic tests in HIV/HTLV-1/2 coinfections. IMPORTANCE HTLV-1 and HTLV-2 are endemic to Brazil, and they have different effects in HIV/AIDS disease progression. HIV/HTLV-1 has been described as accelerating the progression to AIDS and death, while HIV/HTLV-2 slows the progression to AIDS. Provirus mutations of HTLV-1 were implicated in severe leukemia development and in problems in the diagnosis of HTLV-1; in contrast, provirus mutations of HTLV-2 had not been confirmed and associated with problems in HTLV-2 diagnosis or disease outcome. Nevertheless, data obtained here allowed us to recognize and understand the false-negative results in serologic and molecular tests applied for HTLV-1 and HTLV-2 diagnosis. Defective proviruses, as well as synonymous and nonsynonymous mutations, were associated with the diagnosis deficiencies. Additionally, since HIV-1 and HTLV-1 infect the same cells (CD4 positive), the production of HIV-1 pseudotypes with HTLV-1 envelope glycoprotein during HIV/HTLV-1 coinfection cannot be excluded. Defective provirus of HTLV-2 and Tax2c is speculated to influence progression to AIDS.

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Section: Discussionsupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Provirus Mutations of Human T-Lymphotropic Virus 1 and 2 (HTLV-1 and HTLV-2) in HIV-1-Coinfected Individuals

Campos

Caterino–de–Araujo

2020

mSphere

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“…Moreover, some defective proviruses lacking the 5′-LTR due to partial deletion consequently loose transcriptional regulation by Tax. Defective proviruses are rare at the beginning of infection, but later on clones with defective-type proviruses preferentially expand and become predominant [ 152 ].…”

Section: Transactivation: Activation Of Ltrs By Virus-encoded Protmentioning

confidence: 99%

Regulation of Expression and Latency in BLV and HTLV

Pluta

Jaworski

Douville

2020

Viruses

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Human T-lymphotrophic virus type 1 (HTLV-1) and Bovine leukemia virus (BLV) belong to the Deltaretrovirus genus. HTLV-1 is the etiologic agent of the highly aggressive and currently incurable cancer adult T-cell leukemia (ATL) and a neurological disease HTLV-1-associated myelopathy (HAM)/tropical spastic paraparesis (TSP). BLV causes neoplastic proliferation of B cells in cattle: enzootic bovine leucosis (EBL). Despite the severity of these conditions, infection by HTLV-1 and BLV appear in most cases clinically asymptomatic. These viruses can undergo latency in their hosts. The silencing of proviral gene expression and maintenance of latency are central for the establishment of persistent infection, as well as for pathogenesis in vivo. In this review, we will present the mechanisms that control proviral activation and retroviral latency in deltaretroviruses, in comparison with other exogenous retroviruses. The 5′ long terminal repeats (5′-LTRs) play a main role in controlling viral gene expression. While the regulation of transcription initiation is a major mechanism of silencing, we discuss topics that include (i) the epigenetic control of the provirus, (ii) the cis-elements present in the LTR, (iii) enhancers with cell-type specific regulatory functions, (iv) the role of virally-encoded transactivator proteins, (v) the role of repressors in transcription and silencing, (vi) the effect of hormonal signaling, (vii) implications of LTR variability on transcription and latency, and (viii) the regulatory role of non-coding RNAs. Finally, we discuss how a better understanding of these mechanisms may allow for the development of more effective treatments against Deltaretroviruses.

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Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

Kojabad

Farzanehpour

Galeh

et al. 2021

Journal of Medical Virology

145

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High‐throughput droplet‐based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR)‎ methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.

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The Nature of HTLV-1 Provirus in Naturally Infected Individuals Analyzed by Viral DNA-Capture-Seq Approach

Cited by 11 publications

References 0 publications

Provirus Mutations of Human T-Lymphotropic Virus 1 and 2 (HTLV-1 and HTLV-2) in HIV-1-Coinfected Individuals

Provirus Mutations of Human T-Lymphotropic Virus 1 and 2 (HTLV-1 and HTLV-2) in HIV-1-Coinfected Individuals

Regulation of Expression and Latency in BLV and HTLV

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

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