Molecular detection of monkeypox and related viruses: challenges and opportunities

Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing

The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.

In silico identification of potential phytochemical inhibitors for mpox virus: molecular docking, MD simulation, and ADMET studies

The mpox virus (MPXV), a member of the Poxviridae family, which recently appeared outside of the African continent has emerged as a global threat to public health. Given the scarcity of antiviral treatments for mpox disease, there is a pressing need to identify and develop new therapeutics. We investigated 5715 phytochemicals from 266 species available in IMMPAT database as potential inhibitors for six MPXV targets namely thymidylate kinase (A48R), DNA ligase (A50R), rifampicin resistance protein (D13L), palmytilated EEV membrane protein (F13L), viral core cysteine proteinase (I7L), and DNA polymerase (E9L) using molecular docking. The best-performing phytochemicals were also subjected to molecular dynamics (MD) simulations and in silico ADMET analysis. The top phytochemicals were forsythiaside for A48R, ruberythric acid for A50R, theasinensin F for D13L, theasinensin A for F13L, isocinchophyllamine for I7L, and terchebin for E9L. Interestingly, the binding energies of these potential phytochemical inhibitors were far lower than brincidofovir and tecovirimat, the standard drugs used against MPXV, hinting at better binding properties of the former. These findings may pave the way for developing new MPXV inhibitors based on natural product scaffolds. However, they must be further studied to establish their inhibitory efficacy and toxicity in in vitro and in vivo models.

Frontiers of monkeypox research: An analysis from the top 100 most influential articles in the field

BACKGROUND

Monkeypox (MPX) has made recurrence after decades as a neglected zoonotic disease. More nations have reported endemic monkeypox in the past decade than in the previous forty. The World Health Organization has warned that the world may face another significant challenge after dealing with COVID-19, a pandemic, and the Monkeypox outbreak. Early appraisal of monkeypox research and development allows researchers to anticipate solutions for large outbreaks. We conducted a bibliometric analysis of this study's top 100 cited papers to identify regional research patterns.

METHODS

Our method was to search the SCI-Expanded database on Web of Science (WOS) for the top 100 papers that were cited in MPX on this database. We examined relevant literature from different years, journals, countries/regions, institutions, authors, and keywords.In order to create knowledge maps, we used the programs VOSviewer, Citespace, Scimago Graphica and the bibliometric online analysis platform. After compiling the relevant literature in Excel, we could estimate the field's focus and trends.

RESULTS

A total of 47 journals from 36 countries and regions published the top 100 cited papers between 1999 and 2023. The majority of articles were published in EMERGING INFECTIOUS DISEASES, while the highest average number of citations per paper were found in the NEW ENGLAND JOURNAL OF MEDICINE. The UNITED STATES contributed the most publications, followed by ENGLAND and SWITZERLAND. As far as the total number of publications goes, the Centers for Disease Control & Prevention in the USA, the National Institute of Health in the USA, and the World Health Organization each contributed the most papers. The major categories are immunology, virology and infectious diseases. The top five keywords were infection, Congo, virus, smallpox, and transmission. The cluster analysis suggests MPX research will focus on safe and effective vaccines and epidemic prevention.

CONCLUSION

By using bibliometric analysis, MPX researchers can quickly and visually identify their research focus and boundaries. Although studies suggest that antiviral medicine is the best treatment, creating an effective vaccine might lessen and avoid MPX pandemics in the long term. Our findings imply that safe and effective vaccines may be the focus and trends for future MPX research. International coordination for case monitoring and identification is essential to understand monkeypox disease's ever-changing epidemiology.

Oral Infection, Oral Pathology and Salivary Diagnostics of Mpox Disease: Relevance in Dentistry and OMICs Perspectives

In this narrative review, we aim to point out the close relationship between mpox virus (MPXV) infection and the role of saliva as a diagnostic tool for mpox, considering the current molecular approach and in the perspective of OMICs application. The MPXV uses the host cell's rough endoplasmic reticulum, ribosomes, and cytoplasmic proteins to replicate its genome and synthesize virions for cellular exit. The presence of oral mucosa lesions associated with mpox infection is one of the first signs of infection; however, current diagnostic tools find it difficult to detect the virus before the rashes begin. MPXV transmission occurs through direct contact with an infected lesion and infected body fluids, including saliva, presenting a potential use of this fluid for diagnostic purposes. Currently available diagnostic tests for MPXV detection are performed either by real-time quantitative PCR (RT-qPCR) or ELISA, which presents several limitations since they are invasive tests. Despite current clinical trials with restricted sample size, MPXV DNA was detected in saliva with a sensitivity of 85%-100%. In this context, the application of transcriptomics, metabolomics, lipidomics, or proteomics analyses coupled with saliva can identify novel disease biomarkers. Thus, it is important to note that the identification and quantification of salivary DNA, RNA, lipid, protein, and metabolite can provide novel non-invasive biomarkers through the use of OMICs platforms aiding in the early detection and diagnosis of MPXV infection. Untargeted mass spectrometry (MS)-based proteomics reveals that some proteins also expressed in saliva were detected with greater expression differences in blood plasma when comparing mpox patients and healthy subjects, suggesting a promising alternative to be applied in screening or diagnostic platforms for mpox salivary diagnostics coupled to OMICs.

Human monkeypox: history, presentations, transmission, epidemiology, diagnosis, treatment, and prevention

Human monkeypox is a zoonotic infection that is similar to the diseases caused by other poxviruses. It is endemic among wild rodents in the rainforests of Central and Western Africa, and can be transmitted via direct skin contact or mucosal exposure to infected animals. The initial symptoms include fever, headache, myalgia, fatigue, and lymphadenopathy, the last of which is the main symptom that distinguishes it from smallpox. In order to prevent and manage the disease, those who are infected must be rapidly diagnosed and isolated. Several vaccines have already been developed (e.g., JYNNEOS, ACAM2000 and ACAM3000) and antiviral drugs (e.g., cidofovir and tecovirimat) can also be used to treat the disease. In the present study, we reviewed the history, morphology, clinical presentations, transmission routes, diagnosis, prevention, and potential treatment strategies for monkeypox, in order to enable health authorities and physicians to better deal with this emerging crisis.