Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants

shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals

The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately labeled sampling times. Improving accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous sequences. Furthermore, while not all branches of a phylogenetic tree may exhibit a clear temporal signal, specific branches may still adhere to the assumptions, with varying evolutionary rates. Supporting a relaxed molecular clock model better aligns with the complexities of evolution. The root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic signals. Despite its utility, there remains a lack of corresponding software implementations for broader applications. To address this gap, we present shinyTempSignal, an interactive web application implemented with the shiny framework, available as an R package and publicly accessible at https://github.com/YuLab-SMU/shinyTempSignal. This tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed models. By extending the root-to-tip regression method to diverse signals, shinyTempSignal helps in the detection of evolving features or traits, thereby laying the foundation for deeper insights and subsequent analyses.

SARS-CoV-2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control

The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit SARS-CoV-2 are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse and white-tailed deer. Among farmed animals, American mink have the highest likelihood to become infected from humans or animals and further transmit SARS-CoV-2. In the EU, 44 outbreaks were reported in 2021 in mink farms in seven MSs, while only six in 2022 in two MSs, thus representing a decreasing trend. The introduction of SARS-CoV-2 into mink farms is usually via infected humans; this can be controlled by systematically testing people entering farms and adequate biosecurity. The current most appropriate monitoring approach for mink is the outbreak confirmation based on suspicion, testing dead or clinically sick animals in case of increased mortality or positive farm personnel and the genomic surveillance of virus variants. The genomic analysis of SARS-CoV-2 showed mink-specific clusters with a potential to spill back into the human population. Among companion animals, cats, ferrets and hamsters are those at highest risk of SARS-CoV-2 infection, which most likely originates from an infected human, and which has no or very low impact on virus circulation in the human population. Among wild animals (including zoo animals), mostly carnivores, great apes and white-tailed deer have been reported to be naturally infected by SARS-CoV-2. In the EU, no cases of infected wildlife have been reported so far. Proper disposal of human waste is advised to reduce the risks of spill-over of SARS-CoV-2 to wildlife. Furthermore, contact with wildlife, especially if sick or dead, should be minimised. No specific monitoring for wildlife is recommended apart from testing hunter-harvested animals with clinical signs or found-dead. Bats should be monitored as a natural host of many coronaviruses.

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

BACKGROUND

Between November 2021 and February 2022, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events.

METHODS

We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant.

FINDINGS

We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5' end of the viral genome was from the Delta genome and the 3' end from Omicron, including the majority of the spike protein gene, though the breakpoints were different.

CONCLUSIONS

Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared with the circulating Omicron lineages.

FUNDING

This research was supported by the NIH RADx initiative and by the Centers for Disease Control Contract 75D30121C12730 (Helix).

SARS-CoV-2 variants of concerns in animals: An unmonitored rising health threat

Recent findings have highlighted the urgency for rapidly detecting and characterizing SARS-CoV-2 variants of concern in companion and wild animals. The significance of active surveillance and genomic investigation on these animals could pave the way for more understanding of the viral circulation and how the variants emerge. It enables us to predict the next viral challenges and prepare for or prevent these challenges. Horrible neglect of this issue could make the COVID-19 pandemic a continuous threat. Continuing to monitor the animal-origin SARS-CoV-2, and tailoring prevention and control measures to avoid large-scale community transmission in the future caused by the virus leaping from animals to humans, is essential. The reliance on only developing vaccines with ignoring this strategy could cost us many lives. Here, we discuss the most recent data about the transmissibility of SARS-CoV-2 variants of concern (VOCs) among animals and humans.

Human coronaviruses: The emergence of SARS-CoV-2 and management of COVID-19

To date, a total of seven human coronaviruses (HCoVs) have been identified, all of which are important respiratory pathogens. Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has led to a global pandemic causing millions of infections and deaths. Here, we summarize the discovery and fundamental virology of HCoVs, discuss their zoonotic transmission and highlight the weak species barrier of SARS-CoV-2. We also discuss the possible origins of SARS-CoV-2 variants of concern identified to date and discuss the experimental challenges in characterizing mutations of interest and propose methods to circumvent them. As the COVID-19 treatment and prevention landscape rapidly evolves, we summarize current therapeutics and vaccines, and their implications on SARS-CoV-2 variants. Finally, we explore how interspecies transmission of SARS-CoV-2 may drive the emergence of novel strains, how disease severity may evolve and how COVID-19 will likely continue to burden healthcare systems globally.

Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges

Since the 20^th century, humans have lived through five pandemics caused by influenza A viruses (IAVs) (H1N1/1918, H2N2/1957, H3N2/1968, and H1N1/2009) and the coronavirus (CoV) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IAVs and CoVs both have broad host ranges and share multiple hosts. Virus co-circulation and even co-infections facilitate genetic reassortment among IAVs and recombination among CoVs, further altering virus evolution dynamics and generating novel variants with increased cross-species transmission risk. Moreover, SARS-CoV-2 may maintain long-term circulation in humans as seasonal IAVs. Co-existence and co-infection of both viruses in humans could alter disease transmission patterns and aggravate disease burden. Herein, we demonstrate how virus-host ecology correlates with the co-existence and co-infection of IAVs and/or CoVs, further affecting virus evolution and disease dynamics and burden, calling for active virus surveillance and countermeasures for future public health challenges.

Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 spike (S) protein have arisen, culminating in the spread of several variants of concern (VOCs) with various degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we used pseudoviruses that express specific SARS-CoV-2 S protein substitutions and cell lines that express angiotensin-converting enzyme 2 (ACE2) from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the ancestral prototype S at levels comparable to human ACE2. Most single S substitutions did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency. Conversely, combinatorial VOC substitutions in the S protein were associated with increased entry of pseudoviruses. Neutralizing titers in sera from various animal species were significantly reduced against pseudoviruses expressing the S proteins of Beta, Delta, or Omicron VOCs compared to the parental S protein. Especially, substitutions in the S protein of the Omicron variant significantly reduced the neutralizing titers of the sera. This study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication, and antibody-mediated viral neutralization. IMPORTANCE The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to have devastating impacts on global health and socioeconomics. The recent emergence of SARS-CoV-2 variants of concern, which contain mutations that can affect the virulence, transmission, and effectiveness of licensed vaccines and therapeutic antibodies, are currently becoming the common strains circulating in humans worldwide. In addition, SARS-CoV-2 has been shown to infect a wide variety of animal species, which could result in additional mutations of the SARS-CoV-2 virus. In this study, we investigate the effect of mutations present in SARS-CoV-2 variants of concern and determine the effects of these mutations on cell entry, virulence, and antibody neutralization activity in humans and a variety of animals that might be susceptible to SARS-CoV-2 infection. This information is essential to understand the effects of important SARS-CoV-2 mutations and to inform public policy to create better strategies to control the COVID-19 pandemic.

Social Media Efficacy in Crisis Management: Effectiveness of Non-pharmaceutical Interventions to Manage COVID-19 Challenges

The new identified virus COVID-19 has become one of the most contagious diseases in human history. The ongoing coronavirus has created severe threats to global mental health, which have resulted in crisis management challenges and international concerns related to health issues. As of September 9, 2021, there were over 223.4 million patients with COVID-19, including 4.6 million deaths and over 200 million recovered patients reported worldwide, which has made the COVID-19 outbreak one of the deadliest pandemics in human history. The aggressive public health implementations endorsed various precautionary safety and preventive strategies to suppress and minimize COVID-19 disease transmission. The second, third, and fourth waves of COVID-19 continue to pose global challenges to crisis management, as its evolution and implications are still unfolding. This study posits that examining the strategic ripostes and pandemic experiences sheds light on combatting this global emergency. This study recommends two model strategies that help reduce the adverse effects of the pandemic on the immune systems of the general population. This present paper recommends NPI interventions (non-pharmaceutical intervention) to combine various measures, such as the suppression strategy (lockdown and restrictions) and mitigation model to decrease the burden on health systems. The current COVID-19 health crisis has influenced all vital economic sectors and developed crisis management problems. The global supply of vaccines is still not sufficient to manage this global health emergency. In this crisis, NPIs are helpful to manage the spillover impacts of the pandemic. It articulates the prominence of resilience and economic and strategic agility to resume economic activities and resolve healthcare issues. This study primarily focuses on the role of social media to tackle challenges and crises posed by COVID-19 on economies, business activities, healthcare burdens, and government support for societies to resume businesses, and implications for global economic and healthcare provision disruptions. This study suggests that intervention strategies can control the rapid spread of COVID-19 with hands-on crisis management measures, and the healthcare system will resume normal conditions quickly. Global economies will revitalize scientific contributions and collaborations, including social science and business industries, through government support.

Animal models for SARS-CoV-2 infection and pathology

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiology of coronavirus disease 2019 (COVID-19) pandemic. Current variants including Alpha, Beta, Gamma, Delta, and Lambda increase the capacity of infection and transmission of SARS-CoV-2, which might disable the in-used therapies and vaccines. The COVID-19 has now put an enormous strain on health care system all over the world. Therefore, the development of animal models that can capture characteristics and immune responses observed in COVID-19 patients is urgently needed. Appropriate models could accelerate the testing of therapeutic drugs and vaccines against SARS-CoV-2. In this review, we aim to summarize the current animal models for SARS-CoV-2 infection, including mice, hamsters, nonhuman primates, and ferrets, and discuss the details of transmission, pathology, and immunology induced by SARS-CoV-2 in these animal models. We hope this could throw light to the increased usefulness in fundamental studies of COVID-19 and the preclinical analysis of vaccines and therapeutic agents.

Natural and Experimental SARS-CoV-2 Infection in Domestic and Wild Animals

SARS-CoV-2 is the etiological agent responsible for the ongoing COVID-19 pandemic, which continues to spread with devastating effects on global health and socioeconomics. The susceptibility of domestic and wild animal species to infection is a critical facet of SARS-CoV-2 ecology, since reverse zoonotic spillover events resulting in SARS-CoV-2 outbreaks in animal populations could result in the establishment of new virus reservoirs. Adaptive mutations in the virus to new animal species could also complicate ongoing mitigation strategies to combat SARS-CoV-2. In addition, animal species susceptible to SARS-CoV-2 infection are essential as standardized preclinical models for the development and efficacy testing of vaccines and therapeutics. In this review, we summarize the current findings regarding the susceptibility of different domestic and wild animal species to experimental SARS-CoV-2 infection and provide detailed descriptions of the clinical disease and transmissibility in these animals. In addition, we outline the documented natural infections in animals that have occurred at the human-animal interface. A comprehensive understanding of animal susceptibility to SARS-CoV-2 is crucial to inform public health, veterinary, and agricultural systems, and to guide environmental policies.

Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization

SARS-CoV-2 is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 Spike protein (S) have arisen in circulating viral populations, culminating in the spread of several variants of concern (VOC) with varying degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we employed lentivirus-based pseudotyped viruses that express specific SARS-CoV-2 S protein substitutions and cell lines that stably express ACE2 from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the parental (prototype Wuhan-1) S at levels comparable to human ACE2. Most single S substitutions (e.g., 452R, 478K, 501Y) did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency in viral entry. Conversely, combinatorial VOC substitutions in the S protein were associated with significantly increased entry capacity of pseudotyped viruses compared to that of the parental Wuhan-1 pseudotyped virus. Similarly, infection studies using live ancestral (USA-WA1/2020), Alpha, and Beta SARS-CoV-2 viruses in hamsters revealed a higher replication potential for the Beta variant compared to the ancestral prototype virus. Moreover, neutralizing titers in sera from various animal species, including humans, were significantly reduced by single substitutions of 484K or 452R, double substitutions of 501Y-484K, 452R-484K and 452R-478K and the triple substitution of 501Y-484K-417N, suggesting that 484K and 452R are particularly important for evading neutralizing antibodies in human, cat, and rabbit sera. Cumulatively, this study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication and antibody-mediated viral neutralization.

AUTHOR SUMMARY

Cells stably expressing ACE2 from various animals and a lentivirus-based SARS-CoV-2 pseudotyped virus assay were established to study SARS-CoV-2 cell entry. The results demonstrated that ACE2 from a wide range of animal species facilitate S-mediated virus entry into cells, which is supported by in silico data as well as natural and experimental infection studies. Pseudotyped viruses containing mutations in the RBD of S representative of the Alpha, Gamma, and especially Beta, variants of concern demonstrated that certain mutations are associated with increased viral entry compared to the parental S. The Beta variant was also observed to have a replicative advantage in vitro and in vivo compared to the prototype virus. Pseudotyped viruses containing combinatorial substitutions of 501Y-484K-417K, 614G-501Y-484K and 614G-501Y-484K-417N increased viral entry via ACE2 across multiple species. The 501Y or 478K single substitution did not significantly affect neutralizing capacity of immune sera compared to the prototype strain, but the addition of 484K or 452R substitutions significantly reduced the neutralizing titers.