Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses

Optimization of potent, broad-spectrum, and specific anti-influenza compounds targeting RNA polymerase PA-PB1 heterodimerization

Influenza viruses (IV) are single-stranded RNA viruses with a negative-sense genome and have the potential to cause pandemics. While vaccines exist for influenza, their protection is only partial. Additionally, there is only a limited number of approved anti-IV drugs, which are associated to emergence of drug resistance. To address these issues, for years we have focused on the development of small-molecules that can interfere with the heterodimerization of PA and PB1 subunits of the IV RNA-dependent RNA polymerase (RdRP). In this study, starting from a cycloheptathiophene-3-carboxamide compound that we recently identified, we performed iterative cycles of medicinal chemistry optimization that led to the identification of compounds 43 and 45 with activity in the nanomolar range against circulating A and B strains of IV. Mechanistic studies demonstrated the ability of 43 and 45 to interfere with viral RdRP activity by disrupting PA-PB1 subunits heterodimerization and to bind to the PA C-terminal domain through biophysical assays. Most important, ADME studies of 45 also showed an improvement in the pharmacokinetic profile with respect to the starting hit.

Experimental viral spillover across 25 million year gap in Rodentia reveals limited viral transmission and purifying selection of a picornavirus

When a virus crosses from one host species to another, the consequences can be devastating. However, animal models to empirically evaluate cross-species transmission can fail to recapitulate natural transmission routes, physiologically relevant doses of pathogens, and population structures of naturally circulating viruses. Here, we present a new model of cross-species transmission where deer mice (Peromyscus maniculatus) are exposed to the natural virome of pet store mice (Mus musculus). Using RNA sequencing, we tracked viral transmission via fecal-oral routes and found the evidence of transmission of murine astroviruses, coronaviruses, and picornaviruses. Deep sequencing of murine kobuvirus revealed tight bottlenecks during transmission and purifying selection that leaves limited diversity present after transmission from Mus to Peromyscus. This work provides a structure for studying viral bottlenecks across species while keeping natural variation of viral populations intact and a high resolution look at within-host dynamics that occur during the initial stages of cross-species viral transmission.IMPORTANCEViral spillover events can have devastating public health consequences. Tracking cross-species transmission in real-time and evaluating viral evolution during the initial spillover event are useful for understanding how viruses adapt to new hosts. Using our new animal model and next generation sequencing, we develop a framework for understanding intrahost viral evolution and bottleneck events, which are very difficult to study in natural transmission settings.

Filling the knowledge gap: Scoping review regarding sampling methods, assays, and further requirements to assess airborne viruses

Assessment of occupational exposure to viruses is crucial to identify virus reservoirs and sources of dissemination at an early stage and to help prevent spread between employees and to the general population. Measuring workers' exposure can facilitate assessment of the effectiveness of protective and mitigation measures in place. The aim of this scoping review is to give an overview of available methods and those already implemented for airborne virus' exposure assessment in different occupational and indoor environments. The results retrieved from the different studies may contribute to the setting of future standards and guidelines to ensure a reliable risk characterization in the occupational environments crucial for the implementation of effective control measures. The search aimed at selecting studies between January 1st 2010 and June 30th 2023 in the selected databases. Fifty papers on virus exposure assessment fitted the eligibility criteria and were selected for data extraction. Overall, this study identified gaps in knowledge regarding virus assessment and pinpointed the needs for further research. Several discrepancies were found (transport temperatures, elution steps, …), as well as a lack of publication of important data related to the exposure conditions (contextual information). With the available information, it is impossible to compare results between studies employing different methods, and even if the same methods are used, different conclusions/recommendations based on the expert judgment have been reported due to the lack of consensus in the contextual information retrieved and/or data interpretation. Future research on the field targeting sampling methods and in the laboratory regarding the assays to employ should be developed bearing in mind the different goals of the assessment.

RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals

RNA molecules, similar to proteins, fold into complex structures to confer diverse functions in cells. The intertwining of functions with RNA structures offers a new therapeutic opportunity for small molecules to bind and manipulate disease-relevant RNA pathways, thus creating a therapeutic realm of RNA-binding small molecules. The ongoing interest in RNA targeting and subsequent screening campaigns have led to the identification of numerous compounds that can regulate RNAs from splicing, degradation to malfunctions, with therapeutic benefits for a variety of diseases. Moreover, along with the rise of RNA-based therapeutics, RNA-binding small molecules have expanded their application to the modification, regulation, and delivery of RNA drugs, leading to the burgeoning interest in this field. This Perspective overviews the emerging roles of RNA-binding small molecules in drug discovery and delivery, covering aspects from their action fundamentals to therapeutic applications, which may inspire researchers to advance the field.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.

The harms of promoting the lab leak hypothesis for SARS-CoV-2 origins without evidence

Science is humanity's best insurance against threats from nature, but it is a fragile enterprise that must be nourished and protected. The preponderance of scientific evidence indicates a natural origin for SARS-CoV-2. Yet, the theory that SARS-CoV-2 was engineered in and escaped from a lab dominates media attention, even in the absence of strong evidence. We discuss how the resulting anti-science movement puts the research community, scientific research, and pandemic preparedness at risk.

Surveillance strategies for SARS-CoV-2 infections through one health approach

Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), is an emergent disease that threatens global health. Public health structures and economic activities have been disrupted globally by the COVID-19 pandemic. Over 556.3 million confirmed cases and 6.3 million deaths have been reported. However, the exact mechanism of its emergence in humans remains unclear. SARS-CoV-2 is believed to have a zoonotic origin, suggesting a spillover route from animals to humans, which is potentially facilitated by wildlife farming and trade. The COVID-19 pandemic highlighted the importance of the One Health approach in managing threats of zoonosis in the human-animal-environment interaction. Implementing vigilant surveillance programs by adopting the One Health concept at the interfaces between wildlife, livestock, and humans is the most pertinent, practical, and actionable strategy for preventing and preparing for future pandemics of zoonosis, such as COVID-19 infection. This review summarizes the updated evidence of CoV infections in humans and animals and provides an appropriate strategy for preventive measures focused on surveillance systems through an On Health approach.

Detection of SARS-CoV-2 on the environmental surfaces and its implications for pandemic preparedness

Even though death due to COVID-19 is no longer a public health emergency, less virulent but highly transmissible forms of SARS-CoV-2 continue to spread in many countries leading to outbreaks and rise in hospitalizations in the affected regions. Lessons learned during the pandemic must be put into action to protect the world's population from another catastrophe like COVID-19. Novel approaches that were developed for tracking the spread of SARS-CoV-2 included analysis of wastewater, air samples, and various environmental surfaces. We conducted a study in Kuwait during the peak of COVID-19 pandemic to examine if SARS-CoV-2 could be detected in swabs taken from frequently touched environmental surfaces. We selected 12 Cooperative Society Stores-two from each governorate of Kuwait-for collection of surface samples. The Cooperative Society Stores are widely distributed across the whole country and cater to daily household needs including groceries and other essential items. These stores operated even during the "lockdown" imposed at the height of the pandemic. We collected swabs from high-touch surfaces including the handles of the shopping carts and freezers, the elevators, the keypads of the point-of-service terminals of cash counters, and the automated teller machines. All the surfaces tested showed a variable presence of SARS-CoV-2 by reverse transcriptase quantitative PCR, showing the validity of the proof-of-concept study. Monitoring of the presence of SARS-CoV-2 by surface sampling thus offers a cheap but effective means of environmental surveillance for coronaviruses. We therefore strongly recommend the addition of surface environmental sampling as a strategy for pandemic preparedness everywhere.

The Emergence and Evolution of SARS-CoV-2

The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.

Evaluating climate-dependent distribution of orthohantaviruses with monitoring wild rodents: One Health Perspective†

Orthohantaviruses, cause hemorrhagic fever with renal syndrome, nephropathia epidemica, and hantavirus pulmonary syndrome, are major public health problems all over the world. Wild rodent surveillance for orthohantaviruses is of great importance for the preparedness against these human infections and the prediction of possible outbreak regions. Thus, we aimed to screen orthohantaviruses in wild rodents in Southern Anatolia, where the area has some of the glacial period refugia in the Mediterranean Basin, and interpret their current epidemiology with climatic biovariables in comparison with previously positive regions.We trapped muroid rodents between 2015 and 2017, and screened for orthohantaviruses. Then, we evaluated the relationship between orthohantavirus infections and bioclimatic variables. In spite of the long-term and seasonal sampling, we found no evidence for Orthohantavirus infections. The probable absence of orthohantaviruses in the sampling area was further evaluated from the climatic perspective, and results led us suggest that Orthohantavirus epidemiology might be relatively dependent on precipitation levels in driest and warmest quarters, and temperature fluctuations.These initial data might provide necessary perspective on wild rodent surveillance for orthohantaviruses in other regions, and help to collect lacking data for a such habitat suitability study in a bigger scale in the future.

Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges

Wastewater surveillance holds great promise as a sensitive method to detect spillover of zoonotic infections and early pandemic emergence, thereby informing risk mitigation and public health response. Known viruses with pandemic potential are shed in human stool or urine, or both, and the experiences with SARS-CoV-2, monkeypox virus, and Zika virus highlight the feasibility of community-based wastewater surveillance for pandemic viruses that have different transmission routes. We reviewed human shedding and wastewater surveillance data for prototype viruses representing viral families of concern to estimate the likely sensitivity of wastewater surveillance compared with that of clinical surveillance. We examined how data on wastewater surveillance detection, together with viral genetic sequences and animal faecal biomarkers, could be used to identify spillover infections or early human transmission and adaptation. The opportunities and challenges associated with global wastewater surveillance for the prevention of pandemics are described in this Personal View, focusing on low-income and middle-income countries, where the risk of pandemic emergence is the highest. We propose a research and public health agenda to ensure an equitable and sustainable solution to these challenges.

SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity

Circulating bat coronaviruses represent a pandemic threat. However, our understanding of bat coronavirus pathogenesis and transmission potential is limited by the lack of phenotypically characterized strains. We created molecular clones for the two closest known relatives of SARS-CoV-2, BANAL-52 and BANAL-236. We demonstrated that BANAL-CoVs and SARS-CoV-2 have similar replication kinetics in human bronchial epithelial cells. However, BANAL-CoVs have impaired replication in human nasal epithelial cells and in the upper airway of mice. We also observed reduced pathogenesis in mice and diminished transmission in hamsters. Further, we observed that diverse bat coronaviruses evade interferon and downregulate major histocompatibility complex class I. Collectively, our study demonstrates that despite high genetic similarity across bat coronaviruses, prediction of pandemic potential of a virus necessitates functional characterization. Finally, the restriction of bat coronavirus replication in the upper airway highlights that transmission potential and innate immune restriction can be uncoupled in this high-risk family of emerging viruses.

Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.

A One Health framework for exploring zoonotic interactions demonstrated through a case study

The eco-epidemiology of zoonoses is often oversimplified to host-pathogen interactions while findings derived from global datasets are rarely directly transferable to smaller-scale contexts. Through a systematic literature search, we compiled a dataset of naturally occurring zoonotic interactions in Austria, spanning 1975-2022. We introduce the concept of zoonotic web to describe the complex relationships between zoonotic agents, their hosts, vectors, food, and environmental sources. The zoonotic web was explored through network analysis. After controlling for research effort, we demonstrate that, within the projected unipartite source-source network of zoonotic agent sharing, the most influential zoonotic sources are human, cattle, chicken, and some meat products. Analysis of the One Health 3-cliques (triangular sets of nodes representing human, animal, and environment) confirms the increased probability of zoonotic spillover at human-cattle and human-food interfaces. We characterise six communities of zoonotic agent sharing, which assembly patterns are likely driven by highly connected infectious agents in the zoonotic web, proximity to human, and anthropogenic activities. Additionally, we report a frequency of emerging zoonotic diseases in Austria of one every six years. Here, we present a flexible network-based approach that offers insights into zoonotic transmission chains, facilitating the development of locally-relevant One Health strategies against zoonoses.

The reverse zoonotic potential of SARS-CoV-2

There has been considerable emphasis recently on the zoonotic origins of emerging infectious diseases in humans, including the SARS-CoV-2 pandemic; however, reverse zoonoses (infections transmitted from humans to other animals) have received less attention despite their potential importance. The effects can be devastating for the infected species and can also result in transmission of the pathogen back to human populations or other animals either in the original form or as a variant. Humans have transmitted SARS-CoV-2 to other animals, and the virus is able to circulate and evolve in those species. As global travel resumes, the potential of SARS-CoV-2 as a reverse zoonosis threatens humans and endangered species. Nonhuman primates are of particular concern given their susceptibility to human respiratory infections. Enforcing safety measures for all people working in and visiting wildlife areas, especially those with nonhuman primates, and increasing access to safety measures for people living near protected areas that are home to nonhuman primates will help mitigate reverse zoonotic transmission.

Zoonotic spillover and viral mutations from low and middle-income countries: improving prevention strategies and bridging policy gaps

The increasing frequency of zoonotic spillover events and viral mutations in low and middle-income countries presents a critical global health challenge. Contributing factors encompass cultural practices like bushmeat consumption, wildlife trade for traditional medicine, habitat disruption, and the encroachment of impoverished settlements onto natural habitats. The existing "vaccine gap" in many developing countries exacerbates the situation by allowing unchecked viral replication and the emergence of novel mutant viruses. Despite global health policies addressing the root causes of zoonotic disease emergence, there is a significant absence of concrete prevention-oriented initiatives, posing a potential risk to vulnerable populations. This article is targeted at policymakers, public health professionals, researchers, and global health stakeholders, particularly those engaged in zoonotic disease prevention and control in low and middle-income countries. The article underscores the importance of assessing potential zoonotic diseases at the animal-human interface and comprehending historical factors contributing to spillover events. To bridge policy gaps, comprehensive strategies are proposed that include education, collaborations, specialized task forces, environmental sampling, and the establishment of integrated diagnostic laboratories. These strategies advocate simplicity and unity, breaking down barriers, and placing humanity at the forefront of addressing global health challenges. Such a strategic and mental shift is crucial for constructing a more resilient and equitable world in the face of emerging zoonotic threats.

Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses

Nanoparticle vaccines displaying mosaic receptor-binding domains (RBDs) or spike (S) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or other sarbecoviruses are used in preparedness against potential zoonotic outbreaks. Here, we describe a self-assembling nanoparticle using lumazine synthase (LuS) as the scaffold to display RBDs from different sarbecoviruses. Mosaic nanoparticles induce sarbecovirus cross-neutralizing antibodies comparable to a nanoparticle cocktail. We find mosaic nanoparticles elicit a B cell receptor repertoire using an immunodominant germline gene pair of IGHV14-3:IGKV14-111. Most of the tested IGHV14-3:IGKV14-111 monoclonal antibodies (mAbs) are broadly cross-reactive to clade 1a, 1b, and 3 sarbecoviruses. Using mAb competition and cryo-electron microscopy, we determine that a representative IGHV14-3:IGKV14-111 mAb, M2-7, binds to a conserved epitope on the RBD, largely overlapping with the pan-sarbecovirus mAb S2H97. This suggests mosaic nanoparticles expand B cell recognition of the common epitopes shared by different clades of sarbecoviruses. These results provide immunological insights into the cross-reactive responses elicited by mosaic nanoparticles against sarbecoviruses.

Building a pathway to One Health surveillance and response in Asian countries

To detect and respond to emerging diseases more effectively, an integrated surveillance strategy needs to be applied to both human and animal health. Current programs in Asian countries operate separately for the two sectors and are principally concerned with detection of events that represent a short-term disease threat. It is not realistic to either invest only in efforts to detect emerging diseases, or to rely solely on event-based surveillance. A comprehensive strategy is needed, concurrently investigating and managing endemic zoonoses, studying evolving diseases which change their character and importance due to influences such as demographic and climatic change, and enhancing understanding of factors which are likely to influence the emergence of new pathogens. This requires utilisation of additional investigation tools that have become available in recent years but are not yet being used to full effect. As yet there is no fully formed blueprint that can be applied in Asian countries. Hence a three-step pathway is proposed to move towards the goal of comprehensive One Health disease surveillance and response.

"Smart markets": harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets

Emerging and endemic zoonotic diseases continue to threaten human and animal health, our social fabric, and the global economy. Zoonoses frequently emerge from congregate interfaces where multiple animal species and humans coexist, including farms and markets. Traditional food markets are widespread across the globe and create an interface where domestic and wild animals interact among themselves and with humans, increasing the risk of pathogen spillover. Despite decades of evidence linking markets to disease outbreaks across the world, there remains a striking lack of pathogen surveillance programs that can relay timely, cost-effective, and actionable information to decision-makers to protect human and animal health. However, the strategic incorporation of environmental surveillance systems in markets coupled with novel pathogen detection strategies can create an early warning system capable of alerting us to the risk of outbreaks before they happen. Here, we explore the concept of "smart" markets that utilize continuous surveillance systems to monitor the emergence of zoonotic pathogens with spillover potential.IMPORTANCEFast detection and rapid intervention are crucial to mitigate risks of pathogen emergence, spillover and spread-every second counts. However, comprehensive, active, longitudinal surveillance systems at high-risk interfaces that provide real-time data for action remain lacking. This paper proposes "smart market" systems harnessing cutting-edge tools and a range of sampling techniques, including wastewater and air collection, multiplex assays, and metagenomic sequencing. Coupled with robust response pathways, these systems could better enable Early Warning and bolster prevention efforts.

A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects

The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.

Causes and Consequences of Coronavirus Spike Protein Variability

Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.

SARS-CoV-2 surveillance in a veterinary health system provides insight into transmission risks

OBJECTIVE

To investigate the prevalence and seropositivity of SARS-CoV-2 in companion and exotic animals in a veterinary healthcare system.

SAMPLE

A total of 341 animals were sampled by a combination of oral and nasal swabs. Serum from whole blood was collected from a subset of animals (86 canines, 25 felines, and 6 exotic animals).

METHODS

After informed owner consent, convenience samples from client-owned animals and the pets of students and staff members associated with Colorado State University's Veterinary Health System were collected between May 2021 and September 2022. Study samples were collected by trained veterinarians, Veterinary Health System staff, and veterinary students.

RESULTS

SARS-CoV-2 RNA was detected by reverse transcription PCR in 1.6% (95% CI, 0.5% to 4.6%) of domestic canines and 1.1% (95% CI, 0.2% to 6.1%) of domestic felines. No RNA was detected in any of the exotic animal species tested (n = 66). Plaque reduction neutralization tests indicated that 12.8% (95% CI, 7.3% to 21.5%) of canines and 12.0% (95% CI, 4.2% to 30.0%) of felines had neutralizing antibodies against SARS-CoV-2.

CLINICAL RELEVANCE

This study provides insight regarding SARS-CoV-2 spillover in domestic companion and exotic animals and contributes to our understanding of transmission risk in the veterinary setting.

What we can and cannot learn from SARS-CoV-2 and animals in metagenomic samples from the Huanan market

While the exact context of the emergence of SARS-CoV-2 remains uncertain, data accumulated since 2020 have provided an increasingly more precise picture of Wuhan's Huanan Seafood Wholesale Market, to which the earliest clusters of human cases of Covid-19 were linked. After the market closed on January 1st 2020, teams from the Chinese Center for Disease Control and Prevention collected environmental samples, and sequenced them. Metagenomic sequencing data from these samples were shared in early 2023. These data confirmed that non-human animals susceptible to SARS-CoV-2 were present in the market before it closed, but also that these animals were located in the side of the market with most human cases, and in a corner with comparatively more SARS-CoV-2-positive environmental samples. The environmental samples were however collected after abundant human-to-human transmission had taken place in the market, precluding any identification of a non-human animal host. Jesse Bloom recently investigated associations between SARS-CoV-2 and non-human animals, concluding that the data failed to indicate whether non-human animals were infected by SARS-CoV-2, despite this being an already acknowledged limitation of the data. Here I explain why a correlation analysis could not confidently conclude which hosts(s) may have shed SARS-CoV-2 in the market, and I rebut the suggestion that such analyses had been encouraged. I show that Bloom's investigation ignores the temporal and spatial structure of the data, which led to incorrect interpretations. Finally, I show that criteria put forward by Bloom to identify the host(s) that shed environmental SARS-CoV-2 would also exclude humans. Progress on the topic of SARS-CoV-2's origin requires a clear distinction between scientific studies and news articles (mis)interpreting them.

Public awareness of One Health in China

One Health is recognized as an increasingly important approach to global health. It has the potential to inform interventions and governance approaches to prevent future pandemics. Successfully implementing the One Health approach in policy will require active engagement from the public, which begs the question: how aware is the public of One Health? In this study, we examine the level and distribution of One Health awareness among the general public in China using a survey conducted in Beijing (n = 1820). We distinguish between awareness of the term of "One Health" versus awareness of the core set of ideas - the interconnection between the health of people, animals, and the environment. Our analysis shows that 40% of respondents reported that they have heard of the term, but more than double the number indicated that they recognize the core idea of interconnection between people, animals, and the environment. Specifically, about 83% of the respondents said that they believe people's health is closely connected to animal health and 86% believe people's health is closely connected to plant and environmental health. Multiple regression analysis indicates that women, younger people, and individuals with a higher level of education show higher levels of One Health awareness than their counterparts. Being aware of the term is associated with higher recognition of the core ideas. Policymakers and health practitioners should consider these findings when designing public awareness campaigns and educational initiatives to promote One Health principles.

The Question of the Origins of COVID-19 and the Ends of Science

Intense public interest in scientific claims about COVID-19, concerning its origins, modes of spread, evolution, and preventive and therapeutic strategies, has focused attention on the values to which scientists are assumed to be committed and the relationship between science and other public discourses. A much discussed claim, which has stimulated several inquiries and generated far-reaching political and economic consequences, has been that SARS-CoV-2 was deliberately engineered at the Wuhan Institute of Virology and then, either inadvertently or otherwise, released to the public by a laboratory worker. This has been pursued despite a clear refutation, through comprehensive genomic analysis, of the hypothesis that the virus was deliberately engineered and the failure of detailed investigations to identify any evidence in support of a laboratory leak. At the same time a substantial, established body of knowledge about the many factors underlying the emergence of novel zoonotic diseases has been largely ignored-including climate change and other mechanisms of environmental destruction, tourism, patterns of trade, and cultural influences. The existence and conduct of these debates have raised questions about the vulnerability of science to manipulation for political purposes. Scientific discourses are vulnerable because: (i) claims can be made with no more than probabilistic force; (ii) alleged "facts" are always subject to interpretation, which depends on social, ethical, and epistemological assumptions; and (iii) science and scientists are not inherently committed to any single set of values and historically have served diverse, and sometimes perverse, social and political interests. In the face of this complexity, the COVID-19 experience highlights the need for processes of ethical scrutiny of the scientific enterprise and its strategic deployment. To ensure reliability of truth claims and protection from corrupting influences robust ethical discourses are required that are independent of, and at times even contrary to, those of science itself.

The natural virome and pandemic potential: Disease X

Over the last decade, the emergence of several zoonotic viruses has demonstrated that previously unknown or neglected pathogens have the potential to cause epidemics and therefore to pose a threat to global public health. Even more concerning are the estimated 1.7 million still-undiscovered viruses present in the natural environment or 'global virome', with many of these as-yet uncharacterized viruses predicted to be pathogenic for humans. Thus, in order to mitigate disease emergence and prevent future pandemics, it is crucial to identify the global extent of viral threats to which humans may become exposed. This requires cataloguing the viruses that exist in the environment within their various and diverse host species, and also understanding the viral, host, and environmental factors that dictate the circumstances that result in viral spillover into humans. We also address here which strategies can be implemented as countermeasure initiatives to reduce the risk of emergence of new diseases.

Perspectives on research needs in healthcare epidemiology and antimicrobial stewardship: what's on the horizon - Part I

In this overview, we articulate research needs and opportunities in the field of infection prevention that have been identified from insights gained during operative infection prevention work, our own research in healthcare epidemiology, and from reviewing the literature. The 10 areas of research need are: 1) transmissions and interruptions, 2) personal protective equipment and other safety issues in occupational health, 3) climate change and other crises, 4) device, diagnostic, and antimicrobial stewardship, 5) implementation and de-implementation, 6) health care outside the acute care hospital, 7) low- and middle-income countries, 8) networking with the "neighbors", 9) novel research methodologies, and 10) the future state of surveillance. An introduction and chapters 1-5 are presented in part I of the article, and chapters 6-10 and the discussion in part II. There are many barriers to advancing the field, such as finding and motivating the future IP workforce including professionals interested in conducting research, a constant confrontation with challenges and crises, the difficulty of performing studies in a complex environment, the relative lack of adequate incentives and funding streams, and how to disseminate and validate the often very local quality improvement projects. Addressing research gaps now (i.e., in the postpandemic phase) will make healthcare systems more resilient when facing future crises.

Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots

The emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multiple drivers-landscape change, host distribution, and human exposure-associated with the risk of spillover of zoonotic SARS-like coronaviruses to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs before examining how access to healthcare varies within clusters and scenarios. We found 19 clusters with differing risk factor contributions within a single country (N = 9) or transboundary (N = 10). High-risk areas were mainly closer (11-20%) rather than far ( < 1%) from healthcare. Areas far from healthcare reveal healthcare access inequalities, especially Scenario 3, which includes wild mammals and not livestock as secondary hosts. China (N = 2) and Indonesia (N = 1) had clusters with the highest risk. Our findings can help stakeholders in land use planning, integrating healthcare implementation and One Health actions.

Relevance of national, regional and global virome projects on pandemics prediction, prevention, and control: a social network analysis of GVP-citing articles

BACKGROUND

The Global Virome Project (GVP) was proposed in 2018 as an evolution of the USAID PREDICT project and was presented as a "collaborative scientific initiative to discover zoonotic viral threats and stop future pandemics". The immediate response was mixed, with public health and scientific communities representatives showing skepticism, if not direct opposition.

OBJECTIVES

The economic, social, and health consequences of the coronavirus disease 2019 (COVID-19) pandemic demonstrated how unprepared the world was in the face of new pandemics. This paper analyses the impact of the GVP on the scientific and public health communities.

METHODS

Published scientific articles that cited the two 2018 seminal publications proposing the project were analysed using social network analysis methods.

FINDINGS

Encompassing the periods before and after the onset of the Covid-19 pandemic, the results indicate that (i) the concepts of the GVP have received more support than opposition in the scientific literature; (ii) its foundations should be updated to address the specific criticisms.

MAIN CONCLUSIONS

Shifting focus to national virome projects can provide tangible, regional benefits that can positively contribute towards a consensus on achieving a high level of preparedness for the ever-present possibility of the following global viral pandemic.

Data analysis of zoonoses notifications in Aboriginal and Torres Strait Islander populations in Australia 1996-2021: implications for One Health

Introduction

Zoonoses are a health concern for Aboriginal and Torres Strait Islander peoples in Australia that face elevated risk of disease related to the environment and animals. Internationally, One Health is encouraged to effectively manage zoonoses by taking integrated approaches involving animal, human, and environmental health sectors to improve health outcomes. However, Australia's health systems manage zoonotic diseases in animals and people separately which does not support a One Health approach. For the effective management of zoonoses, a strong evidence base and database regarding the epidemiology of zoonotic pathogens is needed. However, we currently lack this evidence limiting our understanding of the impact of zoonoses on Aboriginal and Torres Strait Islander populations.

Methods

As a first step towards building the evidence base, we undertook a descriptive analysis of Aboriginal and Torres Strait Islander zoonotic notifications in Australia from 1996 to 2021. We presented notifications as annual notification rates per 100,000 population, and percentages of notifications by state, remoteness, sex, and age group.

Results

Salmonellosis and campylobacteriosis were the most notified zoonoses with the highest annual notification rates of 99.75 and 87.46 per 100,000 population, respectively. The north of Australia (Queensland, Northern Territory and Western Australia), remote and outer regional areas, and young children (0-4 years of age) had the highest percentages of notifications.

Discussion

To our knowledge, these findings are the first national presentation of the epidemiology of zoonoses within Aboriginal and Torres Strait Islander populations. A greater understanding of transmission, prevalence and impact of zoonoses on Aboriginal and Torres Strait Islander peoples (including animal and environmental health factors) is required to inform their effective management through a One Health approach.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence

Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.

Epidemic intelligence activities among national public and animal health agencies: a European cross-sectional study

Epidemic Intelligence (EI) encompasses all activities related to early identification, verification, analysis, assessment, and investigation of health threats. It integrates an indicator-based (IBS) component using systematically collected surveillance data, and an event-based component (EBS), using non-official, non-verified, non-structured data from multiple sources. We described current EI practices in Europe by conducting a survey of national Public Health (PH) and Animal Health (AH) agencies. We included generic questions on the structure, mandate and scope of the institute, on the existence and coordination of EI activities, followed by a section where respondents provided a description of EI activities for three diseases out of seven disease models. Out of 81 gatekeeper agencies from 41 countries contacted, 34 agencies (42%) from 26 (63%) different countries responded, out of which, 32 conducted EI activities. Less than half (15/32; 47%) had teams dedicated to EI activities and 56% (18/34) had Standard Operating Procedures (SOPs) in place. On a national level, a combination of IBS and EBS was the most common data source. Most respondents monitored the epidemiological situation in bordering countries, the rest of Europe and the world. EI systems were heterogeneous across countries and diseases. National IBS activities strongly relied on mandatory laboratory-based surveillance systems. The collection, analysis and interpretation of IBS information was performed manually for most disease models. Depending on the disease, some respondents did not have any EBS activity. Most respondents conducted signal assessment manually through expert review. Cross-sectoral collaboration was heterogeneous. More than half of the responding institutes collaborated on various levels (data sharing, communication, etc.) with neighbouring countries and/or international structures, across most disease models. Our findings emphasise a notable engagement in EI activities across PH and AH institutes of Europe, but opportunities exist for better integration, standardisation, and automatization of these efforts. A strong reliance on traditional IBS and laboratory-based surveillance systems, emphasises the key role of in-country laboratories networks. EI activities may benefit particularly from investments in cross-border collaboration, the development of methods that can automatise signal assessment in both IBS and EBS data, as well as further investments in the collection of EBS data beyond scientific literature and mainstream media.

The emergence of SARS-CoV-2 lineages and associated saliva antibody responses among asymptomatic individuals in a large university community

SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)-as generated by the immune system following infection or vaccination-has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG), and ACE2 binding inhibition capacity in asymptomatic individuals between January 2021 and May 2022. These data were generated as part of a large university COVID monitoring program in Ohio, United States of America, and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA, and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees' saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data are consistent with COVID vaccines having achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.

The values and risks of an Intergovernmental Panel for One Health to strengthen pandemic prevention, preparedness, and response

The COVID-19 pandemic has shown the need for better global governance of pandemic prevention, preparedness, and response (PPR) and has emphasised the importance of organised knowledge production and uptake. In this Health Policy, we assess the potential values and risks of establishing an Intergovernmental Panel for One Health (IPOH). Similar to the Intergovernmental Panel on Climate Change, an IPOH would facilitate knowledge uptake in policy making via a multisectoral approach, and hence support the addressing of infectious disease emergence and re-emergence at the human-animal-environment interface. The potential benefits to pandemic PPR include a clear, unified, and authoritative voice from the scientific community, support to help donors and institutions to prioritise their investments, evidence-based policies for implementation, and guidance on defragmenting the global health system. Potential risks include a scope not encompassing all pandemic origins, unclear efficacy in fostering knowledge uptake by policy makers, potentially inadequate speed in facilitating response efforts, and coordination challenges among an already dense set of stakeholders. We recommend weighing these factors when designing institutional reforms for a more effective global health system.

Historical RNA expression profiles from the extinct Tasmanian tiger

Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.

Phylogenetic diversity statistics for all clades in a phylogeny

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.

One Health Surveillance Highlights Circulation of Viruses with Zoonotic Potential in Bats, Pigs, and Humans in Viet Nam

A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.

Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region

Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.

SARS-CoV-2 S Glycoprotein Stabilization Strategies

The SARS-CoV-2 pandemic has again shown that structural biology plays an important role in understanding biological mechanisms and exploiting structural data for therapeutic interventions. Notably, previous work on SARS-related glycoproteins has paved the way for the rapid structural determination of the SARS-CoV-2 S glycoprotein, which is the main target for neutralizing antibodies. Therefore, all vaccine approaches aimed to employ S as an immunogen to induce neutralizing antibodies. Like all enveloped virus glycoproteins, SARS-CoV-2 S native prefusion trimers are in a metastable conformation, which primes the glycoprotein for the entry process via membrane fusion. S-mediated entry is associated with major conformational changes in S, which can expose many off-target epitopes that deviate vaccination approaches from the major aim of inducing neutralizing antibodies, which mainly target the native prefusion trimer conformation. Here, we review the viral glycoprotein stabilization methods developed prior to SARS-CoV-2, and applied to SARS-CoV-2 S, in order to stabilize S in the prefusion conformation. The importance of structure-based approaches is highlighted by the benefits of employing stabilized S trimers versus non-stabilized S in vaccines with respect to their protective efficacy.

Pangolin merbecovirus gets down to (poly)basics

Trafficking of live mammals is considered a major risk for emergence of zoonotic viruses. SARS-CoV-2-related coronaviruses have previously been identified in pangolins, the world's most smuggled mammal. A new study identifies a MERS-related coronavirus in trafficked pangolins with broad mammalian tropism and a newly acquired furin cleavage site in Spike.