Chikungunya virus infection prevalence in Africa: a contemporaneous systematic review and meta-analysis.

OBJECTIVES: The (re)emergence of chikungunya virus (CHIKV) in Africa requires better knowledge on the epidemiology of CHIKV infection in the continent for efficient public health strategies. We aimed to describe the epidemiology of CHIKV infection in Africa, a neglected tropical disease (NTD). STUDY DESIGN: This was a systematic review with meta-analysis of studies reporting CHIKV infection prevalence. We searched Embase, PubMed, Africa Journal Online and Global Index Medicus to identify observational studies published from January 2000 to September 2017. METHODS: We used a random-effect model to pool the prevalence of CHIKV infections reported with their 95% confidence interval (CI). Heterogeneity was assessed via the Chi-squared test on Cochran's Q statistic. Review registration is in PROSPERO CRD42017080395. RESULTS: A total of 39 studies (37,881 participants; 18 countries) were included. No study was reported from Southern Africa. Thirty-two (82.0%), seven (18.0%) and no studies had low, moderate and high risk of bias, respectively. Outside outbreak periods, the pooled immunoglobulin M (IgM) and immunoglobulin G (IgG) seroprevalence was 9.7% (95% CI 3.0-19.6; 16 studies) and 16.4% (95% CI 9.1-25.2; 23 studies), respectively. The IgM seroprevalence was lower in Northern Africa, and there was no difference for IgG prevalence across regions in Africa. The IgM and IgG seroprevalences were not different between acute and non-acute febrile participants. The seroprevalence was not associated with GPS coordinates (latitude, longitude and altitude). CONCLUSIONS: Although considered a NTD, we find high prevalence of CHIKV infection in Africa. As such, chikungunya fever should deserve more attention from healthcare providers, researchers, policymakers and stakeholders from many sectors.

Genome-scale phylogeny of the alphavirus genus suggests a marine origin.

The genus Alphavirus comprises a diverse group of viruses, including some that cause severe disease. Using full-length sequences of all known alphaviruses, we produced a robust and comprehensive phylogeny of the Alphavirus genus, presenting a more complete evolutionary history of these viruses compared to previous studies based on partial sequences. Our phylogeny suggests the origin of the alphaviruses occurred in the southern oceans and spread equally through the Old and New World. Since lice appear to be involved in aquatic alphavirus transmission, it is possible that we are missing a louse-borne branch of the alphaviruses. Complete genome sequencing of all members of the genus also revealed conserved residues forming the structural basis of the E1 and E2 protein dimers.

One Health epidemic preparedness: Biosafety quality improvement training in Nigeria.

Background and Aim: One of the key components of the One Health approach to epidemic preparedness is raising awareness and increasing the knowledge of emerging infectious diseases, prevention, and risk reduction. However, related research can involve significant risks to biosafety and biosecurity. For this purpose, we organized a multidisciplinary biosafety hands-on workshop to inform and increase the knowledge of infectious diseases and risk mitigation. This study aimed to describe the process and outcome of a hands-on biosafety training program using a One Health approach across a multidisciplinary and multi-specialty group in Nigeria. Materials and Methods: A face-to-face hands-on training for 48 participants was organized by the West African Center for Emerging Infectious Diseases (WAC-EID) at the Jos University Teaching Hospital, serving as a lead institution for the Nigeria project site. Topics covered included (1) an overview of the WAC-EID research; (2) overview of infection prevention and control; (3) safety in animal handling and restraint, sample collection, and processing; (4) safety in field studies including rodent, bird and bat handling; (5) safety practices in the collection of mosquito and other arthropod vectors; (6) personal protective equipment training (disinfection, donning and doffing); and (7) safety in sample collection, labeling, and transportation. The program was executed using a mixed method of slide presentations, practical hands-on sessions, and video demonstrations. Pre- and post-course evaluation assessments and evaluation measures were used to assess training. Results: A total of 48 trainees participated in this training, with 12 (25%), 16 (33.3%), 14 (29.2%), 6 (12.5%) categorized as ornithology, entomology, mammalogy, and clinical interest groups, respectively. The pass rate for the pre-test was 29.4%, while for the post-test, it was 57.1%, or a 28% improvement. 88.6% of the trainees rated the training as relevant to them. Conclusion: Didactic and hands-on biosafety training is relevant in this era of zoonotic epidemics and pandemic preparedness. During this training program, there was a clear demonstration of knowledge transfer that can change the current practices of participants and improve the safety of infectious diseases research.

Analysis of intrahost variation in Venezuelan equine encephalitis virus reveals repeated deletions in the 6-kilodalton protein gene.

RNA viruses exist as a spectrum of mutants that is generated and maintained during replication within the host. Consensus sequencing overlooks minority genotypes present in the viral sample that may impact the population's phenotype. In-depth sequencing of an original field isolate of subtype IE Venezuelan equine encephalitis virus (VEEV) demonstrated the presence of multiple deletions within the 6,000-molecular-weight (6K) protein gene. Using in vitro and in vivo experiments, similar deletions were generated in an additional VEEV strain originating from an infectious cDNA clone. Time course experiments demonstrated that the deletions are produced during acute infection although not until 24 h postinfection. Molecular clones containing some of these deletions were generated, and although the larger deletions appear to be noninfectious, viruses with the smaller deletions were viable and formed small plaques. Serial passages provided no evidence that these deletion mutants function as defective interfering particles. Furthermore, since wild-type infections generally occur at a low multiplicity of infection, it is unlikely that these deletions are propagated in natural transmission cycles. However, they could affect pathogenesis at later stages of infection. Because they are ubiquitously generated both in vivo and in vitro, further investigation is warranted to understand the generation of these deletions and their significance for disease.

SARS-CoV-2 decontamination of skin with disinfectants active during and after application.

BACKGROUND: The coronavirus disease 2019 pandemic has resulted in high levels of exposure of medical workers to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Hand decontamination is one of the actions recommended to reduce the risk of infection. AIM: Two disinfectants - BIAKOS antimicrobial skin and wound cleanser (AWC) and AWC2 (Sanara MedTech, Fort Worth, TX, USA) - were tested to determine whether they can inactivate SARS-CoV-2 upon contact or as a coating applied before contact with the virus. METHODS: The ability of AWC and AWC2 to inactivate SARS-CoV-2 was tested in liquid and dried form on plastic surfaces and porcine skin. FINDINGS: AWC and AWC2 were effective in reducing the infectious titre of SARS-CoV-2 in liquid form during application and in dried form 4 h after application. Virus on skin was reduced up to 2 log10-fold and 3.5 log10-fold after treatment with AWC and AWC2, respectively. CONCLUSION: Application of AWC and AWC2 to skin reduces the level of SARS-CoV-2 and the risk of infection.

Silent circulation of arboviruses in Cameroon.

OBJECTIVES: To investigate the silent circulation and transmission of arthropod-borne viruses (arboviruses) in the Fako Division of Cameroon. DESIGN: This survey was conducted based on clinical observations and laboratory diagnosis; field collections of mosquitoes. SETTING: This study was conducted in the Fako Division of South West Cameroon. SUBJECTS: One hundred and two sera were obtained from febrile patients (with negative laboratory findings for malaria and typhoid fever) at clinics in the Fako Division, and diurnal anthropophilic mosquitoes (4,764) collected. INTERVENTIONS: Virus isolation was attempted from these, and sera were screened for antibodies against 18 African arboviruses by haemagglutination inhibition (HI) and complement fixation (CF) tests. RESULTS: No virus was isolated. Fifty three of 79 (67.1%) sera reacted with one or more viral antigens. Twenty nine sera (36.7%) reacted with members of the genus Alphavirus, with Chikungunya (CHIKV) and O'nyong-nyong (ONNV) viruses as the most frequent (34.2%). Forty six sera (58.2%) reacted with members of the genus Flavivirus: 24 (30.4%) were cross-reactive, but 11.4% reacted monotypically with Zika, 5.1% with yellow fever virus (YFV), 5.1% with dengue virus-2 (DENV-2), 2.5% with DENV-1 and 1.3% with Wesselsbron virus, respectively. The plaque reduction neutralisation test used to specify the agent that elicited the response could not resolve 33.3% of the cross reactions between CHIKV and ONNV. Neutralising antibody titres against ONNV and CHIKV were very high indicating probable re-infection. CONCLUSION: Our results indicate previously undetected circulation of arboviruses in Cameroon, and suggest that they are important, overlooked public health problems.

GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 5: Entomological aspects.

The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) chikungunya (CHIKV), o'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group has been established to investigate natural history, epidemiology and clinical aspects of infection by these viruses. Here, we present a report dedicated to entomological aspects of CHIKV, ONNV and MAYV. Recent global expansion of chikungunya virus has been possible because CHIKV established a transmission cycle in urban settings using anthropophilic vectors such as Aedes albopictus and Aedes aegypti. MAYV and ONNV have a more limited geographic distribution, being confined to Africa (ONNV) and central-southern America (MAYV). ONNV is probably maintained through an enzootic cycle that has not been characterized yet, with Anopheles species as main vectors and humans as amplification hosts during epidemics. MAYV is transmitted by Haemagogus species in an enzootic cycle using non-human primates as the main amplification and maintenance hosts, and humans becoming sporadically infected when venturing in or nearby forest habitats. Here, we focused on the transmission cycle and natural vectors that sustain circulation of these viruses in their respective locations. The knowledge of the natural ecology of transmission and the capacity of different vectors to transmit these viruses is crucial to understand CHIKV emergence, and to assess the risk that MAYV and ONNV will expand on wide scale using anthropophilic mosquito species not normally considered primary vectors. Finally, the experts identified knowledge gaps and provided adapted recommendations, in order to address future entomological investigations in the right direction.

GloPID-R report on chikungunya, o'nyong-nyong and Mayaro virus, part 2: Epidemiological distribution of o'nyong-nyong virus.

The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) chikungunya (CHIKV), o'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group has been established to identify gaps of knowledge about the natural history, epidemiology and medical management of infection by these viruses, and to provide adapted recommendations for future investigations. Here, we present a report dedicated to ONNV epidemiological distribution. Two large-scale ONNV outbreaks have been identified in Africa in the last 60 years, interspersed with sporadic serosurveys and case reports of returning travelers. The assessment of the real scale of ONNV circulation in Africa remains a difficult task and surveillance studies are necessary to fill this gap. The identification of ONNV etiology is made complicated by the absence of multiplex tools in co-circulation areas and that of reference standards, as well as the high cross-reactivity with related pathogens observed in serological tests, in particular with CHIKV. This is a specific obstacle for seroprevalence studies, that necessitate an improvement of serological tools to provide robust results. The scarcity of existent genetic data currently limits molecular epidemiology studies. ONNV epidemiology would also benefit from reinforced entomological and environmental surveillance. Finally, the natural history of the disease deserves to be further investigated, with a specific attention paid to long-term complications. Considering our incomplete knowledge on ONNV distribution, GloPID-R CHIKV, ONNV and MAYV experts recommend that a major effort should be done to fill existing gaps.

GloPID-R report on Chikungunya, O'nyong-nyong and Mayaro virus, part I: Biological diagnostics.

The GloPID-R (Global Research Collaboration for Infectious Disease Preparedness) Chikungunya (CHIKV), O'nyong-nyong (ONNV) and Mayaro virus (MAYV) Working Group is investigating the natural history, epidemiology and medical management of infection by these viruses, to identify knowledge gaps and to propose recommendations for direct future investigations and rectification measures. Here, we present the first report dedicated to diagnostic aspects of CHIKV, ONNV and MAYV. Regarding diagnosis of the disease at the acute phase, molecular assays previously described for the three viruses require further evaluation, standardized protocols and the availability of international standards representing the genetic diversity of the viruses. Detection of specific IgM would benefit from further investigations to clarify the extent of cross-reactivity among the three viruses, the sensitivity of the assays, and the possible interfering role of cryoglobulinaemia. Implementation of reference panels and external quality assessments for both molecular and serological assays is necessary. Regarding sero-epidemiological studies, there is no reported high-throughput assay that can distinguish among these different viruses in areas of potential co-circulation. New specific tools and/or improved standardized protocols are needed to enable large-scale epidemiological studies of public health relevance to be performed. Considering the high risk of future CHIKV, MAYV and ONNV outbreaks, the Working Group recommends that a major investigation should be initiated to fill the existing diagnostic gaps.

Evolutionary influences in arboviral disease.

Arthropod-borne viruses (arboviruses) generally require horizontal transmission by arthropod vectors among vertebrate hosts for their natural maintenance. This requirement for alternate replication in disparate hosts places unusual evolutionary constraints on these viruses, which have probably limited the evolution of arboviruses to only a few families of RNA viruses (Togaviridae, Flaviviridae, Bunyaviridae, Rhabdoviridae, Reoviridae, and Orthomyxoviridae) and a single DNA virus. Phylogenetic studies have suggested the dominance of purifying selection in the evolution of arboviruses, consistent with constraints imposed by differing replication environments and requirements in arthropod and vertebrate hosts. Molecular genetic studies of alphaviruses and flaviviruses have also identified several mutations that effect differentially the replication in vertebrate and mosquito cells, consistent with the view that arboviruses must adopt compromise fitness characteristics for each host. More recently, evidence of positive selection has also been obtained from these studies. However, experimental model systems employing arthropod and vertebrate cell cultures have yielded conflicting conclusions on the effect of alternating host infections, with host specialization inconsistently resulting in fitness gains or losses in the bypassed host cells. Further studies using in vivo systems to study experimental arbovirus evolution are critical to understanding and predicting disease emergence, which often results from virus adaptation to new vectors or amplification hosts. Reverse genetic technologies that are now available for most arbovirus groups should be exploited to test assumptions and hypotheses derived from retrospective phylogenetic approaches.

Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences.

Local transmission of chikungunya virus (CHIKV) was first detected in the Americas in December 2013, after which it spread rapidly throughout the Caribbean islands and American mainland, causing a major chikungunya fever epidemic. Previous phylogenetic analysis of CHIKV from a limited number of countries in the Americas suggests that an Asian genotype strain was responsible, except in Brazil where both Asian and East/Central/South African (ECSA) lineage strains were detected. In this study, we sequenced thirty-three complete CHIKV genomes from viruses isolated in 2014 from fourteen Caribbean islands, the Bahamas and two mainland countries in the Americas. Phylogenetic analyses confirmed that they all belonged to the Asian genotype and clustered together with other Caribbean and mainland sequences isolated during the American outbreak, forming an 'Asian/American' lineage defined by two amino acid substitutions, E2 V368A and 6K L20M, and divided into two well-supported clades. This lineage is estimated to be evolving at a mean rate of 5 × 10-4 substitutions per site per year (95% higher probability density, 2.9-7.9 × 10-4) and to have arisen from an ancestor introduced to the Caribbean (most likely from Oceania) in about March 2013, 9 months prior to the first report of CHIKV in the Americas. Estimation of evolutionary rates for individual gene regions and selection analyses indicate that (in contrast to the Indian Ocean Lineage that emerged from the ECSA genotype followed by adaptive evolution and with a significantly higher substitution rate) the evolutionary dynamics of the Asian/American lineage are very similar to the rest of the Asian genotype and natural selection does not appear to have played a major role in its emergence. However, several codon sites with evidence of positive selection were identified within the non-structural regions of Asian genotype sequences outside of the Asian/American lineage.

Isolation and Characterization of Madariaga Virus from a Horse in Paraíba State, Brazil.

Madariaga virus (MADV), the new species designation for the South American isolates of eastern equine encephalitis virus (EEEV), is genetically divergent and substantially different in ecology and pathogenesis from North American EEEV strains. We isolated and characterized a MADV isolate obtained from a horse in Brazil. Our results support previous phylogenetic studies showing there are three genetically distinct MADV lineages. The MADV isolate from Paraíba State belongs to the South American lineage III and is closely related to Peruvian, Colombian and Venezuelan isolates.

Host range, amplification and arboviral disease emergence.

Etiologic agents of arboviral diseases are primarily zoonotic pathogens that are maintained in nature in cycles involving arthropod transmission among a variety of susceptible reservoir hosts. In the simplest form of human exposure, spillover occurs from the enzootic cycle when humans enter zoonotic foci and/or enzootic amplification increases circulation near humans. Examples include Eastern (EEEV) and Western equine encephalitis viruses (WEEV), as well as West Nile (WNV), St. Louis encephalitis (SLEV) and Yellow fever viruses. Spillover can involve direct transmission to humans by primary enzootic vectors (e.g. WNV, SLEV and WEEV) and/or bridge vectors with more catholic feeding preferences that include humans (e.g. EEEV). Some viruses, such as Rift Valley fever, Japanese encephalitis and Venezuelan equine encephalitis viruses (VEEV) undergo secondary amplification involving replication in livestock animals, resulting in greater levels of spillover to humans in rural settings. In the case of VEEV, secondary amplification involves equines and requires adaptive mutations in enzootic strains that allow for efficient viremia production. Two of the most important human arboviral pathogens, Yellow fever and dengue viruses (DENV), have gone one step further and adopted humans as their amplification hosts, allowing for urban disease. The ancestral forms of DENV, sylvatic viruses transmitted among nonhuman primate reservoir hosts by arboreal mosquitoes, adapted to efficiently infect the urban mosquito vectors Aedes aegypti and Ae. albopictus during the past few thousand years as civilizations arose. Comparative studies of the sylvatic and urban forms of DENV may elucidate the evolution of arboviral virulence and the prospects for DENV eradication should effective vaccines be implemented.

Seroepidemiology of selected alphaviruses and flaviviruses in bats in Trinidad.

A serosurvey of antibodies against selected flaviviruses and alphaviruses in 384 bats (representing 10 genera and 14 species) was conducted in the Caribbean island of Trinidad. Sera were analysed using epitope-blocking enzyme-linked immunosorbent assays (ELISAs) specific for antibodies against West Nile virus (WNV), Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV), all of which are zoonotic viruses of public health significance in the region. Overall, the ELISAs resulted in the detection of VEEV-specific antibodies in 11 (2.9%) of 384 bats. Antibodies to WNV and EEEV were not detected in any sera. Of the 384 sera, 308 were also screened using hemagglutination inhibition assay (HIA) for antibodies to the aforementioned viruses as well as St. Louis encephalitis virus (SLEV; which also causes epidemic disease in humans), Rio Bravo virus (RBV), Tamana bat virus (TABV) and western equine encephalitis virus (WEEV). Using this approach, antibodies to TABV and RBV were detected in 47 (15.3%) and 3 (1.0%) bats, respectively. HIA results also suggest the presence of antibodies to an undetermined flavivirus(es) in 8 (2.6%) bats. Seropositivity for TABV was significantly (P<0.05; χ2) associated with bat species, location and feeding preference, and for VEEV with roost type and location. Differences in prevalence rates between urban and rural locations were statistically significant (P<0.05; χ2) for TABV only. None of the aforementioned factors was significantly associated with RBV seropositivity rates.

Ultrastructural features of epithelial cell degeneration in rectal crypts of patients with AIDS.

Focal crypt epithelial cell degeneration (apoptosis) of the rectum is a characteristic pathologic feature in AIDS. The presence of apoptosis usually implies cell-mediated cytolysis, which would be an unexpected finding in this disease. We investigated the ultrastructural features of apoptosis in rectal biopsies from five AIDS patients (three homosexual males and two females with i.v. drug abuse), three heterosexual controls, and two homosexual male controls. Apoptosis was found in all AIDS patients and, to a lesser extent, in one heterosexual control. Ultrastructurally, vacuolization of several adjacent cells, leading to extrusion of cellular debris through the basal lamina and phagocytosis by macrophages, was seen. No intracellular or extracellular viral particles were detected in the regions containing apoptotic bodies, in epithelial cells near the crypt bases, in intraepithelial lymphocytes, or in macrophages. In summary, apoptosis in the rectal crypts of patients with AIDS has the same ultrastructural features as in other conditions, which suggests that its pathogenesis is related to immune rather than infectious factors. If this process occurs on a chronic basis in multiple cell types, it would promote general tissue depletion, which has been demonstrated to occur in AIDS. The presence of apoptosis in AIDS is not explained by current concepts of disease pathogenesis.

Genetic determinants of Venezuelan equine encephalitis emergence.

Following a period of inactivity from 1973-1991, Venezuelan equine encephalitis (VEE) reemerged during the past decade in South America and Mexico. Experimental studies of VEE virus (VEEV) infection of horses with virus strains isolated during these outbreaks have revealed considerable variation in the ability of equine-virulent, epizootic strains to exploit horses as efficient amplification hosts. Subtype IC strains from recent outbreaks in Venezuela and Colombia amplify efficiently in equines, with a correlation between maximum viremia titers and the extent of the outbreak from which the virus strain was isolated. Studies of enzootic VEEV strains that are believed to represent progenitors of the epizootic subtypes support the hypothesis that adaptation to efficient replication in equines is a major determinant of emergence and the ability of VEEV to spread geographically. Correlations between the ability of enzootic and epizootic VEEV strains to infect abundant, equiphilic mosquitoes, and the location and extent of these outbreaks, also suggest that specific adaptation to Ochlerotatus taeniorhynchus mosquitoes is a determinant of some but not all emergence events. Genetic studies imply that mutations in the E2 envelope glycoprotein gene are major determinants of adaptation to both equines and mosquito vectors.

Electron microscopic analysis of infection patterns for Venezuelan equine encephalomyelitis virus in the vector mosquito, Culex (Melanoconion) taeniopus.

The infectious process for Venezuelan equine encephalomyelitis virus in an enzootic vector mosquito, Culex (Melanoconion) taeniopus, was examined by transmission electron microscopy. Following large dose oral infection, virus was seen in the abdominal fat body and epidermis within 1 hr of engorgement. Replicated virus appeared to leave the mesenteron 3-4 hr post-infection. Dissemination to other organs occurred between days 1 and 2 of extrinsic incubation, when the hindgut and abdominal nerve ganglia were found to be infected. Virus reached the thoracic nerve ganglia, brain and salivary glands by 4 days post-infection, and flight muscles contained virus by day 6. Virus was never detected in the malphigian tubules or ovaries of infected mosquitoes within 21 days of extrinsic incubation. These results suggest that virus particles penetrate the mesenteron and accumulate in the abdominal fat body prior to replication within the vector. This pattern differs from that reported for other arbovirus-vector pairs.

Ultrastructural aspects of replication of the New Jersey serotype of vesicular stomatitis virus in a suspected sand fly vector, Lutzomyia shannoni (Diptera: Psychodidae).

Transmission electron microscopy was used to examine replication of the New Jersey serotype of vesicular stomatitis virus (VSNJ) (Rhabdoviridae: Vesiculovirus) in Lutzomyia shannoni (Diptera: Psychodidae), a recently implicated sand fly vector. Following ingestion of an infectious blood meal, female sand flies were fixed and examined at approximately 12-hr intervals for six days. The New Jersey serotype of vesicular stomatitis virus was first detected in the abdominal midgut after 34 hr of incubation. Virus next appeared in fat body and the thoracic midgut at 48 hr, while salivary glands first contained visible virus in apical cavities 5-6 days after infection. Flight muscles and nervous tissue occasionally contained small numbers of VSNJ virions, while virus was never detected in the ovaries or malphigian tubules. The midgut and fat body appeared to be major sites of VSNJ virus replication. In all tissues examined, virus matured primarily by budding from the plasma membrane. Virions were occasionally observed within vacuoles, along with nucleocapsids. In the midgut, budding occurred exclusively from the basolateral plasma membrane, while maturation in salivary gland cells involved apical budding. Accumulation of virions adjacent to basal laminae surrounding several tissues suggested that this structure physically impedes virus dissemination within the sandfly. The paucity of virus budding 120-144 hr after infection suggested that the VSNJ virus infection was modulated in Lu. shannoni.