Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo

Insights into the Monkeypox virus: making of another pandemic within the pandemic?

Just when the world started to adapt to the 'new normal' amid the coronavirus disease 19 (COVID-19) pandemic, the world is witnessing the wrath of another viral disease, the monkeypox virus (MPXV). The virus is endemic to African countries, where several outbreaks have been reported in the past. However, the present cases have been reported in non-endemic countries worldwide. Although MPX is considered to be a self-limiting disease, recent reports on its incidence have proved otherwise. The 2022 multi-country MPX outbreak has drawn the attention of global surveillance organizations and epidemiologists to trace its origin, however, there are existing gaps regarding the animal reservoirs, biological implications, and management of MPX. In view of the recent events, the World Health Organization (WHO) has also declared the ongoing MPX outbreak a global health emergency. Hence, the geographically expanding MPXV poses a significant threat to human health and public safety. In this review, the latest insights into the biology of MPXV have been provided by discussing its biological implications on human health, changing epidemiological footprint, and presently available intervention strategies. This review also sheds light on the existing lacunas and possible reasons that may have been responsible for the ongoing MPX outbreak. This article is protected by copyright. All rights reserved.

Human Monkeypox: A Comprehensive Narrative Review and Analysis of the Public Health Implications

Recently, numerous cases of monkeypox were reported from several non-endemic countries in Europe, North America, and Oceania, suggesting an unusual and alarming public health issue, particularly considering that the disease is not directly related to human or animal travels. Attention is currently being drawn to this phenomenon since more than 70% of the global population is no longer vaccinated against smallpox. Indeed, the smallpox vaccination also confers some indirect degree of protection against other poxviruses, including monkeypox. We performed a narrative review to describe the existing literature with regard to monkeypox using the MEDLINE, EMBASE, and Scopus databases. This review aims to provide updated evidence of findings on the epidemiology, clinical features, diagnosis, management, and prevention of monkeypox, also considering the concurrent zoonotic pandemic caused by the COVID-19 coronavirus, SARS-CoV-2.

Assessment of Knowledge of Monkeypox Viral Infection among the General Population in Saudi Arabia

Monkeypox is re-emerging and spreading over the world, posing a serious threat to human life, especially in non-endemic countries, including Saudi Arabia. Due to the paucity of research on knowledge about monkeypox in Saudi Arabia, this study aimed to evaluate the general population’s knowledge of monkeypox in a sample of the country. A web-based cross-sectional survey was conducted from 25 May 2022 to 15 July 2022. Participants’ knowledge about monkeypox on a 23-item scale and socio-demographic characteristics were gathered in the survey. Pearson’s Chi-square test was used to compare knowledge level (categorized into high and low) and explanatory variables. Out of 480, only 48% of the respondents had high knowledge (mean score > 14). Participants’ age, marital status, residential region, living in the urban area, education level, employment status, being a healthcare worker, income, and smoking status were significantly associated with the level of knowledge about monkeypox (p < 0.01). Overall, social media (75.0%) was the most frequently reported source from where participants obtained monkeypox-related information followed by TV and radio (45.6%), family or friend (15.6%), and healthcare provider (13.8%). We found that overall knowledge of monkeypox infection was slightly poor among the Saudi population. These findings highlight the urgent need for public education on monkeypox to promote awareness and engage the public ahead of the outbreak.

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus

The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. 1-6). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018-2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution. An in-depth mutational analysis suggests the action of host APOBEC3 in viral evolution as well as signs of potential MPXV human adaptation in ongoing microevolution. Our findings also indicate that genome sequencing may provide resolution to track the spread and transmission of this presumably slow-evolving double-stranded DNA virus.

Monkeypox: considerations for the understanding and containment of the current outbreak in non-endemic countries

The neglected and rare zoonotic disease caused by monkeypox virus (MPV) has recently spread widely, resulting in the largest known monkeypox outbreak outside of Africa, where it is endemic. MPV belongs to the Poxviridae family, genus Orthopoxvirus. At least two different clades have been identified, each having different fatality rates but recent cases are all phylogenetically related to the West African clade. MPV is transmitted directly by either person-to-person, -animal, or virus-contaminated fomite contact. The disease is often self-limited, and clinical symptoms include fever, skin lesions, and lymphadenopathies. At present, no deaths have been associated with the current outbreak. MPV DNA detection using molecular techniques is recommended for diagnosis. At least two approved drugs for antiviral therapy are available in the USA. Two different vaccines, including the vaccine used in the past for smallpox eradication and a new formulation more recently approved based on a live but non-replicating virus, are available that provide immunity to MPV. These and other clinical and public health considerations pertaining to the recent monkeypox outbreaks together with aspects of MPV biology are discussed in this article.

Monkeypox virus: a re-emergent threat to humans

Human monkeypox (MPX) is a rare zoonotic infection characterized by smallpox-like signs and symptoms. It is caused by monkeypox virus (MPXV), a double stranded DNA virus belonging to the genus Orthopoxvirus. MPX was first identified in 1970 and mostly prevailed in the rural rainforests of Central and West Africa in the past. Outside Africa, MPX was reported in the United Kingdom, the USA, Israel, and Singapore. In 2022, the resurgence of MPX in Europe and elsewhere posed a potential threat to humans. MPXV was transmitted by the animals-human or human-human pathway, and the symptoms of MPXV infection are similar to that of smallpox, but in a milder form and with lower mortality (1%-10%). Although the smallpox vaccination has been shown to provide 85% protection against MPXV infection, and two anti-smallpox virus drugs have been approved to treat MPXV, there are still no specific vaccines and drugs against MPXV infection. Therefore it is urgent to take active measures including the adoption of novel anti-MPXV strategies to control the spread of MPXV and prevent MPX epidemic. In this review, we summarize the biological features, epidemiology, pathogenicity, laboratory diagnosis, and prevention and treatment strategies on MPXV. This review provides the basic knowledge for prevention and control of future outbreaks of this emerging infection.

Monkeypox: A New Threat?

The global vaccination programme against smallpox led to its successful eradication and averted millions of deaths. Monkeypox virus (MPXV) is a close relative of the Variola (smallpox) virus. Due to antigenic similarity, smallpox vaccines cross-protect against MPXV. However, over 70% of people living today were never vaccinated against smallpox. Symptoms of monkeypox (MPX) include fever, head- and muscle ache, lymphadenopathy and a characteristic rash that develops into papules, vesicles and pustules which eventually scab over and heal. MPX is less often fatal (case fatality rates range from <1% to up to 11%) than smallpox (up to 30%). MPXV is endemic in sub-Saharan Africa, infecting wild animals and causing zoonotic outbreaks. Exotic animal trade and international travel, combined with the increasing susceptibility of the human population due to halted vaccination, facilitated the spread of MPXV to new areas. The ongoing outbreak, with >10,000 cases in >50 countries between May and July 2022, shows that MPXV can significantly spread between people and may thus become a serious threat to public health with global consequences. Here, we summarize the current knowledge about this re-emerging virus, discuss available strategies to limit its spread and pathogenicity and evaluate its risk to the human population.

Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage?

Monkeypox is a zoonotic disease with clinical manifestations similar to smallpox in humans. Since May 13, 2022, an increasing number of suspected and confirmed cases have been reported, affecting non-endemic regions across the globe. More strikingly, reports from the current outbreak reveal unique aspects regarding transmission dynamics and an unprecedented, rapidly expanding and sustained community transmission. As demonstrated through the still-ongoing COVID-19 pandemic, genomic surveillance has been an essential resource for monitoring and tracking the evolution of pathogens of public health relevance. Herein, we performed a phylogenomic analysis of available Monkeypox virus (MPXV) genomes to determine their evolution and diversity. Our analysis revealed that all MPXV genomes grouped into three monophyletic clades: two previously characterized clades and a newly emerging clade harboring genomes from the ongoing 2022 multi-country outbreak with 286 genomes comprising the hMPXV-1A clade and the newly classified lineages: A.1 (n = 6), A.1.1 (n = 1), A.2 (n = 3) and B.1 (n = 262), where lineage B.1 includes all MPXV genomes from the 2022 outbreak. Finally, it was estimated that B.1 lineage of this clade emerged in Europe on 03/02/2022 [95%CI = 11/13/2021 to 05/10/2022]. The exceptional surge of cases and the broader geographical expansion suggest multifactorial factors as drivers of the current outbreak dynamics. Such factors may include the cessation of smallpox vaccination and its potential spread across particular networks. Integrating pertinent epidemiological information with genomic surveillance information will help generate real-time data to help implement adequate preventive and control measures by optimizing public health decisions to mitigate this outbreak.

The 2022 outbreak and the pathobiology of the monkeypox virus

Following two reports of monkeypox virus infection in individuals who returned from Nigeria to the USA, one who returned to Texas (July 2021) and the other to the Washington, DC area (November 2021), the number of monkeypox infection have dramatically increased. This sounded an alarm of potential for spreading of the virus throughout the USA. During 2022, there was a report of monkeypox virus infection (May 6, 2022) in a British national following a visit to Nigeria who developed readily recognizable signs and symptoms of monkeypox virus infection. Soon following this report, case numbers climbed. By June 10, 2022, more than 1,500 cases were reported in 43 countries, including Europe and North America. While the prevalence of the monkeypox virus is well known in central and western Africa, its presence in the developed world has raised disturbing signs for worldwide spread. While infection was reported during the past half-century, starting in the Democratic Republic of Congo in 1970, in the United States, only sporadic monkeypox cases have been reported. All cases have been linked to international travel or through African animal imports. The monkeypox virus is transmitted through contact with infected skin, body fluids, or respiratory droplets. The virus spreads from oral and nasopharyngeal fluid exchanges or by intradermal injection; then rapidly replicates at the inoculation site with spreads to adjacent lymph nodes. Monkeypox disease begins with constitutional symptoms that include fever, chills, headache, muscle aches, backache, and fatigue. Phylogenetically the virus has two clades. One clade emerged from West Africa and the other in the Congo Basin of Central Africa. During the most recent outbreak, the identity of the reservoir host or the primary carriage remains unknown. African rodents are the suspected intermediate hosts. At the same time, the Centers for Disease Control (CDC) affirmed that there are no specific treatments for the 2022 monkeypox virus infection; existing antivirals shown to be effective against smallpox may slow monkeypox spread. A smallpox vaccine JYNNEOS (Imvamune or Imvanex) may also be used to prevent infection. The World Health Organization (WHO), has warned that the world could be facing a formidable infectious disease challenge in light of the current status of worldwide affairs. These affairs include the SARS-COVID-19 pandemic and the Ukraine-Russia war. In addition, the recent rise in case of numbers worldwide could continue to pose an international threat. With this in mind, strategies to mitigate the spread of monkeypox virus are warranted.

Human Monkeypox: Fifty-Two Years based analysis and Updates

The growing prevalence of human monkeypox infection has developed an alarming situation worldwide. Monkeypox virus was first time found in 1958 in monkeys and later spread to humans. The first case of human monkeypox was reported in September 1970 in the Democratic Republic of the Congo. Human monkeypox was found outside Africa in the year 2003 in United States. More recently, from May 7 2022 to June 29, 2022, the monkeypox cases are swiftly spread worldwide, involving over 50 countries, and affecting 5115 people in Europe, the United Kingdom, North America, and South America, Asia, Australia, and the Middle East. The confirmed monkeypox cases in the United Kingdom from May 7, 2022 to June 29, 2022, are 1076 (21.03%); Germany 874 (17.08%); Spain 800 (15.64%); France 440 (8.60%); Portugal 391 (7.64%); United States 350 (6.84); Canada 276 (5.39%); Netherlands 257 (5.02%); Italy 159 (3.10); Belgium 117 (2.28%); Switzerland 81 (1.58%); Israel 33 (0.64%), and Ireland 31 (0.60%). However, in about 35 countries, the cases are less than 20 in each country. The epidemiological trends of the human monkeypox infection are swiftly shifting from endemic regions to non-endemic countries. The global health authorities must take priority-based preventive measures to stop the outbreaks of monkeypox disease across the globe.

Preparedness for a monkeypox outbreak

In light of the ongoing COVID-19 pandemic, the unexpected outbreak and worldwide spread of monkeypox has gained global attention. As of June 22, 2022, there were 3340 confirmed cases of monkeypox globally, which is the largest and most widespread monkeypox epidemic outside Africa. Monkeypox virus (MPXV) is transmitted from human-to-human through direct contact with infectious skin or mucosal skin lesions, respiratory droplets, or indirect contact with contaminated objects or materials, as well as mother-to-child vertical transmission. It is also possibly sexually transmitted through semen/vaginal fluid, and the possibility of community transmission cannot be ruled out. Monkeypox is a viral zoonotic disease caused by MPXV, which is an enveloped, linear, double-stranded DNA virus belonging to the Orthopoxvirus genus, of the Chordopoxvirinae subfamily, within the Poxviridae family. Monkeypox is usually a self-limiting infection, with symptoms lasting 2-4 weeks, and has a fatality rate that has historically fluctuated from 0% to 11%. Symptoms of monkeypox include intense headaches, fever, lesions, and lymphadenopathy. Although there is no specific treatment or vaccine for MPXV infection, antiviral drugs and vaccines for smallpox have been approved for use in several countries in response to the monkeypox outbreak. Before the virus can be allowed to establish efficient person-to-person transmission, rapid action must be taken to contain the local spread and, by extension, the multi-country outbreak of monkeypox.

Exportation of Monkeypox Virus From the African Continent

BACKGROUND

The largest West African monkeypox outbreak began September 2017, in Nigeria. Four individuals traveling from Nigeria to the United Kingdom (n = 2), Israel (n = 1), and Singapore (n = 1) became the first human monkeypox cases exported from Africa, and a related nosocomial transmission event in the United Kingdom became the first confirmed human-to-human monkeypox transmission event outside of Africa.

METHODS

Epidemiological and molecular data for exported and Nigerian cases were analyzed jointly to better understand the exportations in the temporal and geographic context of the outbreak.

RESULTS

Isolates from all travelers and a Bayelsa case shared a most recent common ancestor and traveled to Bayelsa, Delta, or Rivers states. Genetic variation for this cluster was lower than would be expected from a random sampling of genomes from this outbreak, but data did not support direct links between travelers.

CONCLUSIONS

Monophyly of exportation cases and the Bayelsa sample, along with the intermediate levels of genetic variation, suggest a small pool of related isolates is the likely source for the exported infections. This may be the result of the level of genetic variation present in monkeypox isolates circulating within the contiguous region of Bayelsa, Delta, and Rivers states, or another more restricted, yet unidentified source pool.

The changing epidemiology of human monkeypox-A potential threat? A systematic review

Monkeypox, a zoonotic disease caused by an orthopoxvirus, results in a smallpox-like disease in humans. Since monkeypox in humans was initially diagnosed in 1970 in the Democratic Republic of the Congo (DRC), it has spread to other regions of Africa (primarily West and Central), and cases outside Africa have emerged in recent years. We conducted a systematic review of peer-reviewed and grey literature on how monkeypox epidemiology has evolved, with particular emphasis on the number of confirmed, probable, and/or possible cases, age at presentation, mortality, and geographical spread. The review is registered with PROSPERO (CRD42020208269). We identified 48 peer-reviewed articles and 18 grey literature sources for data extraction. The number of human monkeypox cases has been on the rise since the 1970s, with the most dramatic increases occurring in the DRC. The median age at presentation has increased from 4 (1970s) to 21 years (2010-2019). There was an overall case fatality rate of 8.7%, with a significant difference between clades-Central African 10.6% (95% CI: 8.4%- 13.3%) vs. West African 3.6% (95% CI: 1.7%- 6.8%). Since 2003, import- and travel-related spread outside of Africa has occasionally resulted in outbreaks. Interactions/activities with infected animals or individuals are risk behaviors associated with acquiring monkeypox. Our review shows an escalation of monkeypox cases, especially in the highly endemic DRC, a spread to other countries, and a growing median age from young children to young adults. These findings may be related to the cessation of smallpox vaccination, which provided some cross-protection against monkeypox, leading to increased human-to-human transmission. The appearance of outbreaks beyond Africa highlights the global relevance of the disease. Increased surveillance and detection of monkeypox cases are essential tools for understanding the continuously changing epidemiology of this resurging disease.

Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution

Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is a member of orthopoxvirus genus. The reemergence of MPXV in 2017 (at Bayelsa state) after 39 years of no reported case in Nigeria, and the export of travelers' monkeypox (MPX) from Nigeria to other parts of the world, in 2018 and 2019, respectively, have raised concern that MPXV may have emerged to occupy the ecological and immunological niche vacated by smallpox virus. This review X-rays the current state of knowledge pertaining the infection biology, epidemiology, and evolution of MPXV in Nigeria and worldwide, especially with regard to the human, cellular, and viral factors that modulate the virus transmission dynamics, infection, and its maintenance in nature. This paper also elucidates the role of recombination, gene loss and gene gain in MPXV evolution, chronicles the role of signaling in MPXV infection, and reviews the current therapeutic options available for the treatment and prevention of MPX. Additionally, genome-wide phylogenetic analysis was undertaken, and we show that MPXV isolates from recent 2017 outbreak in Nigeria were monophyletic with the isolate exported to Israel from Nigeria but do not share the most recent common ancestor with isolates obtained from earlier outbreaks, in 1971 and 1978, respectively. Finally, the review highlighted gaps in knowledge particularly the non-identification of a definitive reservoir host animal for MPXV and proposed future research endeavors to address the unresolved questions.

A systematic review of the epidemiology of human monkeypox outbreaks and implications for outbreak strategy

Monkeypox is a vesicular-pustular illness that carries a secondary attack rate in the order of 10% in contacts unvaccinated against smallpox. Case fatality rates range from 1 to 11%, but scarring and other sequelae are common in survivors. It continues to cause outbreaks in remote populations in Central and West Africa, in areas with poor access and weakened or disrupted surveillance capacity and information networks. Recent outbreaks in Nigeria (2017-18) and Cameroon (2018) have occurred where monkeypox has not been reported for over 20 years. This has prompted concerns over whether there have been changes in the biology and epidemiology of the disease that may in turn have implications for how outbreaks and cases should best be managed. A systematic review was carried out to examine reported data on human monkeypox outbreaks over time, and to identify if and how epidemiology has changed. Published and grey literature were critically analysed, and data extracted to inform recommendations on outbreak response, use of case definitions and public health advice. The level of detail, validity of data, geographical coverage and consistency of reporting varied considerably across the 71 monkeypox outbreak documents obtained. An increase in cases reported over time was supported by literature from the Democratic Republic of Congo (DRC). Data were insufficient to measure trends in secondary attack rates and case fatality rates. Phylogenetic analyses consistently identify two strains of the virus without evidence of emergence of a new strain. Understanding of monkeypox virulence with regard to clinical presentation by strain is minimal, with infrequent sample collection and laboratory analysis. A variety of clinical and surveillance case definitions are described in the literature: two definitions have been formally evaluated and showed high sensitivity but low specificity. These were specific to a Congo-Basin (CB) strain-affected area of the DRC where they were used. Evidence on use of antibiotics for prophylaxis against secondary cutaneous infection is anecdotal and limited. Current evidence suggests there has been an increase in total monkeypox cases reported by year in the DRC irrespective of advancements in the national Integrated Disease Surveillance and Response (IDSR) system. There has been a marked increase in number of individual monkeypox outbreak reports, from outside the DRC in between 2010 and 2018, particularly in the Central African Republic (CAR) although this does not necessarily indicate an increase in annual cases over time in these areas. The geographical pattern reported in the Nigeria outbreak suggests a possible new and widespread zoonotic reservoir requiring further investigation and research. With regards to outbreak response, increased attention is warranted for high-risk patient groups, and nosocomial transmission risks. The animal reservoir remains unknown and there is a dearth of literature informing case management and successful outbreak response strategies. Up-to-date complete, consistent and longer-term research is sorely needed to inform and guide evidence-based response and management of monkeypox outbreaks.

A review of the monkeypox virus and a recent outbreak of skin rash disease in Nigeria

Since the eradication of smallpox approximately 39 years ago, monkeypox virus remains the most pathogenic poxvirus, being mainly restricted to Central and West Africa. Before 1970, there were no reports of human monkeypox in Nigeria, while between 1971 and 1978 there were three cases, with none having been reported thereafter. However, in September 2017, a case of contagious skin rash disease, typical of monkeypox, was observed in an 11-year-old boy from the southern part of the country and confirmed to be associated with the monkeypox virus. This large outbreak consisted of 262 suspected, 115 confirmed cases, and 7 mortalities across 26 states and the Federal Capital Territory (FCT), Abuja. The aim of this manuscript is to provide an updated, comprehensive, and timely review of monkeypox, an important emerging infection in Nigeria. Monkeypox is now a major threat to global health security, requiring an urgent multidisciplinary approach involving veterinarians, physicians, virologists, and public health experts to fast-track the development of diagnostic assays, vaccines, antivirals, and other control strategies.

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus

The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.

Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly

The orthopoxviruses (OPV) comprise several emerging viruses with great importance to human and veterinary medicine, including vaccinia virus (VACV), which causes outbreaks of bovine vaccinia (BV) in South America. Historically, VACV is the most comprehensively studied virus, however, its origin and natural hosts remain unknown. VACV was the primary component of the smallpox vaccine, largely used during the smallpox eradication campaign. After smallpox was declared eradicated, the vaccination that conferred immunity to OPV was discontinued, favoring a new contingent of susceptible individuals to OPV. VACV infections occur naturally after direct contact with infected dairy cattle, in recently vaccinated individuals, or through alternative routes of exposure. In Brazil, VACV outbreaks are frequently reported in rural areas, affecting mainly farm animals and humans. Recent studies have shown the role of wildlife in the VACV transmission chain, exploring the role of wild rodents as reservoirs that facilitate VACV spread throughout rural areas. Furthermore, VACV circulation in urban environments and the significance of this with respect to public health, have also been explored. In this review, we discuss the history, epidemiological, ecological and clinical aspects of natural VACV infections in Brazil, also highlighting alternative routes of VACV transmission, the factors involved in susceptibility to infection, and the natural history of the disease in humans and animals, and the potential for dissemination to urban environments.

A Nosocomial Outbreak of Human Monkeypox in the Central African Republic

An outbreak of familial monkeypox occurred in the Central African Republic in 2015/2016 by 3 transmission modes: familial, health care–related, and transport-related. Ten people (3 children and 7 adults) were infected. Most presented with cutaneous lesions and fever, and 2 children died. The viral strain responsible was a Zaire genotype strain.

Varicella Coinfection in Patients with Active Monkeypox in the Democratic Republic of the Congo

From 2006 to 2007, an active surveillance program for human monkeypox (MPX) in the Democratic Republic of the Congo identified 151 cases of coinfection with monkeypox virus and varicella zoster virus from 1158 suspected cases of human MPX (13%). Using clinical and socio-demographic data collected with standardized instruments by trained, local nurse supervisors, we examined a variety of hypotheses to explain the unexpectedly high proportion of coinfections among the sample, including the hypothesis that the two viruses occur independently. The probabilities of disease incidence and selection necessary to yield the observed sample proportion of coinfections under an assumption of independence are plausible given what is known and assumed about human MPX incidence. Cases of human MPX are expected to be underreported, and more coinfections are expected with improved surveillance.

Emerging Foodborne and Agriculture-Related Viruses

Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.

Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections

Outbreaks associated with emerging and re-emerging viral pathogens continue to increase in frequency and are associated with an increasing burden to global health. In light of this, there is a need to integrate basic and clinical research for investigating the connections between molecular and clinical pathogenesis and for therapeutic development strategies. Here, we will discuss this approach with a focus on the emerging viral pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola virus (EBOV), and monkeypox virus (MPXV) from the context of clinical presentation, immunological and molecular features of the diseases, and OMICS-based analyses of pathogenesis. Furthermore, we will highlight the role of global investigations of host kinases, the kinome, for investigating emerging and re-emerging viral pathogens from the context of characterizing cellular responses and identifying novel therapeutic targets. Lastly, we will address how increased integration of clinical and basic research will assist treatment and prevention efforts for emerging pathogens.

Finishing monkeypox genomes from short reads: assembly analysis and a neural network method

BACKGROUND

Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses, the emergence of monkeypox outbreaks in humans and the need to monitor potential malicious release of smallpox virus requires development of methods for rapid virus identification. Whole-genome sequencing (WGS) is an emergent technology with increasing application to the diagnosis of diseases and the identification of outbreak pathogens. But "finishing" such a genome is a laborious and time-consuming process, not easily automated. To date the large, complete poxvirus genomes have not been studied comprehensively in terms of applying WGS techniques and evaluating genome assembly algorithms.

RESULTS

To explore the limitations to finishing a poxvirus genome from short reads, we first analyze the repetitive regions in a monkeypox genome and evaluate genome assembly on the simulated reads. We also report on procedures and insights relevant to the assembly (from realistically short reads) of genomes. Finally, we propose a neural network method (namely Neural-KSP) to "finish" the process by closing gaps remaining after conventional assembly, as the final stage in a protocol to elucidate clinical poxvirus genomic sequences.

CONCLUSIONS

The protocol may prove useful in any clinical viral isolate (regardless if a reference-strain sequence is available) and especially useful in genomes confounded by many global and local repetitive sequences embedded in them. This work highlights the feasibility of finishing real, complex genomes by systematically analyzing genetic characteristics, thus remedying existing assembly shortcomings with a neural network method. Such finished sequences may enable clinicians to track genetic distance between viral isolates that provides a powerful epidemiological tool.

A phylogeographic investigation of African monkeypox

Monkeypox is a zoonotic disease caused by a virus member of the genus Orthopoxvirus and is endemic to Central and Western African countries. Previous work has identified two geographically disjuct clades of monkeypox virus based on the analysis of a few genomes coupled with epidemiological and clinical analyses; however, environmental and geographic causes of this differentiation have not been explored. Here, we expand previous phylogenetic studies by analyzing a larger set of monkeypox virus genomes originating throughout Sub-Saharan Africa to identify possible biogeographic barriers associated with genetic differentiation; and projected ecological niche models onto environmental conditions at three periods in the past to explore the potential role of climate oscillations in the evolution of the two primary clades. Analyses supported the separation of the Congo Basin and West Africa clades; the Congo Basin clade shows much shorter branches, which likely indicate a more recent diversification of isolates within this clade. The area between the Sanaga and Cross Rivers divides the two clades and the Dahomey Gap seems to have also served as a barrier within the West African clade. Contraction of areas with suitable environments for monkeypox virus during the Last Glacial Maximum, suggests that the Congo Basin clade of monkeypox virus experienced a severe bottleneck and has since expanded its geographic range.

From lesions to viral clones: biological and molecular diversity amongst autochthonous Brazilian vaccinia virus

Vaccinia virus (VACV) has had an important role for humanity because of its use during the smallpox eradication campaign. VACV is the etiologic agent of the bovine vaccinia (BV), an emerging zoonosis that has been associated with economic, social, veterinary and public health problems, mainly in Brazil and India. Despite the current and historical VACV importance, there is little information about its circulation, prevalence, origins and maintenance in the environment, natural reservoirs and diversity. Brazilian VACV (VACV-BR) are grouped into at least two groups based on genetic and biological diversity: group 1 (G1) and group 2 (G2). In this study, we went to the field and investigated VACV clonal diversity directly from exanthemous lesions, during BV outbreaks. Our results demonstrate that the G1 VACV-BR were more frequently isolated. Furthermore, we were able to co-detect the two variants (G1 and G2) in the same sample. Molecular and biological analysis corroborated previous reports and confirmed the co-circulation of two VACV-BR lineages. The detected G2 clones presented exclusive genetic and biological markers, distinct to reference isolates, including VACV-Western Reserve. Two clones presented a mosaic profile, with both G1 and G2 features based on the molecular analysis of A56R, A26L and C23L genes. Indeed, some SNPs and INDELs in A56R nucleotide sequences were observed among clones of the same virus population, maybe as a result of an increased mutation rate in a mixed population. These results provide information about the diversity profile in VACV populations, highlighting its importance to VACV evolution and maintenance in the environment.

Cytokine modulation correlates with severity of monkeypox disease in humans

BACKGROUND

Human monkeypox is a zoonotic disease endemic to parts of Africa. Similar to other orthopoxviruses, virus and host have considerable interactions through immunomodulation. These interactions likely drive the establishment of a productive infection and disease progression, resulting in the range of disease presentations and case fatality rates observed for members of the Orthopoxvirus genus.

OBJECTIVES

Much of our understanding about the immune response to orthopoxvirus infection comes from either in vitro or in vivo studies performed in small animals or non-human primates. Here, we conducted a detailed assessment of cytokine responses to monkeypox virus using serum from acutely ill humans collected during monkeypox active disease surveillance (2005-2007) in the Democratic Republic of the Congo.

STUDY DESIGN

Nineteen serum samples that were from patients with confirmed monkeypox virus infections were selected for cytokine profiling. Cytokine profiling was performed on the Bio-Rad Bioplex 100 system using a 30-plex human cytokine panel.

RESULTS

Cytokine profiling revealed elevated cytokine concentrations in all samples. Overproduction of certain cytokines (interleukin [IL]-2R, IL-10, and granulocyte macrophage-colony stimulating factor were observed in patients with serious disease (defined as >250 lesions based on the World Health Organization scoring system).

CONCLUSIONS

The data suggest that cytokine modulation affects monkeypox disease severity in humans.

Inactivation of bacterial and viral biothreat agents on metallic copper surfaces

In recent years several studies in laboratory settings and in hospital environments have demonstrated that surfaces of massive metallic copper have intrinsic antibacterial and antiviral properties. Microbes are rapidly inactivated by a quick, sharp shock known as contact killing. The underlying mechanism is not yet fully understood; however, in this process the cytoplasmic membrane is severely damaged. Pathogenic bacterial and viral high-consequence species able to evade the host immune system are among the most serious lethal microbial challenges to human health. Here, we investigated contact-killing mediated by copper surfaces of Gram-negative bacteria (Brucella melitensis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis tularensis and Yersinia pestis) and of Gram-positive endospore-forming Bacillus anthracis. Additionally, we also tested inactivation of monkeypox virus and vaccinia virus on copper. This group of pathogens comprises biothreat species (or their close relatives) classified by the Center for Disease and Control and Prevention (CDC) as microbial select agents posing severe threats to public health and having the potential to be deliberately released. All agents were rapidly inactivated on copper between 30 s and 5 min with the exception of B. anthracis endospores. For vegetative bacterial cells prolonged contact to metallic copper resulted in the destruction of cell structure.