Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport

Assessing the microbial diversity and proximate composition of smoked-fermented bushmeat from four different bushmeat samples

The ever-increasing demand for wildlife-derived raw or processed meat commonly known as bushmeat, has been identified as one of the critical factors driving the emergence of infectious diseases. This study focused on examining the bacterial community composition of smoked and fermented bushmeats, specifically grasscutter, rat, rabbit, and mona monkey. The analysis involved exploring 16Sr RNA amplicon sequences isolated from bushmeat using QIIME2. Microbiome profiles and their correlation with proximate components (PLS regression) were computed in STAMP and XLSTAT, respectively. Results indicate the predominance of Firmicutes (70.9%), Actinobacteria (18.58%), and Proteobacteria (9.12%) in bushmeat samples at the phylum level. Staphylococcus, Arthrobacter, Macrococcus, and Proteus constituted the core microbiomes in bushmeat samples, ranked in descending order. Notably, significant differences were observed between the bacterial communities of bushmeat obtained from omnivores and herbivores (rat and mona monkey, and grasscutter and mona monkey), as well as those with similar feeding habits (rat and monkey, and grasscutter and rabbit) at the family and genus levels. Each type of bushmeat possessed unique microbial diversity, with some proximate components such as fat in rat samples correlating with Staphylococcus, while proteins in Mona monkey correlated with Arthrobacter and Brevibacterium, respectively. The study underscores public health concerns and highlights probiotic benefits, as bushmeat samples contained both pathogenic and beneficial bacteria. Therefore, future research efforts could focus on improving bushmeat quality.

A systematic mapping review of links between handling wild meat and zoonotic diseases

1.Hunting, trade, and consumption of wildlife present a serious threat to global public health as it places humans in close contact with zoonotic pathogens.2.We systematically mapped the literature on wild meat handling and zoonotic disease transmission (1996-2022) using the online database Web of Science and Google search engine and identified 6229 articles out of which 253 were finally selected for use in our mapping review; 51 of these provided specific information regarding transmission risks.3.The reviewed studies reported 43 zoonotic pathogens (17 bacteria, 15 viruses, and 11 parasites) that could pose a potential risk to human health.4.Sixteen hygienic and sanitary behaviours were described in the reviewed studies. Disease surveillance was the most frequent. Most of the surveillance studies were carried out in Europe and were less common in the tropics.5.To inform policy and practical actions effectively, it is imperative to broaden our understanding of how various mitigation behaviours can be employed to minimize the risk of transmission.

A systematic review of the intercontinental movement of unregulated African meat imports into and through European border checkpoints

There is an urgent need for biosurveillance of unregulated African meat imports at border points of entry in destination markets. This is underscored by recent pandemics linked to exotic wildlife products. Our objective was to catalog the quantity of meat that is informally transported from Africa into and through Europe often without any veterinary or sanitary checks. We searched and included peer-reviewed studies that contained data on the intercontinental movement of unregulated meat from the African continent. This was followed by an investigation of the reported contamination of such meat. We included fifteen airport studies with limited data on this topic. The references included in this review describe the quantity of meat found at border inspection posts and the presence of pathogens. Disease-causing pathogens were found to be present, and the results are organized into bacteria, virus, and parasite categories. The species of animal meat found in this review were linked to CITES-protected species some of which are known reservoir hosts for infectious diseases. This represents a potential and unquantified human health risk to populations along the supply chain, and a loss to biodiversity in supply countries. Meat samples described in this review were primarily found opportunistically by Customs officials, indicating that any estimate of the total quantities passing undetected through border checkpoints must remain tentative, and cannot rule out the possibility that it is indeed considerably higher. We propose a template for future studies regarding African meat imports at border points of entry. The result of this review illustrates a gap in knowledge and lacunae regarding the amount of unregulated African meat imports worldwide, the pathogens it may contain, and the resulting biodiversity loss that occurs from the intercontinental movement of this meat.

Zoonoses in a changing world

Animals are continuously exposed to pathogens but rarely get infected, because pathogens must overcome barriers to establish successful infections. Ongoing planetary changes affect factors relevant for such infections, such as pathogen pressure and pathogen exposure. The replacement of wildlife with domestic animals shrinks the original host reservoirs, whereas expanding agricultural frontiers lead to increased contact between natural and altered ecosystems, increasing pathogen exposure and reducing the area where the original hosts can live. Climate change alters species' distributions and phenology, pathogens included, resulting in exposure to pathogens that have colonized or recolonized new areas. Globalization leads to unwilling movement of and exposure to pathogens. Because people and domestic animals are overdominant planetwide, there is increased selective pressure for pathogens to infect them. Nature conservation measures can slow down but not fully prevent spillovers. Additional and enhanced surveillance methods in potential spillover hotspots should improve early detection and allow swifter responses to emerging outbreaks.

Illegal Wildlife Trade and Emerging Infectious Diseases: Pervasive Impacts to Species, Ecosystems and Human Health

Simple Summary

Wildlife is trafficked illegally across the globe every day. The illegal wildlife trade (IWT) creates opportunity for emerging infectious disease (EID) events to occur. EIDs are a major threat to wildlife, ecosystems, and public health. This study addresses the lack of comprehensive review of pathogens identified in IWT and highlights the expansion of literature on this subject over the past 30 years. We reviewed 82 scientific papers and conference proceedings from 1990 to 2020. Trends in EIDs identified in IWT have significantly increased over the past decade. Cases covered 240 pathogens across all taxa. Approximately 60% of the pathogens identified were zoonotic (transmissible between animals and humans) and threaten public health. Based on our findings, we recommend further research is needed to monitor and prevent the IWT.

Abstract

Emerging infectious disease (EID) events can be traced to anthropogenic factors, including the movement of wildlife through legal and illegal trade. This paper focuses on the link between illegal wildlife trade (IWT) and infectious disease pathogens. A literature review through Web of Science and relevant conference proceedings from 1990 to 2020 resulted in documenting 82 papers and 240 identified pathogen cases. Over 60% of the findings referred to pathogens with known zoonotic potential and five cases directly referenced zoonotic spillover events. The diversity of pathogens by taxa included 44 different pathogens in birds, 47 in mammals, 16 in reptiles, two in amphibians, two in fish, and one in invertebrates. This is the highest diversity of pathogen types in reported literature related to IWT. However, it is likely not a fully representative sample due to needed augmentation of surveillance and monitoring of IWT and more frequent pathogen testing on recovered shipments. The emergence of infectious disease through human globalization has resulted in several pandemics in the last decade including SARS, MERS, avian influenza H1N1,and Ebola. We detailed the growing body of literature on this topic since 2008 and highlight the need to detect, document, and prevent spillovers from high-risk human activities, such as IWT.

Detection of zoonotic pathogens in animals performed at the University Hospital Institute Méditerranée Infection (Marseille - France)

At the University Hospital Institute Méditerranée Infection (IHU, Marseille, France), for almost thirty years, veterinarians have been carrying out epidemiological investigations, together with doctors, on animals living near human cases of zoonoses, on the one hand, and on the other hand, transverse and longitudinal epidemiological surveillance studies on animals which are reservoirs, vectors or sentinels of potentially zoonotic infections,. This article presents the methods adopted and the results obtained from these studies. They have been the subject of 76 peer-reviewed publications relating to wild animals (37 publications) and/or domestic animals (48 publications). These studies were often carried out in the field with veterinarians from the French army's health service (39 publications). They were at the origin of the detection of some thirty zoonotic pathogens in the laboratories of the IHU (64 publications) and/or other French laboratories (18 publications). Our approach is an original embodiment of the "One Health" concept.

Exploring the characteristics of a local demand for African wild meat: A focus group study of long-term Ghanaian residents in the Netherlands

While there is a growing body of research documenting unregulated African wild meat imports into Europe from the Africa continent, the drivers of this demand are virtually unknown. This study employs focus group discussions and a survey questionnaire to examine the attitudes and practices related to African wild meat consumption in the city of Amsterdam, Netherlands. The Ghanaian community was selected as the object of this study, as it is the largest West African population in the Netherlands and represents an important part of Dutch society. We model our report on a recent US study of the Liberian community of Minneapolis, Minnesota, which allows for the comparison of results between two Western countries. The overall perceived health risk of consuming African wild meat in The Netherlands is low and unlikely to deter consumption. However, local prices for the meat may be prohibitive in some cases. Incentives include health benefits, cultural drivers and a strong preference for the taste of African wild meat over all local meat alternatives. The study calls for further research into the nature of the drivers of demand for African wild meat as well as its public health consequences, in the Netherlands and beyond.

Bushmeat Species Identification: Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow (LF) Strip for Identification of Formosan Reeves' Muntjac (Muntiacus reevesi micrurus)

Simple Summary

Illegal hunting of wild animals and the consumption of bushmeat are recognized not only as a threat to biodiversity, but also as a risk for transmitting zoonotic diseases. Illegal sales of meat products from Formosan Reeves’ muntjac (Muntiacus reevesi micrurus) is a growing issue in Taiwan, bringing forth the demand for a fast and cost-effective technique for meat species identification. In this study, a new recombinase polymerase amplification combined with a lateral flow strip to identify Formosan Reeves’ muntjac in meat products was described. This method only requires minimal sample preparation and an isothermal heating process. The result can be interpreted by the naked eye within 30 min. The system we designed efficiently detected a variety of meat products, and no cross-reactions were observed with other animal species. This simple assay provides a sensitive and specific method to identify bushmeat sources in various meat products, which holds the potential for on-field application in the future.

Abstract

The identification of animal species of meat in meat products is of great concern for various reasons, such as public health, religious beliefs, food allergies, legal perspectives, and bushmeat control. In this study, we developed a new technique to identify Formosan Reeves’ muntjac in meat using recombinase polymerase amplification (RPA) in combination with a lateral flow (LF) strip. The DNA extracted from a piece of Formosan Reeves’ muntjac meat was amplified by a pair of specific primers based on its mitochondrial cytochrome b gene for 10 min at a constant temperature ranging from 30 to 45 °C using RPA. Using the specific probe added to the RPA reaction system, the amplified products were visualized on the LF strip within 5 min. The total operating time from quick DNA extraction to visualizing the result was approximately 30 min. The RPA-LF system we designed was efficient when using boiled, pan-fried, roasted, stir-fried, or stewed samples. The advantages of simple operation, speediness, and cost-effectiveness make our RPA-LF method a promising molecular detection tool for meat species identification of either raw or variously cooked Formosan Reeves’ muntjac meat. It is also possible to apply this method to identify the meat of other wildlife sources.

Zoonoses

The selection of papers included in this issue of Microbiology Australia present a broad brush of zoonotic diseases, from those known or described in ancient times such as rabies, first described in the Eshnunna cuneiform law tablets from ancient Mesopotamia dating back to the 18th–19th centuries BC, and glanders, thought to be first described in donkeys by Aristotle in Ancient Greece in 420–450 BC and subsequently by the Romans, to some discovered or recognised as zoonotic within the past 30 years, such as the recently described zoonotic bat-borne pathogens in Australia, and Clostridium difficile, only recently recognised as a zoonotic pathogen. The selection of papers also demonstrates the wide range of zoonotic origins, including arthropod-borne viruses and potentially seafood-borne parasites.

Infectious Disease Risk Across the Growing Human-Non Human Primate Interface: A Review of the Evidence

Most of the human pandemics reported to date can be classified as zoonoses. Among these, there is a long history of infectious diseases that have spread from non-human primates (NHP) to humans. For millennia, indigenous groups that depend on wildlife for their survival were exposed to the risk of NHP pathogens' transmission through animal hunting and wild meat consumption. Usually, exposure is of no consequence or is limited to mild infections. In rare situations, it can be more severe or even become a real public health concern. Since the emergence of acquired immune deficiency syndrome (AIDS), nobody can ignore that an emerging infectious diseases (EID) might spread from NHP into the human population. In large parts of Central Africa and Asia, wildlife remains the primary source of meat and income for millions of people living in rural areas. However, in the past few decades the risk of exposure to an NHP pathogen has taken on a new dimension. Unprecedented breaking down of natural barriers between NHP and humans has increased exposure to health risks for a much larger population, including people living in urban areas. There are several reasons for this: (i) due to road development and massive destruction of ecosystems for agricultural needs, wildlife and humans come into contact more frequently; (ii) due to ecological awareness, many long distance travelers are in search of wildlife discovery, with a particular fascination for African great apes; (iii) due to the attraction for ancient temples and mystical practices, others travelers visit Asian places colonized by NHP. In each case, there is a risk of pathogen transmission through a bite or another route of infection. Beside the individual risk of contracting a pathogen, there is also the possibility of starting a new pandemic. This article reviews the known cases of NHP pathogens' transmission to humans whether they are hunters, travelers, ecotourists, veterinarians, or scientists working on NHP. Although pathogen transmission is supposed to be a rare outcome, Rabies virus, Herpes B virus, Monkeypox virus, Ebola virus, or Yellow fever virus infections are of greater concern and require quick countermeasures from public health professionals.

Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere

The history of giant viruses began in 2003 with the identification of Acanthamoeba polyphaga mimivirus. Since then, giant viruses of amoeba enlightened an unknown part of the viral world, and every discovery and characterization of a new giant virus modifies our perception of the virosphere. This notably includes their exceptional virion sizes from 200 nm to 2 µm and their genomic complexity with length, number of genes, and functions such as translational components never seen before. Even more surprising, Mimivirus possesses a unique mobilome composed of virophages, transpovirons, and a defense system against virophages named Mimivirus virophage resistance element (MIMIVIRE). From the discovery and isolation of new giant viruses to their possible roles in humans, this review shows the active contribution of the University Hospital Institute (IHU) Mediterranee Infection to the growing knowledge of the giant viruses' field.

New Isolates of Pandoraviruses: Contribution to the Study of Replication Cycle Steps

Giant viruses are complex members of the virosphere, exhibiting outstanding structural and genomic features. Among these viruses, the pandoraviruses are some of the most intriguing members, exhibiting giant particles and genomes presenting at up to 2.5 Mb, with many genes having no known function. In this work, we analyzed, by virological and microscopic methods, the replication cycle steps of three new pandoravirus isolates from samples collected in different regions of Brazil. Our data indicate that all analyzed pandoravirus isolates can deeply modify the Acanthamoeba cytoplasmic environment, recruiting mitochondria and membranes into and around the electron-lucent viral factories. We also observed that the viral factories start forming before the complete degradation of the cellular nucleus. Various patterns of pandoravirus particle morphogenesis were observed, and the assembly of the particles seemed to be started either by the apex or by the opposite side. On the basis of the counting of viral particles during the infection time course, we observed that pandoravirus particles could undergo exocytosis after their morphogenesis in a process that involved intense recruitment of membranes that wrapped the just-formed particles. The treatment of infected cells with brefeldin affected particle exocytosis in two of the three analyzed strains, indicating biological variability among isolates. Despite such particle exocytosis, the lysis of host cells also contributed to viral release. This work reinforces knowledge of and reveals important steps in the replication cycle of pandoraviruses.IMPORTANCE The emerging Pandoraviridae family is composed of some of the most complex viruses known to date. Only a few pandoravirus isolates have been described until now, and many aspects of their life cycle remain to be elucidated. A comprehensive description of the replication cycle is pivotal to a better understanding of the biology of the virus. For this report, we describe new pandoraviruses and used different methods to better characterize the steps of the replication cycle of this new group of viruses. Our results provide new information about the diversity and biology of these giant viruses.

Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa

Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.

A Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses

Giant viruses of amoebae are distinct from classical viruses by the giant size of their virions and genomes. Pandoraviruses are the record holders in size of genomes and number of predicted genes. Three strains, P. salinus, P. dulcis, and P. inopinatum, have been described to date. We isolated three new ones, namely P. massiliensis, P. braziliensis, and P. pampulha, from environmental samples collected in Brazil. We describe here their genomes, the transcriptome and proteome of P. massiliensis, and the pangenome of the group encompassing the six pandoravirus isolates. Genome sequencing was performed with an Illumina MiSeq instrument. Genome annotation was performed using GeneMarkS and Prodigal softwares and comparative genomic analyses. The core genome and pangenome were determined using notably ProteinOrtho and CD-HIT programs. Transcriptomics was performed for P. massiliensis with the Illumina MiSeq instrument; proteomics was also performed for this virus using 1D/2D gel electrophoresis and mass spectrometry on a Synapt G2Si Q-TOF traveling wave mobility spectrometer. The genomes of the three new pandoraviruses are comprised between 1.6 and 1.8 Mbp. The genomes of P. massiliensis, P. pampulha, and P. braziliensis were predicted to harbor 1,414, 2,368, and 2,696 genes, respectively. These genes comprise up to 67% of ORFans. Phylogenomic analyses showed that P. massiliensis and P. braziliensis were more closely related to each other than to the other pandoraviruses. The core genome of pandoraviruses comprises 352 clusters of genes, and the ratio core genome/pangenome is less than 0.05. The extinction curve shows clearly that the pangenome is still open. A quarter of the gene content of P. massiliensis was detected by transcriptomics. In addition, a product for a total of 162 open reading frames were found by proteomic analysis of P. massiliensis virions, including notably the products of 28 ORFans, 99 hypothetical proteins, and 90 core genes. Further analyses should allow to gain a better knowledge and understanding of the evolution and origin of these giant pandoraviruses, and of their relationships with viruses and cellular microorganisms.

Primates on display: Potential disease consequences beyond bushmeat

Human interactions with nonhuman primates vary tremendously, from daily cultural engagements and food commodities, to pet ownership and tourist encounters. These interactions provide opportunities for the exchange of pathogenic organisms (both zoonoses and anthroponoses). As exposures are not limited to areas where bushmeat usage continues to be a major problem, we must work to understand better our motivations for engaging in activities like owning primates as pets and having direct physical contact with wild primates within the context of nature-based tourism. These topics, and the theoretical potential for pathogen transmission, are reviewed in the present manuscript. This is followed by a case study utilizing 3845 survey responses collected from four international locations known for primate-based tourism, with results indicating that while a majority of people understand that they can give/get diseases to/from wild primates, a surprising percentage would still touch or feed these animals if given the opportunity. Many people still choose to touch and/or own primates, as their drive to bond with animals outweighs some basic health behaviors. Desires to tame, control, or otherwise establish emotional connections with other species, combined with the central role of touch for exploring our environment, necessitate the development of better communication and educational campaigns to minimize risks of emerging infectious diseases.

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples.