Analysis of the nucleotide sequence of 23.8 kbp from the left terminus of the genome of variola major virus strain India-1967

Genomic and transcriptomic analysis of the recent Mpox outbreak

The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Genome Sequences of Akhmeta Virus, an Early Divergent Old World Orthopoxvirus

Annotated whole genome sequences of three isolates of the Akhmeta virus (AKMV), a novel species of orthopoxvirus (OPXV), isolated from the Akhmeta and Vani regions of the country Georgia, are presented and discussed. The AKMV genome is similar in genomic content and structure to that of the cowpox virus (CPXV), but a lower sequence identity was found between AKMV and Old World OPXVs than between other known species of Old World OPXVs. Phylogenetic analysis showed that AKMV diverged prior to other Old World OPXV. AKMV isolates formed a monophyletic clade in the OPXV phylogeny, yet the sequence variability between AKMV isolates was higher than between the monkeypox virus strains in the Congo basin and West Africa. An AKMV isolate from Vani contained approximately six kb sequence in the left terminal region that shared a higher similarity with CPXV than with other AKMV isolates, whereas the rest of the genome was most similar to AKMV, suggesting recombination between AKMV and CPXV in a region containing several host range and virulence genes.

The complete genome sequence of the Alphaentomopoxvirus Anomala cuprea entomopoxvirus, including its terminal hairpin loop sequences, suggests a potentially unique mode of apoptosis inhibition and mode of DNA replication

Complete genome sequence of Anomala cuprea entomopoxvirus, which belongs to the genus Alphaentomopoxvirus, including its terminal hairpin loop sequences, is reported. This is the first genome sequence of Alphaentomopoxvirus reported, and hairpin loops in entomopoxviruses have not previously been sequenced. The genome is 245,717 bp, which is smaller than had previously been estimated for Alphaentomopoxvirus. The inverted terminal repeats are quite long, and experimental results suggest that one genome molecule has one type of hairpin at one end and another type at the other end. The genome contains unexpected ORFs, e.g., that for the ubiquitin-conjugating enzyme E2 of eukaryotes. The BIR and RING domains found in a single ORF for an inhibitor of apoptosis in baculoviruses and entomopoxviruses occurred in two different, widely separated ORFs. Furthermore, an ORF in the genome contains a serpin domain that was previously found in vertebrate poxviruses for apoptosis inhibition but not in insect viruses.

Interaction of orthopoxviruses with the cellular ubiquitin-ligase system

Protein modification by ubiquitin or ubiquitin-like polypeptides is important for the fate and functions of the majority of proteins in the eukaryotic cell and can be involved in regulation of various biological processes, including protein metabolism (degradation), protein transport to several cellular compartments, rearrangement of cytoskeleton, and transcription of cytoprotective genes. The accumulated experimental data suggest that the ankyrin-F-box-like and BTB-kelch-like proteins of orthopoxviruses, represented by the largest viral multigene families, interact with the cellular Cullin-1- and Cullin-3-containing ubiquitin-protein ligases, respectively. In addition, orthopoxviruses code for their own RING-domain-containing ubiquitin ligase. In this review, this author discusses the differences between variola (smallpox), monkeypox, cowpox, vaccinia, and ectromelia (mousepox) viruses in the organization of ankyrin-F-box and BTB-kelch protein families and their likely functions.

MHC-I-restricted epitopes conserved among variola and other related orthopoxviruses are recognized by T cells 30 years after vaccination

It is many years since the general population has been vaccinated against smallpox virus. Here, we report that human leukocyte antigen (HLA) class I restricted T cell epitopes can be recognized more than 30 years after vaccination. Using bioinformatic methods, we predicted 177 potential cytotoxic T lymphocyte epitopes. Eight epitopes were confirmed to stimulate IFN-gamma release by T cells in smallpox-vaccinated subjects. The epitopes were restricted by five supertypes (HLA-A1, -A2, -A24 -A26 and -B44). Significant T cell responses were detected against 8 of 45 peptides with an HLA class I affinity of K(D) less than or equal to 5 nM, whereas no T cell responses were detected against 60 peptides with an HLA affinity of K(D) more than 5 nM. All epitopes were fully conserved in seven variola, vaccinia and cowpox strains. Knowledge of the long-term response to smallpox vaccination may lead to a better understanding of poxvirus immunity and may aid in the development of new improved vaccines and diagnostic tools.

Characterization of the vaccinia virus A35R protein and its role in virulence

The vaccinia virus A35R gene is highly conserved among poxviruses and encodes a previously uncharacterized hydrophobic acidic protein. Western blotting with anti-A35R peptide antibodies indicated that the protein is expressed early in infection and resolved as a single sharp band of approximately 23 kDa, slightly higher than the 20 kDa predicted from its sequence. The protein band appeared to be the same molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, whether expressed in an in vitro transcription/translation system without microsomes or expressed in infected cells, suggesting that it was not glycosylated. A mutant virus with the A35R gene deleted (vA35Delta) formed wild-type-sized plaques on all cell lines tested (human, monkey, mouse, and rabbit); thus, A35R is not required for replication and does not appear to be a host range gene. Although the A35R protein is hydrophobic, it is unlikely to be an integral membrane protein, as it partitioned to the aqueous phase during TX-114 partitioning. The protein could not be detected in virus-infected cell supernatants. A35R localized intracellularly to the virus factories, where the first stages of morphogenesis occur. The vA35Delta mutant formed near-normal levels of the various morphogenic stages of infectious virus particles and supported normal acid-induced fusion of virus-infected cells. Despite normal growth and morphogenesis in vitro, the vA35Delta mutant virus was attenuated in intranasal challenge of mice compared to wild-type and A35R rescue virus. Thus, the intracellular A35R protein plays a role in virulence. The A35R has little homology to any protein outside of poxviruses, suggesting a novel virulence mechanism.

An alternative genetic method to test essential vaccinia virus early genes

The vaccinia virus F11L gene product was identified during search for additional factors involved in the control of post-replicative viral gene transcription elongation. F11L is a 1065 base pairs (354 aminoacids) gene expressed early during infection with no attributed function. The F11L gene is conserved in many but not all poxviruses. The essential presence of the F11L gene was tested using two different genetic methods. F11L gene disruption by insertion of a selectable cassette containing the Escherichia coli guanine phosphoribosyl transferase gene driven by the viral early-late 7.5K transcriptional promoter resulted exclusively in recombinant viruses containing both the wild type and disrupted alleles, indicating that the F11L gene was essential. However, an alternative test, using transient dominant selection to insert nonsense mutations into the F11L gene, proved that the F11L gene was non-essential for growth in culture. These experiments suggest that misleading results can be obtained using gene insertional mutagenesis as a test of essential presence of the gene. The experiments also provide genetic data on the probability of co-insertion of linked mutations in vaccinia virus genome using transient dominant selection.

Extensive gene gain associated with adaptive evolution of poxviruses

Previous studies of genome evolution usually have involved one or two genomes and have thus been limited in their ability to detect the direction and rate of evolutionary change. Here, we use complete genome data from 20 poxvirus genomes to build a robust phylogeny of the Poxviridae and to study patterns of genome evolution. We show that, although there has been little gene order evolution, there are substantial differences between poxviruses in terms of genome content. Furthermore, we show that the rate of gene acquisition is not constant over time and that it has increased in the orthopox lineage (which includes smallpox and vaccinia). We also tested for positive selection on 204 groups of genes and show that a disproportionately high proportion of genes in the orthopox clade are under positive selection. The association of an increased rate of gene gain and positive selection is indicative of adaptive genome evolution. Many of the genes involved in these processes are likely to be associated with host-parasite coevolution.

Variola virus immune evasion proteins

Variola virus, the causative agent of smallpox, encodes approximately 200 proteins. Over 80 of these proteins are located in the terminal regions of the genome, where proteins associated with host immune evasion are encoded. To date, only two variola proteins have been characterized. Both are located in the terminal regions and demonstrate immunoregulatory functions. One protein, the smallpox inhibitor of complement enzymes (SPICE), is homologous to a vaccinia virus virulence factor, the vaccinia virus complement-control protein (VCP), which has been found experimentally to be expressed early in the course of vaccinia infection. Both SPICE and VCP are similar in structure and function to the family of mammalian complement regulatory proteins, which function to prevent inadvertent injury to adjacent cells and tissues during complement activation. The second variola protein is the variola virus high-affinity secreted chemokine-binding protein type II (CKBP-II, CBP-II, vCCI), which binds CC-chemokine receptors. The vaccinia homologue of CKBP-II is secreted both early and late in infection. CKBP-II proteins are highly conserved among orthopoxviruses, sharing approximately 85% homology, but are absent in eukaryotes. This characteristic sets it apart from other known virulence factors in orthopoxviruses, which share sequence homology with known mammalian immune regulatory gene products. Future studies of additional variola proteins may help illuminate factors associated with its virulence, pathogenesis and strict human tropism. In addition, these studies may also assist in the development of targeted therapies for the treatment of both smallpox and human immune-related diseases.

Poxvirus orthologous clusters: toward defining the minimum essential poxvirus genome

Increasingly complex bioinformatic analysis is necessitated by the plethora of sequence information currently available. A total of 21 poxvirus genomes have now been completely sequenced and annotated, and many more genomes will be available in the next few years. First, we describe the creation of a database of continuously corrected and updated genome sequences and an easy-to-use and extremely powerful suite of software tools for the analysis of genomes, genes, and proteins. These tools are available free to all researchers and, in most cases, alleviate the need for using multiple Internet sites for analysis. Further, we describe the use of these programs to identify conserved families of genes (poxvirus orthologous clusters) and have named the software suite POCs, which is available at www.poxvirus.org. Using POCs, we have identified a set of 49 absolutely conserved gene families-those which are conserved between the highly diverged families of insect-infecting entomopoxviruses and vertebrate-infecting chordopoxviruses. An additional set of 41 gene families conserved in chordopoxviruses was also identified. Thus, 90 genes are completely conserved in chordopoxviruses and comprise the minimum essential genome, and these will make excellent drug, antibody, vaccine, and detection targets. Finally, we describe the use of these tools to identify necessary annotation and sequencing updates in poxvirus genomes. For example, using POCs, we identified 19 genes that were widely conserved in poxviruses but missing from the vaccinia virus strain Tian Tan 1998 GenBank file. We have reannotated and resequenced fragments of this genome and verified that these genes are conserved in Tian Tan. The results for poxvirus genes and genomes are discussed in light of evolutionary processes.

Species-specific differences in the structure of orthopoxvirus complement-binding protein

Vaccinia virus complement-binding protein (VCP) is secreted from the cells infected with the virus and controls the complement activation reactions. This protein contains four short consensus repeats (SCR), typical of the protein family of complement activation regulators. Organization of the VCP genes/proteins of orthopoxviruses-monkeypox (MPV), variola, cowpox and vaccinia viruses-and their cellular homologues (DAF and C4BP) were studied comparatively. For this purpose, VCP genes of three MPV strains were sequenced. VCP gene sequences of other human-pathogenic orthopoxvirus species and strains determined earlier were involved in the analysis. It has been demonstrated that a premature termination of the MPV VCP open reading frame results in a truncated protein sequence carrying a deletion of the C-terminal SCR4. This is an essential distinction of MPV from other orthopoxvirus species.

Alastrim smallpox variola minor virus genome DNA sequences

Alastrim variola minor virus, which causes mild smallpox, was first recognized in Florida and South America in the late 19th century. Genome linear double-stranded DNA sequences (186,986 bp) of the alastrim virus Garcia-1966, a laboratory reference strain from an outbreak associated with 0.8% case fatalities in Brazil in 1966, were determined except for a 530-bp fragment of hairpin-loop sequences at each terminus. The DNA sequences (EMBL Accession No. Y16780) showed 206 potential open reading frames for proteins containing >/=60 amino acids. The amino acid sequences of the putative proteins were compared with those reported for vaccinia virus strain Copenhagen and the Asian variola major strains India-1967 and Bangladesh-1975. About one-third of the alastrim viral proteins were 100% identical to correlates in the variola major strains and the remainder were >/=95% identical. Compared with variola major virus DNA, alastrim virus DNA has additional segments of 898 and 627 bp, respectively, within the left and right terminal regions. The former segment aligns well with sequences in other orthopoxviruses, particularly cowpox and vaccinia viruses, and the latter is apparently alastrim-specific.

Smallpox: gone but not forgotten

Smallpox represents both the acme of man's efforts to combat infectious diseases and one of his greatest fears. The disease emerged in prehistoric times to spread throughout the world causing blindness and death in millions of people. An acute infection caused by variola virus, one of the Orthopoxviruses, with skin eruption and marked toxemia had an average case fatality rate of 30%. Variola minor, a milder form of the disease, had a case fatality of one percent. Humans are the sole host, and survival confers lifelong immunity. Immunization was practiced since ancient times by inoculation with the variola virus until Jenner's demonstration of the efficacy and safety of vaccination with vaccinia virus. Following an intensive eradication effort by the World Health Organization, the world was declared to be free of smallpox in 1979. The decision to destroy all remaining stocks of variola virus in 1999 has met with some controversy.

The genomic sequence analysis of the left and right species-specific terminal region of a cowpox virus strain reveals unique sequences and a cluster of intact ORFs for immunomodulatory and host range proteins

Sequencing and computer analysis of the left (52,283 bp) and right (49,649 bp) variable DNA regions of the cowpox virus strain GRI-90 (CPV-GRI) has revealed 51 and 37 potential open reading frames (ORFs), respectively. Comparison of the structure-function organization of these DNA regions of CPV-GRI with those previously published for corresponding regions of genomes of vaccinia virus, strains Copenhagen (VAC-COP) and Western Reserve (VAC-WR); and variola major virus, strains India-1967 (VAR-IND), Bangladesh-1975 (VAR-BSH); and alastrim variola minor virus, strain Garcia-1966 (VAR-GAR), was performed. Within the left terminal region under study, an extended DNA sequence (14,171 bp), unique to CPV, has been found. Within the right region of the CPV-GRI genome two segments, which are unique to CPV DNA (1579 and 3585 bp) have been found. Numerous differences have been revealed in the genetic structure of CPV-GRI DNA regions, homologous to fragments of the genomes of the above-mentioned orthopoxvirus strains. A cluster of ORFs with structural similarity ot immunomodulatory and host range function of other poxviruses have also been detected. A comparison of the sequences of ORF B, crmA, crmB, crmC, IMP, and CHO hr genes of CPV Brighton strain (CPV-BRI) with the corresponding genes in strain GRI-90 have revealed an identity at the amino acid level ranging from 82 to 96% between the two strains. The findings are significant in light of the recent demonstration of CPV as an important poxvirus model system to probe the precise in vivo role(s) of the unique virally encoded immunomodulatory proteins. Also, the presence of a complete and intact repertoire of immunomodulatory proteins, ring canal proteins family, and host range genes indicates that CPV may have been the most ancient of all studied orthopoxviruses.