A combined approach of rolling-circle amplification-single site restriction endonuclease digestion followed by next generation sequencing to characterize the whole genome and intra-host variants of human Torque teno virus

Cancela, Florencia; Marandino, Ana; Panzera, Yanina; Betancour, Gabriela; Mirazo, Santiago; Arbiza, Juan; Ramos, Natália

doi:10.1016/j.virusres.2022.198974

Cited by 1 publication

(2 citation statements)

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“…In this study, SNVs will be determined by comparing the within‐host consensus HPV genome to their respective sublineages reference genomes (Figure 1). Furthermore, our investigation extends to the deep‐sequenced viral genomic diversity of a virus population within an individual sample, that is, iSNVs 27,28 …”

Section: Introductionmentioning

confidence: 96%

“…Furthermore, our investigation extends to the deep-sequenced viral genomic diversity of a virus population within an individual sample, that is, iSNVs. 27,28 It has been hypothesized that iSNVs could serve as markers for the potential progression of an HPV infection to cervical cancer. 21,24,25 A lower amount of iSNVs has previously been associated with cervical precancerous lesions/cancers when compared to normal/low-grade lesion cases.…”

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confidence: 99%

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Changes in intrahost genetic diversity according to lesion severity in longitudinal HPV16 samples

Costanzi,

Stosic,

Løvestad

et al. 2024

Journal of Medical Virology

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Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient with lesions not progressing to cancer. There is a lack of specific biomarkers for early cancer risk stratification. This study aimed to explore the intrahost HPV16 genomic variation in longitudinal samples from HPV16‐infected women with different cervical lesion severity (normal, low‐grade, and high‐grade). The TaME‐seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intrahost SNVs (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3‐induced iSNVs were significantly lower in high‐grade relative to normal and low‐grade samples. A significant increase in the number of APOBEC3‐induced iSNVs over time was observed for normal samples when compared to high‐grade. Our results indicates that the lower incidence of iSNVs and APOBEC3‐induced iSNVs in high‐grade lesions may have implications for novel biomarkers discoveries, potentially aiding early stratification of HPV‐induced cervical precancerous lesions.

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Section: Introductionmentioning

confidence: 96%

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confidence: 99%