Evolutionary dissection of monkeypox virus: Positive Darwinian selection drives the adaptation of virus-host interaction proteins

Vaccinia Virus Vector Bivalent Norovirus Vaccine

Norovirus is a major etiological agent of nonbacterial gastroenteritis around the world. Due to its in vitro culture complexity, high genome diversity, and the lack of cross-reactive immunity between genogroups, there is an unmet urgent need for polyvalent norovirus vaccines that provide broad-spectrum protection, and no vaccine has gained global approval to date. In this study, we constructed a bivalent norovirus vaccine, based on the highly attenuated poxvirus [strain VG9] vector, expressing the major capsid protein VP1 from genotypes GII.4 and GII.17. VG9-NOR exhibited a comparable replication ability to the authentic virus while preserving good safety. After the intramuscular and intranasal immunization of mice, VG9-NOR induced high IgG- and IgA-binding antibody (Ab) titers against GII.4 and GII.17, increased the secretion of GII.4 and GII.17-specific HGBA-blocking antibodies, and enhanced GII.17-specific mucosal immunity. Furthermore, VG9-NOR also induced a Th1-mediated cellular response. These results demonstrate that the polyvalent poxvirus vector vaccine expressing VP1 variants from different subtypes is able to elicit effective protection. Our study highlights the VG9 vector as a highly promising candidate for the development of polyvalent norovirus vaccines.

Establishment of an animal model for monkeypox virus infection in dormice

This study aims to establish an animal model of monkeypox virus (MPXV) infection in dormice through intranasal inoculation. Male dormice aged 4-5 months were selected as experimental subjects and administered different titers of MPXV (103.5 PFU, 104.5 PFU, and 105.5 PFU, respectively) via nasal instillation. Within 14 days post-infection, clinical indicators such as survival rate, body weight changes, respiratory status, and mental state were continuously monitored. Additionally, tissue samples from the lungs, liver, spleen, and trachea of dormice from each group were collected on the 5th and 10th days for virus titer detection, and histopathological analysis was performed on lung samples collected on the 5th and 10th days. Dormice infected with MPXV exhibited typical symptoms such as appetite loss, continuous body weight reduction, aggravated respiratory difficulties, accompanied by lethargy, chills, and other clinical manifestations similar to human monkeypox infection. Virological tests further confirmed the distribution of MPXV in multiple vital organs of dormice, including the lungs, liver, spleen, and trachea, with particularly significant pathological damage observed in lung tissue. An MPXV infection model in dormice was successfully established through intranasal inoculation with a titer of 105.5 PFU MPXV, which can be used for studying the infection mechanism and pharmacology of MPXV.

Estimating the Current Routes of Transmission in HIV-1 F1 Subtype Infected Persons in Romania: Differences Between Self-Reporting and Phylogenetic Data

Monitoring the HIV epidemic in Romania has proven challenging due to many factors, including the reluctance of newly diagnosed patients to disclose relevant epidemiological aspects during the clinical interview, such as sexual orientation or the existence of previous issues with injectable drug usage. We propose in this study a molecular approach to mitigate this problem with the help of bioinformatic tools, such as cluster analysis of phylogenetic trees. Both a maximum likelihood estimation, as implemented with FastTree, and a Bayesian approach, as used in BEAST, have been applied to our data set of 312 HIV subtype F1 pol gene sequences. ClusterPicker was used in order to identify groups of sequences and indicate similarities possibly related to the route of transmission. An important observation from this analysis is that transmission between men who have sex with men (MSM) is likely occurring in networks significantly larger than previously assessed by self-reported data (65% from the phylogenetic tree versus 37% from self-declared affiliation). Cluster analysis can help identify risk factors, reveal transmission trends, and, consequently, advise prevention programs.

Strengthening Africa's response to Mpox (monkeypox): insights from historical outbreaks and the present global spread

Mpox, formerly known as Monkeypox, is a viral zoonotic disease endemic to Central and West Africa that has posed significant public health challenges since its identification in 1970. Despite decades of experience in managing outbreaks, the 2022-2024 Mpox outbreaks exposed substantial gaps in global preparedness and response, leading the World Health Organization (WHO) to declare a Public Health Emergency of International Concern (PHEIC) in 2022. The resurgence of cases in Europe in 2022 and the more recent emergence of the virulent clade Ⅰb in the Democratic Republic of the Congo (DRC) in 2024 have highlighted a critical need for improved proactive and response strategies to curb the epidemic. This narrative review examines the historical and recent epidemiology of Mpox in Africa and explores the factors that have limited effective management. These include objective influences such as viral mutations, zoonotic transmission patterns, and environmental changes like deforestation, as well as subjective factors, including delayed responses, limited vaccine availability, cessation of smallpox vaccinations, and inequitable access to healthcare. In particular, the review emphasizes the ongoing disparities in global health equity, as wealthier nations have been able to secure vaccines and therapeutics quickly, while endemic regions in Africa continue to struggle with limited resources. The review also discusses how socio-economic and cultural factors, combined with weak public health infrastructure and inadequate surveillance systems, perpetuate cycles of outbreak in vulnerable populations. Furthermore, the emergence of clade Ⅰb in 2024, with its higher virulence and mortality rates among children, particularly in rural areas, underscores the urgency of addressing the evolving epidemiological landscape of Mpox. In response to these challenges, this review recommends strengthening healthcare infrastructure, enhancing surveillance systems, ensuring equitable access to vaccines and treatments, and integrating environmental management into public health strategies. Global collaboration remains essential to provide African countries with the resources and support needed to manage and prevent future outbreaks effectively. Without these measures, the world risks a prolonged public health crisis with far-reaching consequences for both Africa and the global community.

Recombination and selection trajectory of the monkeypox virus during its adaptation in the human population

Monkeypox, caused by the monkeypox virus (MPXV), was historically confined to West and Central Africa but has now spread globally. Recombination and selection play crucial roles in the evolutionary adaptation of MPXV; however, the evolution of MPXV and its relationship with the recent, ground-breaking monkeypox epidemic remains poorly understood. To gain insights into the evolutionary dynamics of MPXV, comprehensive in silico recombination and selection analyses were conducted based on MPXV whole genome sequence data. Three types of recombination were identified: five ancestor-sharing interspecies recombination events, six specific interspecies recombination events and four intraspecies recombination events. The results highlight the prevalent occurrence of recombination in MPXV, with 73.3% occurring in variable regions of the genome. Selection analysis was performed from three dimensions: proteins around recombination regions, proteins from recombinant ancestors and MPXV branches, and whole-genome gene analysis. Results revealed 2 and 7 proteins under positive selection in the first two dimensions, respectively. These proteins are mainly involved in infection immunity, apoptosis regulation and viral virulence. Whole-genome analysis detected 25 genes under positive selection, mainly associated with immune response and viral regulation. Understanding their evolutionary patterns will help predict and prevent cross-species transmission, zoonotic outbreaks and potential human epidemics.

In silico development of a novel anti-mutation, multi-epitope mRNA vaccine against MPXV variants of emerging lineage and sub-lineages by using immunoinformatics approaches

Over the past year, an unexpected surge in human monkeypox (hMPX) cases has been observed. This outbreak differs from previous ones, displaying distinct epidemiological characteristics and transmission patterns, believed to be influenced by a newly emerging monkeypox virus (MPXV) lineage. Notably, this emerging MPXV lineage has exhibited several non-synonymous mutations, some of which are linked to immunomodulatory activities and antigenic characteristics that aid in host detection. However, specific treatments or vaccines for human monkeypox are currently lacking. Hence, we aim to develop a multi-epitope mRNA vaccine by using immunoinformatics approaches against the MPXV, particularly its emerging variants. Six proteins (A29L, A35R, B6R, M1R, H3L, and E8L) were chosen for epitope and mutation site identification. Seventeen top-performing epitopes and eight epitopes containing mutation sites were selected and combined with adjuvants, the PADRE sequence, and linkers for vaccine development. The molecular and physical properties of the designed vaccine (WLmpx) were favorable. Immunological characteristics of WLmpx were assessed through molecular docking, molecular dynamics (MD) simulations, and immune simulations. Finally, the vaccine sequence was utilized to formulate an mRNA-based vaccine. The informatics-based predicted results indicated that the designed vaccine exhibits significant potential in eliciting high-level humoral and cellular immune responses, but further validation through in vivo and vitro studies is warranted.

Genetic insights into the microevolutionary dynamics and early introductions of human monkeypox virus in Mexico

The recent global outbreak of mpox, caused by monkeypox virus (MPV) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. In this study, we analyzed 880 MPV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than single-nucleotide polymorphisms (SNPs), which do not contribute significantly to genome diversity. Although the genome contains multiple SNPs in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is amino acid position 63 of the protein encoded by the Cop-A4L gene, which is intricately related to viral maturity, which we found to be under strong positive selection. Ancestral state reconstruction indicated that the ancestral state at position 63 corresponds to the amino acid valine, which is present only in isolates of clade I. However, the isolates from the current outbreak contained threonine at position 63. Our findings contribute new information about the evolution of monkeypox virus.

Genomic characterization and molecular evolution of human monkeypox viruses

Monkeypox virus is a member of the family Poxviridae, as are variola virus and vaccinia virus. It has a linear double-strand DNA genome approximately 197 kb long, containing ~190 non-overlapping ORFs. Comparison of members of the Central and West African clades shows the presence of unique genes that are associated with different disease presentations, depending on the strain. The last smallpox vaccination efforts ended in the mid-1980s, and there is concern about the recent spread of human monkeypox disease around the world. Almost 87,000 human monkeypox cases have been diagnosed in the world, of which more than 10,900 were in Brazil. The aim of this study was to evaluate the epidemiology and molecular evolution of hMpxV. From computational biology analysis of 640 hMpxV genomes from 1962 to 2022, synteny breaks and gene conservation were observed between Central and West clade genomes, and strains belonged with the 2022 outbreak assigned to the West African clade. Evidence was found for diversifying selective pressure at specific sites within protein coding sequences, acting on immunomodulatory processes. The existence of different sites under diversifying and purifying selection in paralog genes indicates adaptive mechanisms underlying the host-pathogen interaction of monkeypox virus in humans.

Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology

During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.

Monkeypox (Mpox) virus isolation and ultrastructural characterisation from a Brazilian human sample case

BACKGROUND

According to the last 2023 Monkeypox (Mpox) Outbreak Global Map from the Centres for Disease Control and Prevention (CDC), more than 100 countries with no Mpox infection report cases. Brazil stands out in this group and is the second country with the highest number of cases in the last outbreak.

OBJECTIVE

To contribute to knowledge of the virus infection effects in a cellular model, which is important for diagnosis infections not yet included in a provider´s differential diagnosis and for developing viral inhibition strategies.

METHODS

We describe a virus isolation protocol for a human clinical sample from a patient from Brazil, the viral growth in a cell model through plaque forming units (PFU) assay, reverse transcriptase polymerase chain reaction (RT-PCR) and transmission electron microscopy (TEM).

FINDINGS

We follow the viral isolation in Vero cell culture from a Mpox positive clinically diagnosed sample and show the infection effects on cellular structures using a TEM.

MAIN CONCLUSIONS

Understanding the impact of viral growth on cellular structures and its replication kinetics may offer better strategies for the development of new drugs with antiviral properties.

Mpox virus mRNA-lipid nanoparticle vaccine candidates evoke antibody responses and drive protection against the Vaccinia virus challenge in mice

In response to the human Mpox (hMPX) epidemic that began in 2022, there is an urgent need for a monkeypox vaccine. Here, we have developed a series of mRNA-lipid nanoparticle (mRNA-LNP)-based vaccine candidates that encode a collection of four highly conserved Mpox virus (MPXV) surface proteins involved in virus attachment, entry, and transmission, namely A29L, A35R, B6R, and M1R, which are homologs to Vaccinia virus (VACV) A27, A33, B5, and L1, respectively. Despite possible differences in immunogenicity among the four antigenic mRNA-LNPs, administering these antigenic mRNA-LNPs individually (5 μg each) or an average mixture of these mRNA-LNPs at a low dose (0.5 μg each) twice elicited MPXV-specific IgG antibodies and potent VACV-specific neutralizing antibodies. Furthermore, two doses of 5 μg of A27, B5, and L1 mRNA-LNPs or a 2 μg average mixture of the four antigenic mRNA-LNPs protected mice against weight loss and death after the VACV challenge. Overall, our data suggest that these antigenic mRNA-LNP vaccine candidates are both safe and efficacious against MPXV, as well as diseases caused by other orthopoxviruses.

Selective events at individual sites underlie the evolution of monkeypox virus clades

In endemic regions (West Africa and the Congo Basin), the genetic diversity of monkeypox virus (MPXV) is geographically structured into two major clades (Clades I and II) that differ in virulence and host associations. Clade IIb is closely related to the B.1 lineage, which is dominating a worldwide outbreak initiated in 2022. Lineage B.1 has however accumulated mutations of unknown significance that most likely result from apolipoprotein B mRNA editing catalytic polypeptide-like 3 (APOBEC3) editing. We applied a population genetics-phylogenetics approach to investigate the evolution of MPXV during historical viral spread in Africa and to infer the distribution of fitness effects. We observed a high preponderance of codons evolving under strong purifying selection, particularly in viral genes involved in morphogenesis and replication or transcription. However, signals of positive selection were also detected and were enriched in genes involved in immunomodulation and/or virulence. In particular, several genes showing evidence of positive selection were found to hijack different steps of the cellular pathway that senses cytosolic DNA. Also, a few selected sites in genes that are not directly involved in immunomodulation are suggestive of antibody escape or other immune-mediated pressures. Because orthopoxvirus host range is primarily determined by the interaction with the host immune system, we suggest that the positive selection signals represent signatures of host adaptation and contribute to the different virulence of Clade I and II MPXVs. We also used the calculated selection coefficients to infer the effects of mutations that define the predominant human MPXV1 (hMPXV1) lineage B.1, as well as the changes that have been accumulating during the worldwide outbreak. Results indicated that a proportion of deleterious mutations were purged from the predominant outbreak lineage, whose spread was not driven by the presence of beneficial changes. Polymorphic mutations with a predicted beneficial effect on fitness are few and have a low frequency. It remains to be determined whether they have any significance for ongoing virus evolution.