2022

DOI: 10.3389/fviro.2022.821298

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Can a Torque Teno Virus (TTV) Be a Naked DNA Particle Without a Virion Structure?

Perumal Arumugam Desingu

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Cited by 10 publications

(8 citation statements)

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“…It is also observed that the BA.3 lineage spread slowly and causing very fewer cases which may be due to the loss of six mutations. As reported, the S‐protein of BA.1 contains 37 mutations, BA.2 contains 31 mutations, whereas BA.3 contains 33 mutations [7] …”

Section: Acknowledgementssupporting

confidence: 54%

“…As per a recent study, there are no specific mutations observed for the BA.3 lineage in spike protein. However, it is a combination of mutations in BA.2 and BA.1 S‐proteins [7] . As these lineages are developed simultaneously and probably from the same place (Botswana, South Africa), so they may have equal chances of spreading worldwide however, the rate of spread may be different.…”

Section: Acknowledgementsmentioning

confidence: 99%

See 1 more Smart Citation

Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective

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et al. 2022

Self Cite

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The SARS-CoV-2 virus has shown increased ability to mutate over the past two years, especially in the regions of the spike protein and receptor binding sites. Omicron (B.1.1.529) is the fifth variant of concern (VOC) after the emergence of the Alpha,

“…It is also observed that the BA.3 lineage spread slowly and causing very fewer cases which may be due to the loss of six mutations. As reported, the S‐protein of BA.1 contains 37 mutations, BA.2 contains 31 mutations, whereas BA.3 contains 33 mutations [7] …”

Section: Acknowledgementssupporting

confidence: 54%

“…As per a recent study, there are no specific mutations observed for the BA.3 lineage in spike protein. However, it is a combination of mutations in BA.2 and BA.1 S‐proteins [7] . As these lineages are developed simultaneously and probably from the same place (Botswana, South Africa), so they may have equal chances of spreading worldwide however, the rate of spread may be different.…”

Section: Acknowledgementsmentioning

confidence: 99%

Challenges of the Omicron (B.1.1.529) Variant and Its Lineages: A Global Perspective

²

,

³

et al. 2022

Self Cite

View full text Add to dashboard Cite

The SARS-CoV-2 virus has shown increased ability to mutate over the past two years, especially in the regions of the spike protein and receptor binding sites. Omicron (B.1.1.529) is the fifth variant of concern (VOC) after the emergence of the Alpha,

“…Despite anelloviruses constituting the majority of the human virome, their capsid structure was unknown and the identity of the capsid protein itself had not been established experimentally 21 . Our determination of the LY1 structure demonstrates that ORF1 encodes the capsid protein and that anelloviruses evolved a novel spike domain that extends around the 5-fold axis to form a crown structure.…”

Section: Discussionmentioning

confidence: 99%

“…Despite anelloviruses constituting the majority of the human virome, their capsid structure was unknown and the identity of the capsid protein itself had not been established experimentally 21 .…”

Section: Discussionmentioning

confidence: 99%

Anellovirus Structure Reveals a Mechanism for Immune Evasion

Liou²,

et al. 2022

Preprint

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The significant impact of the human virome on human physiology is beginning to emerge thanks to modern sequencing methods and bioinformatic tools. Anelloviruses, the principal constituent of the commensal human virome, are universally acquired in infancy and found throughout the body. Since the discovery of the original torque teno virus in 1997, three genera of the Anelloviridae family, each extremely diverse genetically, have been found in humans. These viruses elicit weak immune responses that permit multiple strains to co-exist and persist for years in a typical individual. However, because they do not cause disease and due to the lack of an in vitro culture system, anelloviruses remain poorly understood. Basic features of the virus, such as the identity of its structural protein, have been unclear until now. Here, we describe the first structure of an anellovirus particle, which includes a jelly roll domain that forms a 60-mer icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axes to form crown-like features. Relatively conserved patches of amino acids are near the base of the spike domain while a hypervariable region is at the apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved epitopes while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. This would contrast with viruses such as beak and feather disease virus, canine parvovirus or adeno-associated virus which lack such pronounced surface features. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.

“…TTV, a dsDNA virus belonging to the Anelloviridae family, had considerable genetic variability and extreme diversity [ 44 ]. In previous reports, the TTV DNA was detected in secretions of healthy humans, such as blood, saliva, breast milk, tears, bile, and urine [ 45 , 46 ]. The TTVs DNA level was also considered the marker of the immunological status, hepatitis, gastroenteritis, periodontitis, multiple sclerosis, and cancer [ 47 , 48 ].…”

Section: Discussionmentioning

confidence: 99%

Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome

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Mauleekoonphairoj

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et al. 2022

Genomics Inform

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Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performed a new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipeline was applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had no viral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases and controls by blastn and blastx analysis. This study is the first report on the full-length HERV-K assembled genomes in the Thai population. Furthermore, the HERV-K integration breakpoint positions were validated and compared between the case and control datasets. Interestingly, Brugada cases contained HERV-K integration breakpoints at promoters five times more often than controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positions that were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and long non-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the human genome.

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