https://doi.org/10.1016/j.scitotenv.2022.159166

Monkeypox outbreak: Wastewater and environmental surveillance perspective

https://doi.org/10.1016/j.scitotenv.2022.161023

Occurrence of multiple respiratory viruses in wastewater in Queensland, Australia: Potential for community disease surveillance

Reviewing methods of deep learning for diagnosing COVID-19, its variants and synergistic medicine combinations

Monkeypox virus has remained the most virulent poxvirus since the elimination of smallpox approximately 41 years ago, with distribution mostly in Central and West Africa. Monkeypox (Mpox) in humans is a zoonotically transferred disease that results in a smallpox-like disease. It was first diagnosed in 1970 in the Democratic Republic of the Congo (DRC), and the disease has spread over West and Central Africa. The purpose of this review was to give an up-to-date, thorough, and timely overview on the genomic diversity and evolution of a re-emerging infectious disease. The genetic profile of Mpox may also be helpful in targeting new therapeutic options based on genes, mutations, and phylogeny. Mpox has become a major threat to global health security, necessitating a quick response by virologists, veterinarians, public health professionals, doctors, and researchers to create high-efficiency diagnostic tests, vaccinations, antivirals, and other infection control techniques. The emergence of epidemics outside of Africa emphasizes the disease’s global significance. Increased monitoring and identification of Mpox cases are critical tools for obtaining a better knowledge of the ever-changing epidemiology of this disease.

/pdf/an-updated-review-on-monkeypox-viral-disease-emphasis-on-2854ydxg.pdf

An Updated Review on Monkeypox Viral Disease: Emphasis on Genomic Diversity

Clinical and laboratory diagnosis of monkeypox (mpox): Current status and future directions

A monkeypox virus outbreak is currently spreading in multiple non-endemic countries since May 2022. The atypical clinical profile of patients has led to a very likely underestimation of the number of cases at the beginning of epidemic. The detection and quantification of the Monkeypox virus genome in sewersheds in Paris (France) correlated temporally with the identification of the first case of infection and the spread of the disease within the population connected to the sewage system.

First detection of Monkeypox virus genome in sewersheds in France

https://doi.org/10.1016/j.scitotenv.2022.157740

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

Numerous SARS-CoV-2 variants are emerging as the epidemic continues, inducing new waves of contamination. In July 2023, a new variant named BA.2.86 was identified, raising concerns about its potential for viral escape, even in an immune population. The reduction in patient-centered testing and the identification of variants by sequencing means that we are now blind to the spread of this new variant. The aim of this study was to track the signature of this variant in wastewater in Paris, France. This variant showed a very rapid spread, highly correlated with national flash studies involving sequencing of clinical samples, but with a moderate impact on virus circulation. This easy-to-implement approach enabled us to monitor the emergence and spread of this new variant in real time at low cost. 

BA.2.86 variant emergence and spread dynamics through wastewater monitoring in Paris, France.


 The development of high-throughput sequencing has greatly improved our knowledge of microbial diversity in aquatic environments and its evolution in highly diverse ecosystems. Relevant microbial diversity description based on high throughput sequencing relies on good quality of the nucleic acid recovered. Indeed, long genetic fragments are more informative for identifying mutation combinations that characterize variants or species in complex samples. This study describes a new analytical method based on digital PCR partitioning technology for assessing the fragmentation of nucleic acid and more specifically viral RNA. This method allows to overcome limits associated to hydrolysis probe-based assay by focusing on the distance between different amplicons, and not as usually on the size of amplicons. RNA integrity can thus be determined as a new fragmentation index, so called Fragment size 50. Application of this method has provided information on issues that are inerrant in environmental analyses, such as the storage impact of raw samples or extracted RNA, extraction methods or the nature of the sample on the integrity of viral RNA. Finally, the estimation of fragment size by dPCR showed a very strong similarity with the fragment size sequenced using Oxford Nanopore Technology. In addition to enabling objective improvements in analytical methods, this approach could become a systematic quality control prior to any long-read sequencing, avoiding insufficiently productive sequencing runs or biases in the representativeness of sequenced fragments.

Assessing RNA Integrity by Digital RT-PCR: Influence of Extraction, Storage, and Matrices

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First detection of Monkeypox virus genome in sewersheds in France

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

BA.2.86 variant emergence and spread dynamics through wastewater monitoring in Paris, France.

Assessing RNA Integrity by Digital RT-PCR: Influence of Extraction, Storage, and Matrices