https://doi.org/10.1016/j.jiph.2023.02.003

Monkeypox (mpox) virus: Classification, origin, transmission, genome organization, antiviral drugs, and molecular diagnosis

As we set into the second half of 2022, the world is still recovering from the two-year COVID-19 pandemic. However, over the past three months, the outbreak of the Monkeypox Virus (MPV) has led to fifty-two thousand confirmed cases and over one hundred deaths. This caused the World Health Organisation to declare the outbreak a Public Health Emergency of International Concern (PHEIC). If this outbreak worsens, we could be looking at the Monkeypox virus causing the next global pandemic. As Monkeypox affects the human skin, the symptoms can be captured with regular imaging. Large samples of these images can be used as a training dataset for machine learning-based detection tools. Using a regular camera to capture the skin image of the infected person and running it against computer vision models is beneficial. In this research, we use deep learning to diagnose monkeypox from skin lesion images. Using a publicly available dataset, we tested the dataset on five pre-trained deep neural networks: GoogLeNet, Places365-GoogLeNet, SqueezeNet, AlexNet and ResNet-18. Hyperparameter was done to choose the best parameters. Performance metrics such as accuracy, precision, recall, f1-score and AUC were considered. Among the above models, ResNet18 was able to obtain the highest accuracy of 99.49%. The modified models obtained validation accuracies above 95%. The results prove that deep learning models such as the proposed model based on ResNet-18 can be deployed and can be crucial in battling the monkeypox virus. Since the used networks are optimized for efficiency, they can be used on performance limited devices such as smartphones with cameras. The addition of explainable artificial intelligence techniques LIME and GradCAM enables visual interpretation of the prediction made, helping health professionals using the model. 

https://doi.org/10.1016/j.medntd.2023.100243

Deep learning based detection of monkeypox virus using skin lesion images

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9783225

Evaluation and clinical validation of monkeypox (mpox) virus real-time PCR assays

The RAA-Cas12a-MPXV assay via fluorescence reader and lateral flow strip. 

CRISPR/Cas12a-mediated ultrasensitive and on-site monkeypox viral testing

/pdf/recent-advances-in-molecular-and-immunological-diagnostic-25ylix0s.pdf

Recent Advances in Molecular and Immunological Diagnostic Platform for Virus Detection: A Review

Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which ‘m’ stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest. mEnrich-seq leverages DNA methylation differences between bacteria to enrich taxa of interest from metagenomic samples for selective sequencing.

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.

Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that can sequence specific bacterial taxa of interest (pathogens, beneficial microbes, or low-abundance taxa), but not the vast background of other taxa in a microbiome sample. To address this need, we developed mEnrich-seq, a method that can enrich taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self vs. non-self genome differentiation provided by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes (REs), individually or in combination, to deplete host DNA and most background microbial DNA while enriching bacterial taxa of interest. This core idea is integrated with library preparation procedures in a way that only non-digested DNA libraries are sequenced. We performed in-depth evaluations of mEnrich-seq and demonstrated its use in several applications to enrich (up to 117-fold) genomic DNA of pathogenic or beneficial bacteria from human urine and fecal samples, including several species that are hard to culture or of low abundance. We also assessed the broad applicability of mEnrich-seq and found that 3130 (68.03%) of the 4601 strains with mapped methylomes to date can be targeted by at least one commercially available RE, representing 54.78% of the species examined in this analysis. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest directly from the microbiome.

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever‐increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real‐time PCR‐assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration‐cleared pan‐Orthopox RT‐PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT‐PCR assay targeting the viral F3L‐gene. In addition, we further evaluated MPXV‐PCR‐positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT‐PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jmv.28247

Evaluation and validation of an RT‐PCR assay for specific detection of monkeypox virus (MPXV)

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mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Evaluation and validation of an RT‐PCR assay for specific detection of monkeypox virus (MPXV)