Preparing for Emerging Zoonotic Viruses

Rodriguez-Morales A, Furqan Ilyas M, Santos Ferreira MDN, Singh Malik Y, Kalantari R, Shahrokhabadi A, Jafari N, Shahabinejad F, Maleki Y, Montajeb S, Mehrpouya R, Ahmadi H, Vazir B, Kabir F, Rehman A, Elmi Z, Hajipour P, El-Seedi HR, Eisenreich W, Shehata AA. Migratory Wave due to Conflicts: Risk of Increased Infection From Zoonotic Diseases

Wars have devastating effects on all the components of the One Health approach: humans, animals, and ecosystems. Wars and the resulting migratory waves massively disrupt normal animal health services and surveillance. Among other consequences, they adversely impact the early detection, prevention, and control of animal diseases. Uncontrolled movement of animals or their undisposed carcasses, the destruction of wildlife habitats, and the increased interface between humans, wildlife, and domestic animals contribute to uncontrolled transmission and spread of zoonotic pathogens from animals to humans. In the last millennium, zoonotic diseases such as the "Black Death" were triggered by devastating wars and led to the deaths of a large fraction of the human population. However, also recent and ongoing wars carry the risk of an uncontrollable increase in zoonotic diseases. The most significant zoonotic diseases reported during the recent wars are African swine fever, highly pathogenic avian influenza, rabies, leptospirosis, and brucellosis, as well as foodborne and waterborne zoonotic diseases. Indeed, alarming rates of infections by antimicrobial-resistant pathogens such as Mycobacterium tuberculosis go along with wars, as seen in the current Ukraine-Russia conflict. Considering human migration, foodborne and waterborne zoonotic diseases are key health threats for refugees due to the consumption of unsafe food, lack of safe water, and disruption of the water supply and sanitation system. This review summarizes the potential factors and some data associated with the increased risk of zoonotic disease emergence and transmission during recent and ongoing conflicts.

First Detection of Alphacoronavirus in Bats from the World's Largest Wetland, the Pantanal, Brazil

Coronaviruses (CoV) infect a wide variety of hosts, causing epidemics in humans, birds, and mammals over the years. Bats (order Chiroptera) are one of the natural hosts of the Coronaviridae family. They represent 40% of the total number of mammal species in the Pantanal, a biodiversity hotspot in South America. Given the recent SARS-CoV-2 pandemic, we investigated the presence of CoV in bats captured in the Brazilian Pantanal. Oral and rectal swabs collected in 2021 from 419 bats were analyzed using Pancoronavirus-nested PCR targeting the RNA-dependent RNA-polymerase (RdRp) gene. Orthocoronavirinae was detected in 16.7% (70/419) of the bats; nine samples were sequenced, confirming that Carollia perspicillata (4), Phyllostomus hastatus (2), Desmodus rotundus (1), Molossus rufus (1), and Myotis cf. nigricans (1) collected in buildings formally used by humans were infected by Alphacoronavirus genera. This is the first description of Alphacoronavirus in bats from the Pantanal. As they are natural reservoirs of CoVs, constant monitoring of bats is important to comprehend the epidemiology of emerging viruses, especially in the Pantanal biome.

A high-throughput, polymerase-targeted RT-PCR for broad detection of mammalian filoviruses

Filoviruses are some of the most lethal viruses in the modern world, and increasing numbers of filovirus species and genera have been discovered in recent years. Despite the potential severity of filovirus outbreaks in the human population, comparably few sensitive pan-filovirus RT-PCR assays have been described that might facilitate early detection and prevention. Here, we present a new pan-filovirus RT-PCR assay targeting the L polymerase gene for detection of all known mammalian filoviruses. We demonstrate the detection of 10 synthetic filovirus RNA templates with analytical sensitivity ranging from 178 to 3,354 copies/mL, without cross-reactivity on 10 non-filoviral human viral species. We verified assay performance on 10 inactivated filovirus isolates, yielding initial sensitivities of 0.012-44.17 TCID50/mL. We coupled this broadly reactive RT-PCR with a deep sequencing workflow that is amenable to high-throughput pooling to maximize detection and discovery potential. In summary, this pan-filovirus RT-PCR assay targets the most conserved filovirus gene, offers the widest breadth of coverage to date, and may help in the detection and discovery of novel filoviruses.IMPORTANCEFiloviruses remain some of the most mysterious viruses known to the world, with extremely high lethality rates and significant pandemic potential. Yet comparably few filovirus species and genera have been discovered to date and questions surround the definitive host species for zoonotic infections. Here, we describe a novel broadly reactive RT-PCR assay targeting the conserved L polymerase gene for high-throughput screening for filoviruses in a variety of clinical and environmental specimens. We demonstrate the assay can detect all known mammalian filoviruses and determine the sensitivity and specificity of the assay on synthetic RNA sequences, inactivated filovirus isolates, and non-filoviral species.

Serological Survey of Retrovirus and Coronavirus Infections, including SARS-CoV-2, in Rural Stray Cats in The Netherlands, 2020-2022

Stray cats can host (zoonotic) viral pathogens and act as a source of infection for domestic cats or humans. In this cross-sectional (sero)prevalence study, sera from 580 stray cats living in 56 different cat groups in rural areas in The Netherlands were collected from October 2020 to July 2022. These were used to investigate the prevalence of the cat-specific feline leukemia virus (FeLV, n = 580), the seroprevalence of the cat-specific feline viruses feline immunodeficiency virus (FIV, n = 580) and feline coronavirus (FCoV, n = 407), and the zoonotic virus severe acute respiratory coronavirus-2 (SARS-CoV-2, n = 407) using enzyme-linked immunosorbent assays (ELISAs). ELISA-positive results were confirmed using Western blot (FIV) or pseudovirus neutralization test (SARS-CoV-2). The FIV seroprevalence was 5.0% (95% CI (Confidence Interval) 3.4-7.1) and ranged from 0-19.0% among groups. FIV-specific antibodies were more often detected in male cats, cats ≥ 3 years and cats with reported health problems. No FeLV-positive cats were found (95% CI 0.0-0.6). The FCoV seroprevalence was 33.7% (95% CI 29.1-38.5) and ranged from 4.7-85.7% among groups. FCoV-specific antibodies were more often detected in cats ≥ 3 years, cats with reported health problems and cats living in industrial areas or countryside residences compared to cats living at holiday parks or campsites. SARS-CoV-2 antibodies against the subunit 1 (S1) and receptor binding domain (RBD) protein were detected in 2.7% (95% CI 1.4-4.8) of stray cats, but sera were negative in the pseudovirus neutralization test and therefore were considered SARS-CoV-2 suspected. Our findings suggest that rural stray cats in The Netherlands can be a source of FIV and FCoV, indicating a potential risk for transmission to other cats, while the risk for FeLV is low. However, suspected SARS-CoV-2 infections in these cats were uncommon. We found no evidence of SARS-CoV-2 cat-to-cat spread in the studied stray cat groups and consider the likelihood of spillover to humans as low.

Modern vaccine strategies for emerging zoonotic viruses

INTRODUCTION

The significant increase in the emergence of notable zoonotic viruses in the previous decades has become a serious concern to global public health. Ninety-nine percent of infectious diseases have originated from zoonotic viruses with immense potential for dissemination, infecting the susceptible population completely lacking herd immunity.

AREAS COVERED

Zoonotic viruses appear in the last two decades as a major health threat either newly evolved or previously present with elevated prevalence in the last few years are selected to explain their current prophylactic measures. In this review, modern generation vaccines including viral vector vaccines, mRNA vaccines, DNA vaccines, synthetic vaccines, virus-like particles, and plant-based vaccines are discussed with their benefits and challenges. Moreover, the traditional vaccines and their efficacy are also compared with the latest vaccines.

EXPERT OPINION

The emergence and reemergence of viruses that constantly mutate themselves have greatly increased the chance of transmission and immune escape mechanisms in humans. Therefore, the only possible solution to prevent viral infection is the use of vaccines with improved safety profile and efficacy, which becomes the basis of modern generation vaccines.

The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond

The human population has doubled in the last 50 years from about 3.7 billion to approximately 7.8 billion. With this rapid expansion, more people live in close contact with wildlife, livestock, and pets, which in turn creates increasing opportunities for zoonotic diseases to pass between animals and people. At present an estimated 75% of all emerging virus-associated infectious diseases possess a zoonotic origin, and outbreaks of Zika, Ebola and COVID-19 in the past decade showed their huge disruptive potential on the global economy. Here, we describe how One Health inspired environmental surveillance campaigns have emerged as the preferred tools to monitor human-adjacent environments for known and yet to be discovered infectious diseases, and how they can complement classical clinical diagnostics. We highlight the importance of environmental factors concerning interactions between animals, pathogens and/or humans that drive the emergence of zoonoses, and the methodologies currently proposed to monitor them-the surveillance of wastewater, for example, was identified as one of the main tools to assess the spread of SARS-CoV-2 by public health professionals and policy makers during the COVID-19 pandemic. One-Health driven approaches that facilitate surveillance, thus harbour the potential of preparing humanity for future pandemics caused by aetiological agents with environmental reservoirs. Via the example of COVID-19 and other viral diseases, we propose that wastewater surveillance is a useful complement to clinical diagnosis as it is centralized, robust, cost-effective, and relatively easy to implement.

Next-Generation Sequencing for Confronting Virus Pandemics

Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.

Microorganisms as Shapers of Human Civilization, from Pandemics to Even Our Genomes: Villains or Friends? A Historical Approach

Universal history is characterized by continuous evolution, in which civilizations are born and die. This evolution is associated with multiple factors, among which the role of microorganisms is often overlooked. Viruses and bacteria have written or decisively contributed to terrible episodes of history, such as the Black Death in 14th century Europe, the annihilation of pre-Columbian American civilizations, and pandemics such as the 1918 Spanish flu or the current COVID-19 pandemic caused by the coronavirus SARS-CoV-2. Nevertheless, it is clear that we could not live in a world without these tiny beings. Endogenous retroviruses have been key to our evolution and for the regulation of gene expression, and the gut microbiota helps us digest compounds that we could not otherwise process. In addition, we have used microorganisms to preserve or prepare food for millennia and more recently to obtain drugs such as antibiotics or to develop recombinant DNA technologies. Due to the enormous importance of microorganisms for our survival, they have significantly influenced the population genetics of different human groups. This paper will review the role of microorganisms as "villains" who have been responsible for tremendous mortality throughout history but also as "friends" who help us survive and evolve.

Pandemics- One Health preparedness for the next

The majority of emerging infectious diseases originate in animals. Current routine surveillance is focused on known diseases and clinical syndromes, but the increasing likelihood of emerging disease outbreaks shows the critical importance of early detection of unusual illness or circulation of pathogens - prior to human disease manifestation. In this Viewpoint, we focus on one key pillar of preparedness—the need for early warning surveillance at the human, animal, environmental interface. The COVID-19 pandemic has revolutionized the scale of sequencing of pathogen genomes, and the current investments in global genomic surveillance offer great potential for a novel, truly integrated Disease X (with epidemic or pandemic potential) surveillance arm provided we do not make the mistake of developing them solely for the case at hand. Generic tools include metagenomic sequencing as a catch-all technique, rather than detection and sequencing protocols focusing on what we know. Developing agnostic or more targeted metagenomic sequencing to assess unusual disease in humans and animals, combined with random sampling of environmental samples capturing pathogen circulation is technically challenging, but could provide a true early warning system. Rather than rebuilding and reinforcing the pre-existing silo's, a real step forward would be to take the lessons learned and bring in novel essential partnerships in a One Health approach to preparedness.

Industrial Animal Farming and Zoonotic Risk: COVID-19 as a Gateway to Sustainable Change? A Scoping Study

The threat of zoonoses (i.e., human infectious diseases transmitted from animals) because of industrial animal farming may be receiving less attention in society due to the putative wildlife origin of COVID-19. To identify societal responses to COVID-19 that do address or affect the risk of future zoonoses associated with industrial animal farming, the literature was screened for measures, actions, proposals and attitudes following the guidelines of a scoping review. Forty-one articles with relevant information published between 1 January 2020 and 30 April 2021 were identified directly or indirectly via bibliographies from 138 records retrieved via Google Scholar. Analysis of relevant content revealed ten fields of policy action amongst which biosecurity and change in dietary habits were the dominant topics. Further searches for relevant records within each field of policy action retrieved another eight articles. Identified responses were furthermore classified and evaluated according to groups of societal actors, implying different modes of regulation and governance. Based on the results, a suggested policy strategy is presented for moving away from food production in factory farms and supporting sustainable farming, involving the introduction of a tax on the demand side and subsidies for the development and production of alternative meat.