A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

Ma, Zhihai; Gharizadeh, Baback; Cai, Xingsheng; Li, Mengzhen; Fellner, Marı́a Dolores; Basiletti, Jorge; Correa, Rita Mariel; Colucci, María Celeste; Baldoni, Gabriela; Vacchino, M; Galarza, Patricia Denisse Barrientos; Picconi, Marı́a Alejandra; Wang, Chunlin

doi:10.1186/s13027-022-00420-8

Cited by 7 publications

(7 citation statements)

References 40 publications

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“…NGS can also be applied to HPV genotyping instead of PCR-based methods on MB samples. The applications of NGS-based methods in the detection of STDs and HPV have been widely explored [40][41][42]. However, no investigations on the use of NGS in HPV detection and genotyping have been performed on MB.…”

Section: Discussionmentioning

confidence: 99%

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool

Tsang,

Cheung,

et al. 2024

Diagnostics

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Background: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women. Method: Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed. Results: MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing. Conclusions: In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women’s health.

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Section: Discussionmentioning

confidence: 99%

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool

Tsang,

Cheung,

et al. 2024

Diagnostics

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“…Although identification of Salmonella at the serogroup level can be rapidly achieved at most diagnostic laboratories, final serovar identification often takes several weeks because of the limited number of reference laboratories performing the complex task of serotyping. While MLSTnext characterizes many more loci than traditional MLST, with ChapterDX proprietary amplification strategy 16 , all 47 loci can be amplified with single-tube, single-step PCR (Figure 1). With a next-generation sequencing (NGS) platform such as Illumina sequencing machine, hundreds to thousands of samples can be analyzed in the same sequencing run within a 22-hour period.…”

Section: Discussionmentioning

confidence: 99%

“…It has been applied to subtype not only bacteria such as Listeria , Legionella , Shiga toxin-producing E. coli (STEC), parasites such as Cyclospora , but also viruses such as Hepatitis A virus. Coupled with the ChapterDx amplification technology 16 and NGS, MLSTnext could be a straightforward, effective, widely applicable and cost-efficient method to address increasingly complex food safety issues.…”

Section: Discussionmentioning

confidence: 99%

High ResolutionSalmonellaSubtyping by the MLSTnext Method

Ma¹,

Gharizadeh²,

Huang³

et al. 2023

Preprint

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The food industry needs a straightforward, efficient, widely applicable and cost-efficient method to not only detect, but also determine serovar and potential sources of multiple strains in food and environment. While Whole Genome Sequencing (WGS) can generate complete genomic profile of food pathogens, it is a laborious, time-consuming, and expensive method that necessitates pure isolates. As a result, it is unsuitable for samples with complex background, limiting its widespread application by food industry. However, traditional multilocus sequence typing (MLST) approaches do not provide sufficient single nucleotide polymorphism (SNP) information to effectively track-and-trace sources of contamination. In contrast, ChapterDx MLSTnext-NGS (next-generation sequencing) Salmonella assay amplifies and sequences 47 polymorphic loci, evenly spanning the Salmonella enterica genome. As demonstrated in this study, the ChapterDx MLSTnext-NGS Salmonella can identify serovar with high resolution, distinguishing between various strains of the same serovar and resolve co-presence of different strains in a single sample. Additionally, this assay can analyze up to thousand samples in a single sequencing run within 22 hours, making it a highly efficient and scalable method for the food industry. Moreover, the cost per sample of the ChapterDx MLSTnext-NGS Salmonella assay is comparable to that of quantitative Polymerase Chain Reaction (qPCR), making it an affordable option. The assay uses ChapterDx amplification technology, allowing for the amplification of all 47 loci in a single-tube, single-step PCR reaction. This makes it one of the simplest NGS applications available. In summary, ChapterDx MLSTnext-NGS Salmonella assay can be implemented in many diagnostic laboratories to address increasingly complex food safety issues.

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“…Human papillomavirus (HPV) is one of the most common causes of sexually transmitted diseases worldwide, infecting numerous people every year, and is closely related to cervical cancer. This virus generally affects the epithelial tissue of the genital area, especially in women, and its infection is resolved by the individual's immune system [1,2]. Furthermore, sexually transmitted infections (STIs) are common around the world and pose a dramatic burden on individual health and public health systems.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, sexually transmitted infections (STIs) are common around the world and pose a dramatic burden on individual health and public health systems. Missed diagnosis and late cure of STIs can lead to severe problems, for instance, infertility and cervical cancer [2,3].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the prevalent genotypes of human papillomavirus in the population of women in Golestan province in the northeastern of Iran

Vosoo,

Sarli,

Yousefi

et al. 2023

Cell. Mol. Biomed. Rep.

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Human papillomavirus (HPV) is a viral infection that usually causes growths on mucous membranes or skin (warts). It has been confirmed that there are more than 100 types of human papillomavirus (HPV). Some types of HPV infections cause warts, and some of them may cause different types of cancer. One of the most common ways of transmitting the HPV virus is unprotected sex, and this virus is the leading cause of cancers of the urinary and genital tracts. Cervical cancer is the fourth cause of cancer death in women, and more than 90% are associated with persistent infection by one of the most dangerous types of the virus. This research aimed to determine the genotypes of the HPV virus in DNA extracted from people suspected of being infected with HPV. In this cross-sectional epidemiological study, 225 cytology samples have been obtained from people suspected of being infected with the HPV virus, who had been referred to the Pardis laboratory of medical genetics in the Gonbad for diagnosis from 2022 to 2023. DNA extraction was done by CEDBIO kit and the determination of HPV virus genotypes was done by a GENOVA kit. The analysis of the data was done by Excel software. In this research, 225 samples have been studied. 106 women were positive while 118 women were negative. Furthermore, the most common high-risk genotypes were (16, 31, 33, 35, 39, 45, 52, 58, 59, and 67) and (18) while the most common low-risk genotypes were (40, 42, 43, 44, 54, 61, 62, 81, 83, and 89) and (6 and 11). Moreover, the maximum age range of positive women is between 28 and 35. This study has demonstrated that the determining of dangerous genotypes is considered an essential measure in managing people infected with HPV, especially persistent infection and prevention of cervical cancer.

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A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

Cited by 7 publications

References 40 publications

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool

High ResolutionSalmonellaSubtyping by the MLSTnext Method

Evaluation of the prevalent genotypes of human papillomavirus in the population of women in Golestan province in the northeastern of Iran

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