Dataset Information

GenomeBits Characterization of MPXV.

ABSTRACT: Genome sequences of the monkeypox virus (MPXV) causing the current outbreak are being reported from an increasing number of countries. We present a letter-to-numerical sequence study via GenomeBits signal mapping in order to characterize the evolution of the MPXV via simple statistical analysis. Histograms, empirical and theoretical cumulative distribution curves and the resulting scatter plots for the base nucleotides A and C versus their complementary base nucleotides T and G are discussed. GenomeBits may help the surveillance of emergent infectious diseases.

SUBMITTER: Canessa E

PROVIDER: S-EPMC9777858 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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GenomeBits Characterization of MPXV.

Canessa Enrique E

Genes 20221127 12

Genome sequences of the monkeypox virus (MPXV) causing the current outbreak are being reported from an increasing number of countries. We present a letter-to-numerical sequence study via GenomeBits signal mapping in order to characterize the evolution of the MPXV via simple statistical analysis. Histograms, empirical and theoretical cumulative distribution curves and the resulting scatter plots for the base nucleotides A and C versus their complementary base nucleotides T and G are discussed. Ge ...[more]

PMID: 36553490

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Project description:Monkeypox virus (MPXV) poses a global health threat. Droplet digital PCR (ddPCR) holds potential as an accurate diagnostic tool for clinical microbiology. However, there is limited literature on the applicability of ddPCR in clinical settings. In this study, the clinical features of patients with MPXV during the initial outbreak in China in June 2023 were reviewed, and an optimized ddPCR method with dilution and/or inhibitor removal was developed to enhance MPXV detection efficiency. Eighty-two MPXV samples were tested from nine different clinical specimen types, including feces, urine, pharyngeal swabs, anal swabs, saliva, herpes fluid, crust, and semen, and the viral load of each specimen was quantified. A comparative analysis was performed with qPCR to assess sensitivity and specificity and to investigate the characteristics of MPXV infection by analyzing viral loads in different clinical specimens. Consequently, common pharyngeal and gastrointestinal symptoms were observed in patients with MPXV. The optimized ddPCR method demonstrated relatively high sensitivity for MPXV quantification in the clinical materials, with a limit of detection of 0.1 copies/μL. This was particularly evident in low-concentration samples like whole blood, semen, and urine. The optimized ddPCR demonstrated greater detection accuracy compared with normal ddPCR and qPCR, with an area under the curve (AUC) of 0.939. Except for crust samples, viral loads in the specimens gradually decreased as the disease progressed. Virus levels in feces and anal swabs kept a high detection rate at each stage of post-symptom onset, and feces and anal swabs samples may be suitable for clinical diagnosis and continuous monitoring of MPXV.ImportanceThe ddPCR technique proved to be a sensitive and valuable tool for accurately quantifying MPXV viral loads in various clinical specimen types. The findings provided valuable insights into the necessary pre-treatment protocols for MPXV diagnosis in ddPCR detection and the potentially suitable sample types for collection. Therefore, such results can aid in comprehending the potential characteristics of MPXV infection and the usage of ddPCR in clinical settings.

Project description:Mpox is a great public health concern worldwide currently; thus, a global primary epidemiological analysis of mpox and a phylogenetic analysis of currently circulating MPXV strains based on open-source data is necessary. A total of 83,419 confirmed cases with 72 deaths were reported from 7 May to 23 December 2022, representing an ongoing increasing trend. Mpox was largely restricted to being endemic in children in West Africa (WA) before 2022, and it mainly spread from animals to humans. Our analysis highlights that mpox has not only spread across regions within Africa but has also led to most infection events outside Africa. Currently, mpox has been dominated by human-to-human spread in 110 countries, with the majority of cases distributed in the non-endemic regions of Europe and North America. These data indicate that the geographic range, transmission route, vulnerable populations, and clinical manifestations of mpox have changed, which suggests that the niche of mpox has the potential to change. Remarkably, approximately 38,025 suspected mpox cases were recorded in West and Central Africa during 1970-2022, which implied that the epidemiology of mpox in the two regions remained cryptic, suggesting that strengthening the accuracy of molecular diagnosis on this continent is a priority. Moreover, 617 mpox genomes have been obtained from 12 different hosts; these data imply that the high host diversity may contribute to its ongoing circulation and global outbreak. Furthermore, a phylogenetic analysis of 175 MPXV genome sequences from 38 countries (regions) showed that the current global mpox outbreak was caused by multiple sub-clades in the clade IIb lineage. These data suggest that MPXV strains from the clade IIb lineage may play a predominated role in the spread of mpox worldwide, implying that the current mpox outbreak has a single infection source. However, further investigations into the origin of the new global mpox outbreak are necessary. Therefore, our analysis highlights that adjusted timely interventive measures and surveillance programs, especially using cheap and quick strategies such as wastewater monitoring the DNA of MPXV in Africa (WA), are important for uncovering this disease's transmission source and chain, which will help curb its further spread.

Project description:Monkeypox (MPX) is a zoonotic infectious disease caused by Monkeypox virus (MPXV), an enveloped DNA virus belonging to the Poxviridae family and the Orthopoxvirus genus. Since early May 2022, a growing number of human cases of Monkeypox have been reported in non-endemic countries, with no history of contact with animals imported from endemic and enzootic areas, or travel to an area where the virus usually circulated before May 2022. This qualitative risk assessment aimed to investigate the probability that MPXV transmission occurs through food during its handling and consumption. The risk assessment used "top-down" (based on epidemiological data) and "bottom-up" (following the agent through the food chain to assess the risk of foodborne transmission to human) approaches, which were combined. The "top-down" approach first concluded that bushmeat was the only food suspected as a source of contamination in recorded cases of MPXV, by contact or ingestion. The "bottom-up" approach then evaluated the chain of events required for a human to become ill after handling or consuming food. This approach involves several conditions: (i) the food must be contaminated with MPXV (naturally, by an infected handler or after contact with a contaminated surface); (ii) the food must contain viable virus when it reaches the handler or consumer; (iii) the person must be exposed to the virus and; (iv) the person must be infected after exposure. Throughout the risk assessment, some data gaps were identified and highlighted. The conclusions of the top-down and bottom-up approaches are consistent and suggest that the risk of transmission of MPXV through food is hypothetical and that such an occurrence was never reported. In case of contamination, cooking (e.g., 12 min at 70°C) could be considered effective in inactivating Poxviridae in foods. Recommendations for risk management are proposed. To our knowledge, this is the first risk assessment performed on foodborne transmission of MPXV.

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GenomeBits Characterization of MPXV.

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GenomeBits Characterization of MPXV.

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