Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission

Pathological findings in raccoon dogs (Nyctereutes procyonoides) in Schleswig-Holstein, Germany

Raccoon dogs (Nyctereutes procyonoides) originated from East Asia and are listed as invasive alien species of Union concern in the European Union. Apart from their potential negative impact on native fauna as predators and competitors, they are discussed as reservoirs and vectors for various infectious diseases. Between 2021 and 2022, comprehensive post-mortem examinations of 110 raccoon dogs were performed as part of a health and risk assessment study of selected invasive alien species in Schleswig-Holstein, Germany. Parasitic infections, often accompanied by eosinophilic and/or granulomatous inflammation, were one of the most common and significant findings. In total, 64% animals had an ectoparasitosis and up to 76% an endoparasitosis. Alaria alata and Trichinella spp were the most relevant endoparasite species found. Eggs of A. alata were detected in 30% of faecal samples, while the prevalence of Trichinella spp in muscle samples was 0.9%. Influenza A virus, canine distemper virus, rustrela virus, Borna disease virus 1 and severe acute respiratory syndrome corona virus 2 were not detected. Carnivore protoparvovirus 1 was detected with a prevalence of 3%, but was not associated with pathognomonic lesions. In general, most of the pathological findings were of minor significance regardless of whether pathogens were detected or not, and therefore did not appear to affect the overall health status of the examined animals. Our study shows that raccoon dogs may contribute to the spread and persistence of certain pathogens by acting as carriers of infectious diseases. This underpins the need to further investigate the risk they pose to endemic European wildlife, livestock and human health.

Detection of avian, murine, bovine, shrew, and bat coronaviruses in wild mammals from Mexico

Coronaviruses infect a wide range of animal and human hosts. Some human coronaviruses, such as SARS-CoV, MERS-CoV, and SARS-CoV-2, originated in animals, with bats often serving as ancestral hosts. This study analyzed samples from wild animals in three Mexican states, using an RT-PCR assay targeting the RdRp gene to detect and genotype coronaviruses, assessing their potential role as reservoirs. Phylogenetic analysis was conducted to determine the genetic relationships of the identified coronaviruses. Gammacoronavirus RNA was identified in fallow deer, llamas, spider monkeys, and mouflons; Betacoronavirus RNA in mouflons and dwarf goats; and Alphacoronavirus RNA in dwarf goats and ponies. The detected viral sequences exhibited high nucleotide identity with known coronaviruses, including Avian coronavirus (Gammacoronavirus), Murine coronavirus (Betacoronavirus), Betacoronavirus 1 (Betacoronavirus), Wénchéng shrew coronavirus (unclassified Alphacoronavirus), and Bat coronavirus HKU10 (Alphacoronavirus). These findings represent the first report of Avian coronavirus, Murine coronavirus, Wénchéng shrew coronavirus, and Bat coronavirus HKU10 in these species, as well as the first detection of Avian coronavirus in llamas, spider monkeys, and mouflons. This study provides valuable insights into the potential role of wildlife as coronavirus reservoirs, highlighting the importance of monitoring these viruses to mitigate future zoonotic transmission risks.

Molecular characteristics of the immune escape of coronavirus PEDV under the pressure of vaccine immunity

Coronaviruses have undergone evolutionary changes and mutations in response to the immune pressures exerted by vaccines and environmental factors, resulting in more severe consequences during breakthrough infections. Nevertheless, the specific correlation between the evolutionary mutations of coronaviruses and immune pressures remains ambiguous. Swine coronavirus-porcine epidemic diarrhea virus (PEDV)-has existed for decades. This study utilized in vivo preparation of polyclonal antibodies against the PEDV and identified critical neutralizing epitopes through serial in vitro passaging. Then, the recombinant mutated strains were successfully constructed. In vitro experiments confirmed the ability of the rA1273P strain to escape neutralization by polyclonal antibodies. Both in vitro cell studies and in vivo animal experiments revealed that the strain maintains virulence and pathogenicity while evading antibody pressure post-vaccination. The pathogenicity of the strain while evading immune pressure is comparable to wild-type strains. A comparison of the S protein gene between vaccine strains and clinical strains identified mutations in 1273 amino acid positions in clinical strains. In conclusion, this study identified a novel PEDV S protein neutralizing site under immune pressure through serial passaging, indicating that the 1,273th amino acid position is prone to mutation under prolonged antibody pressure, enhancing the virus's ability to escape hosts. This study offers new insights into the interpretation of coronavirus escape immune pressure and provides technical support for monitoring and predicting the variation and evolution of coronavirus.IMPORTANCECoronaviruses represent an ongoing public health threat because of high variability. Since 2010, the emergence of highly pathogenic porcine epidemic diarrhea virus (PEDV) strains has resulted in significant economic losses to the global pig industry. PEDV undergoes evolution and mutation under external immune pressure, rendering it an increasingly challenging target for prevention and control measures. Here, we prepared the polyclonal antibodies against PEDV and identified a novel neutralization epitope on the S protein (1,273th amino acids) through serial in vitro passaging. Furthermore, our findings indicate that the mutation of A1273P in the S protein did not alter the virulence of the PEDV but significantly enhanced its ability to escape and infect the host in vitro and in vivo. Finally, we found that the 1,273 amino acid position of the S gene has been mutated to varying degrees in clinical PEDV strains. This work provides a specific correlation between the evolutionary mutations of coronaviruses and immune pressures.

Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics

Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon usage (RSCU) of virus genomes together with other genomic properties are predictive of virus host codon fitness through tree-based machine learning. Statistical analysis on the RSCU data matrix also revealed that the wobble position of the virus codons is critically important for the host codon fitness distinction. As the trained models can well characterise the host codon fitness of the viruses, the frequency and other details stored at the leaf nodes of these models can be reliably translated into human virus codon fitness score (HVCF score) as a readout of codon fitness of any virus infecting human. Specifically, we evaluated and compared HVCF of virus genome sequences from human sources and others and evaluated HVCF of SARS-CoV-2 genome sequences from NCBI virus database, where we found no obvious shifting trend in host codon fitness towards human-non-infectious. We also developed a bioinformatics tool to simulate codon-based virus fitness shifting using codon compositions of the viruses, and we found that Tylonycteris bat coronavirus HKU4 related viruses may have close relationship with SARS-CoV-2 in terms of human codon fitness. The finding of abundant synonymous mutations in the predicted codon fitness shifting path also provides new insights for evolution research and virus monitoring in environmental surveillance.

Bats as a mixing vessel for generation of novel coronaviruses: Co-circulation and co-infection of coronaviruses and other viruses

Bats are the hosts of a wide variety of coronaviruses (CoVs) of the genera Alphacoronavirus and Betacoronavirus. The presence of more than one CoV species or strain in a single bat species greatly enhances the chance of genetic exchange among the CoVs, mainly through homologous recombination, and hence enhance the generation of novel CoV species or strains that may adapt to human or other animals and result in future epidemics. In this article, we review the evidence for co-circulation and/or co-infection of two or more CoVs in the same bat species, including co-infection with different strains of a CoV, co-circulation/co-infection of different alphaCoVs or betaCoVs, and co-circulation/co-infection of alphaCoVs and betaCoVs together. With next-generation sequencing, there has been a recent explosion of such discoveries. It is anticipated that countless more similar findings will be made in the near future.

Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion

Coronaviruses express their structural and accessory genes via a set of subgenomic RNAs, whose synthesis is directed by transcription regulatory sequences (TRSs) in the 5' genomic leader and upstream of each body open reading frame. In SARS-CoV-2, the TRS has the consensus AAACGAAC; upon searching for emergence of this motif in the global SARS-CoV-2 sequences, we find that it evolves frequently, especially in the 3' end of the genome. We show well-supported examples upstream of the Spike gene-within the nsp16 coding region of ORF1b-which is expressed during human infection, and upstream of the canonical Envelope gene TRS, both of which have evolved convergently in multiple lineages. The most frequent neo-TRS is within the coding region of the Nucleocapsid gene, and is present in virtually all viruses from the B.1.1 lineage, including the variants of concern Alpha, Gamma, Omicron and descendants thereof. Here, we demonstrate that this TRS leads to the expression of a novel subgenomic mRNA encoding a truncated C-terminal portion of Nucleocapsid, which is an antagonist of type I interferon production and contributes to viral fitness during infection. We observe distinct phenotypes when the Nucleocapsid coding sequence is mutated compared to when the TRS alone is ablated. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level.

Origin and cross-species transmission of bat coronaviruses in China

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 589 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Recombination across distant coronavirid species and genera is a rare event with distinct genomic features

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; family Coronaviridae, genus Betacoronavirus, subgenus Sarbecovirus) has caused millions of deaths, prompting a need for better understanding of coronavirid emergence and spillover to humans. As an evaluation of how some features of SARS-CoV-2, unique among sarbecoviruses, may have been acquired from related viruses, we conducted phylogenetic and recombination analyses to compare the frequency of recombination among coronavirids across vs within genera, subgenera, and species. Among known betacoronaviruses, we identified 199 (183 intraspecies, 16 interspecies, but no intersubgenera) recombination events. Phylogenetic analyses revealed that the ancestry of interspecies events was limited and less prone to affect 5' regions of coronavirid genome open reading frame 1 (ORF1) than intraspecies events. On the contrary, interspecies events were significantly more prone to impact the 3' end (ORF6-ORF8 and the nucleocapsid protein [N] ORF), suggesting the existence of region-specific constraints on recombination. This work substantiated that recombination among betacoronaviruses is limited by the genome similarity between their parental viruses. We conclude that SARS-CoV-2 likely acquired unique features through recombination with closely related circulating sarbecoviruses (most likely from the same species) that co-existed geographically.

IMPORTANCE

Understanding the evolutionary events that led to SARS-CoV-2 emergence, spillover, and spread is crucial to prevent, or at least be prepared for, the same type of occurrence in the future. Given that SARS-CoV-2 has some characteristics not found in other closely related viruses, we aimed to systematically assess how likely these unique features may have been acquired through recombination. We found that, although recombination is a frequent phenomenon among betacoronaviruses, it is mostly limited to closely related members of the same species. Therefore, we conclude that the most likely scenario involved feature acquisition from recombination with a closely related virus that was circulating in a geographically overlapping area or through a different biological process, but not recombination from a virus of a different species, genus, or subgenus.

Novel coronaviruses and mammarenaviruses of hedgehogs from Russia including the comparison of viral communities of hibernating and active specimens

Introduction

Small mammals, especially rodents and bats, are known reservoirs of zoonotic viruses, but little is known about the viromes of insectivorous species including hedgehogs (order Eulipotyphla), which often live near human settlements and come into contact with humans.

Methods

We used high-throughput sequencing and metaviromic analysis to describe the viromes of 21 hedgehogs (Erinaceus sp.) sampled from summer 2022 to spring 2023. We captured 14 active animals from the wild (seven in European Russia and the other seven in Central Siberia). The remaining 7 animals were hibernating in captivity (captured in European Russia before the experiment).

Results and discussion

The diversity of identified viral taxa as well as the total number of reads classified as viral was high in all active animals (up to eight different viral families per animal), but significantly lower in hibernating animals (zero or no more than three different viral families per animal). The present study reports, for the first time, betacoronaviruses and mammasrenaviruses in hedgehogs from Russia. Erinaceus coronaviruses (EriCoVs) were found in 4 of 7 active animals captured in the wild, in European Russia, making it is the easiest finding of EriCoVs in Europe. One animal was found to carry of two different EriCoVs. Both strains belong to the same phylogenetic clade as other coronaviruses from European hedgehogs. Pairwise comparative analysis suggested that one of these two strains arose by recombination with an unknown coronavirus, since all of identified SNPs (n = 288) were found only in the local genome region (the part of ORF1b and S gene). The novel mammarenaviruses (EriAreVs) were detected in 2 out of 7 active and in 2 out of 7 hibernating animals from the European Russia. Several complete L and S segments of EriAreVs were assembled. All identified EriAreVs belonged to the same clade as the recently described MEMV virus from Hungarian hedgehogs. As the hibernating hedgehogs were positive for EriAreVs when kept in controlled conditions without contact with each other, we suggest the possibility of persistent arenavirus infection in hedgehogs, but further experiments are needed to prove this.

Electron microscopy images and morphometric data of SARS-CoV-2 variants in ultrathin plastic sections

Conventional thin section electron microscopy of viral pathogens, such as the pandemic SARS-CoV-2, can provide structural information on the virus particle phenotype and its evolution. We recorded about 900 transmission electron microscopy images of different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron BA.2 (B.1.1.529) and determined various morphometric parameters, such as maximal diameter and spike number, using a previously published measurement method. The datasets of the evolved virus variants were supplemented with images and measurements of the early SARS-CoV-2 isolates Munich929 and Italy-INMI1 to allow direct comparison. Infected Vero cell cultures were cultivated under comparable conditions to produce the viruses for imaging and morphometric analysis. The images and measurements can be used as a basis to analyse the morphometric changes of further evolving viruses at the particle level or for developing automated image processing workflows and analysis.

Genomic characterization and cross-species transmission potential of hedgehog coronavirus

In the 21st century, three betacoronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have emerged in humans worldwide as a result of animal spillover, causing severe respiratory infections and resulting in more than seven million deaths. In 2013, a novel Betacoronavirus closely related to MERS-CoV (Betacoronavirus cameli) was discovered in European hedgehogs (Erinaceus europaeus), raising questions on the possibility of hedgehog-to-human transmission. Hence, the present study aimed to investigate and characterize the presence and genetic diversity of coronaviruses in hedgehogs from Portugal, as well as their potential for cross-species transmission. To achieve this, fecal samples from 110 hedgehogs at two recovery centers and one environmental non-governmental organization were tested for coronaviruses using a broad-spectrum nested RT-PCR assay targeting the RdRp gene. Of these samples, 24.5 % tested positive, most belonging to the Betacoronavirus genus. However, the present study also reports, for the first time, Alphacoronaviruses in hedgehogs, showing 100 % identity with a Bat coronavirus (a variant of Alphacoronavirus miniopteri). The genome sequencing of one betacoronavirus-positive sample yielded 65 % of a full-length genome, with the closest homology (93.5 %) to Betacoronavirus erinacei from the United Kingdom. Computational protein-protein docking studies predicted the binding affinity between the spike protein of hedgehog coronavirus and cell receptors of mammal species that interact with hedgehogs. The results obtained raise the question of whether hedgehog CoV uses the same receptor as MERS-CoV or a different receptor to enter host cells. Thus, this study enhances our understanding of the epidemiology of coronaviruses, emphasizing the need for further investigation into cross-species transmission risks.

Two fitness inference schemes compared using allele frequencies from 1068 391 sequences sampled in the UK during the COVID-19 pandemic

Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population genetics theory but with different assumptions. One approach, tQLE, features an epistatic fitness landscape and assumes that alleles are nearly in linkage equilibrium. Another approach, MPL, assumes a simple, additive fitness landscape, but allows for any level of correlation between alleles. We characterized differences in the distributions of fitness values inferred by each approach and in the ranks of fitness values that they assign to sequences across time. We find that in a large fraction of weeks the two methods are in good agreement as to their top-ranked sequences, i.e. as to which sequences observed that week are most fit. We also find that agreement between the ranking of sequences varies with genetic unimodality in the population in a given week.

Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus

There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and Embecovirus-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major Embecovirus member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.IMPORTANCEThe Betacoronavirus subgenus Embecovirus contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.

SARS-CoV-2 replication and drug discovery

The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.

COVID-19 mutations: An overview

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.

Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic

The global prevalence of the XBB lineage presents a formidable challenge posed by the recombinant SARS-CoV-2 virus. The understanding of SARS-CoV-2's recombination preference assumes utmost significance in predicting future recombinant variants and adequately preparing for subsequent pandemics. Thus, an urgent need arises to establish a comprehensive landscape concerning SARS-CoV-2 recombinants worldwide and elucidate their evolutionary mechanisms. However, the initial step, involving the detection of potential recombinants from a vast pool of over 10 million sequences, presents a significant obstacle. In this study, we present CovRecomb, a lightweight methodology specifically designed to effectively identify and dissect interlineage SARS-CoV-2 recombinants. Leveraging CovRecomb, we successfully detected 135,567 putative recombinants across the entirety of 14.5 million accessed SARS-CoV-2 genomes. These putative recombinants could be classified into 1451 distinct recombination events, of which 206 demonstrated transmission spanning multiple countries, continents, or globally. Hotspot regions were identified in six specific areas, with prominence observed in the latter halves of the N-terminal domain and receptor-binding domain within the spike (S) gene. Epidemiological investigations revealed extensive recombination events occurring among different SARS-CoV-2 (sub)lineages, independent of lineage prevalence frequencies.

Cellular dynamics shape recombination frequency in coronaviruses

Coronavirus genomes have evolutionary histories shaped extensively by recombination. Yet, how often recombination occurs at a cellular level, or the factors that regulate recombination rates, are poorly understood. Utilizing experimental co-infections with pairs of genetically distinct coronaviruses, we found that recombination is both frequent and rare during coinfection. Recombination occurred in every instance of co-infection yet resulted in relatively few recombinant RNAs. By integrating a discrete-time Susceptible-Infected-Removed (SIR) model, we found that rates of recombination are determined primarily by rates of cellular co-infection, rather than other possible barriers such as RNA compartmentalization. By staggering the order and timing of infection with each virus we also found that rates of co-infection are themselves heavily influenced by genetic and ecological mechanisms, including superinfection exclusion and the relative fitness of competing viruses. Our study highlights recombination as a potent yet regulated force: frequent enough to ensure a steady influx of genetic variation but also infrequent enough to maintain genomic integrity. As recombination is thought to be an important driver of host-switching and disease emergence, our study provides new insights into the factors that regulate coronavirus recombination and evolution more broadly.

Emergence of crucial evidence catalyzing the origin tracing of SARS-CoV-2

Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), its genetic and geographical origins remain unclear, resulting in suspicions about its natural origin. In one of our previous studies, we reported the presence of a furin cleavage site RRAR in the junction region between S1 and S2 subunits of the spike protein, which was discovered as the first crucial clue for the origin tracing of SARS-CoV-2. In the present study, we conducted an integrative analysis of new genome data from bat Sarbecovirus strains reported after the COVID-19 outbreak. The primary results included the identification of BANAL-20-52, Rp22DB159, and S18CXBatR24 as three close relatives of SARS-CoV-2 and the successful detection of seven out of nine key genomic features (designated as RC0-7 and ORF8) observed in wild types of SARS-CoV-2 in the three close relatives from Laos, Vietnam, and Yunnan province of China, respectively. The most significant contribution of the present study lies in the detection of RC1 in wild genotype in a bat Sarbecovirus population BANAL-20-52 belonging to. Encoding a segment of the NSP3 protein, RC1 was discovered as the second crucial clue for the origin tracing of SARS-CoV-2. Although RC0, encoding the junction furin cleavage site, remains undetected outside of the SARS-CoV-2 genome, Feuang of Laos is the sole place where eight of the nine wild-type features (RC1-7 and ORF8) have been detected.

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

Several coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversification versus recent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus-host codiversification have been largely over-estimated.

Structural basis for mouse receptor recognition by bat SARS2-like coronaviruses

The animal origin of SARS-CoV-2 remains elusive, lacking a plausible evolutionary narrative that may account for its emergence. Its spike protein resembles certain segments of BANAL-236 and RaTG13, two bat coronaviruses considered possible progenitors of SARS-CoV-2. Additionally, its spike contains a furin motif, a common feature of rodent coronaviruses. To explore the possible involvement of rodents in the emergence of SARS-CoV-2 spike, we examined the crystal structures of the spike receptor-binding domains (RBDs) of BANAL-236 and RaTG13 each complexed with mouse receptor ACE2. Both RBDs have residues at positions 493 and 498 that align well with two virus-binding hotspots on mouse ACE2. Our biochemical evidence supports that both BANAL-236 and RaTG13 spikes can use mouse ACE2 as their entry receptor. These findings point to a scenario in which these bat coronaviruses may have coinfected rodents, leading to a recombination of their spike genes and a subsequent acquisition of a furin motif in rodents, culminating in the emergence of SARS-CoV-2.

Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2

The SARS-CoV-2 Spike glycoprotein (S) utilizes a unique trimeric conformation to interact with the ACE2 receptor on host cells, making it a prime target for inhibitors that block viral entry. We have previously identified a novel proteinaceous cavity within the Spike protein homotrimer that could serve as a binding site for small molecules. However, it is not known whether these molecules would inhibit, stimulate, or have no effect on viral replication. To address this, we employed structural-based screening to identify small molecules that dock into the trimer cavity and assessed their impact on viral replication. Our findings show that a cohort of identified small molecules binding to the Spike trimer cavity effectively reduces the replication of various SARS-CoV-2 variants. These molecules exhibited inhibitory effects on B.1 (European original, D614G, EDB2) and B.1.617.2 (δ) variants, while showing moderate activity against the B.1.1.7 (α) variant. We further categorized these molecules into distinct groups based on their structural similarities. Our experiments demonstrated a dose-dependent viral replication inhibitory activity of these compounds, with some, like BCC0040453 exhibiting no adverse effects on cell viability even at high concentrations. Further investigation revealed that pre-incubating virions with compounds like BCC0031216 at different temperatures significantly inhibited viral replication, suggesting their specificity towards the S protein. Overall, our study highlights the inhibitory impact of a diverse set of chemical molecules on the biological activity of the Spike protein. These findings provide valuable insights into the role of the trimer cavity in the viral replication cycle and aid drug discovery programs aimed at targeting the coronavirus family.

Genomic Context of SARS-CoV-2 Outbreaks in Farmed Mink in Spain during Pandemic: Unveiling Host Adaptation Mechanisms

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.

Structural basis for raccoon dog receptor recognition by SARS-CoV-2

Since the COVID-19 outbreak, raccoon dogs have been suggested as a potential intermediary in transmitting SARS-CoV-2 to humans. To understand their role in the COVID-19 pandemic and the species barrier for SARS-CoV-2 transmission to humans, we analyzed how their ACE2 protein interacts with SARS-CoV-2 spike protein. Biochemical data showed that raccoon dog ACE2 is an effective receptor for SARS-CoV-2 spike protein, though not as effective as human ACE2. Structural comparisons highlighted differences in the virus-binding residues of raccoon dog ACE2 compared to human ACE2 (L24Q, Y34H, E38D, T82M, R353K), explaining their varied effectiveness as receptors for SARS-CoV-2. These variations contribute to the species barrier that exists between raccoon dogs and humans regarding SARS-CoV-2 transmission. Identifying these barriers can help assess the susceptibility of other mammals to SARS-CoV-2. Our research underscores the potential of raccoon dogs as SARS-CoV-2 carriers and identifies molecular barriers that affect the virus's ability to jump between species.

Serial passage of PDCoV in cell culture reduces its pathogenicity and its damage of gut microbiota homeostasis in piglets

Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that mainly causes diarrhea in suckling piglets, and also has the potential for cross-species transmission. However, there are still no commercial vaccines available to prevent and control PDCoV infection. In this study, PDCoV strain HNZK-02 was serially propagated in vitro for up to 150 passages and the amino acid changes have mainly occurred in the S protein during serial passage which caused structure change. PDCoV HNZK-02-passage 5 (P5)-infected piglets exhibited acute and severe watery diarrhea, an obvious intestinal damage, while the piglets infected with PDCoV HNZK-02-P150 showed no obvious clinical signs, weak intestinal lesions, and lower viral loads in rectal swabs and various tissues. Compared with the PDCoV HNZK-02-P5 infection, HNZK-02-P150 infection resulted in a decrease in intestinal mucosal permeability and pro-inflammatory cytokines. Moreover, PDCoV HNZK-02-P5 infection had significantly reduced bacterial diversity and increased relative abundance of opportunistic pathogens, while PDCoV HNZK-02-P150 infection did not significantly affect the bacterial diversity, and the relative abundance of probiotics increased. Furthermore, the alterations of gut microbiota were closely related to the change of pro-inflammatory factor. Metagenomics prediction analysis demonstrated that HNZK-02-P150 modulated the tyrosine metabolism, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, and lipopolysaccharide biosynthesis, which coincided with lower inflammatory response and intestinal permeability in the piglets infected with HNZK-02-P150. In conclusion, the PDCoV HNZK-02 was successfully attenuated by serial passage in vitro, and the changes of S gene, metabolic function, and gut microbiota may contribute to the attenuation. The PDCoV HNZK-02-P150 may have the potential for developing live-attenuated vaccine.IMPORTANCEPorcine deltacoronavirus (PDCoV) is an enteropathogen causing severe diarrhea, dehydration, and death in nursing piglets, devastating great economic losses for the global swine industry, and has cross-species transmission and zoonotic potential. There are currently no approved treatments or vaccines available for PDCoV. In addition, gut microbiota has an important relationship with the development of many diseases. Here, the PDCoV virulent HNZK-02 strain was successfully attenuated by serial passage on cell cultures, and the pathogenesis and effects on the gut microbiota composition and metabolic function of the PDCoV HNZK-02-P5 and P150 strains were investigated in piglets. We also found the genetic changes in the S protein during passage in vitro and the gut microbiota may contribute to the pathogenesis of PDCoV, while their interaction molecular mechanism would need to be explored further.

The Nucleocapsid Protein of SARS-CoV-2, Combined with ODN-39M, Is a Potential Component for an Intranasal Bivalent Vaccine with Broader Functionality

Despite the rapid development of vaccines against COVID-19, they have important limitations, such as safety issues, the scope of their efficacy, and the induction of mucosal immunity. The present study proposes a potential component for a new generation of vaccines. The recombinant nucleocapsid (N) protein from the SARS-CoV-2 Delta variant was combined with the ODN-39M, a synthetic 39 mer unmethylated cytosine-phosphate-guanine oligodeoxynucleotide (CpG ODN), used as an adjuvant. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive, cell-mediated immunity (CMI). In turn, this combination was able to induce anti-N IgA in the lungs, which, along with the specific IgG in sera and CMI in the spleen, was cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N + ODN-39M preparation, combined with RBD Delta protein, enhanced the local and systemic immune response against RBD, with a neutralizing capacity. Results make the N + ODN-39M preparation a suitable component for a future intranasal vaccine with broader functionality against Sarbecoviruses.

A novel recombination porcine epidemic diarrhea virus isolated from Gansu, China: Genetic characterization and pathogenicity

Porcine epidemic diarrhea virus (PEDV) is an acute and highly contagious porcine enteric coronavirus. It has caused serious economic losses of pig industry in China. Here we insolated a current PEDV field strain named GS2022, analyzed the characters of genetic variation and pathogenicity. The results demonstrated that the GS2022 strain was belong to a newly defined subgroup G2 d, forming an independent branch which mainly contains strains isolated in China from 2017 to 2023. Notably, there are multiple mutations and extensive N-glycosylation compared to CV777 strain and PT-P5 strain, therefore the structure of GS2022 strain is different from 6U7K and 7W6M. Animal pathogenicity test showed that GS2022 strain could cause severe clinical signs and the high level of virus shedding in 7-day-old piglets. But recovery of diarrhea after 5 days, and no pathological damage to important organs. Further study on 3-day-old piglets also indicated GS2022 strain have pathogenicity. In this study no piglets died, which make it possible for that GS2022 strain become a candidate vaccine. These results are helpful to understand the epidemiology, molecular characteristics, evolution, and antigenicity of PEDV circulating in China. It also provides reference for designing effective vaccines against PEDV.

Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.

Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination

Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.

Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing

Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and CCMV. Intra-segmental crosses were more frequent than the inter-segmental ones. Most intra-segmental junctions carried short insertions/deletions (indels) and caused frameshift mutations. The mutation hotspots clustered mainly within the open reading frames. Substitutions of various lengths were also identified, whereas a small fraction of crosses occurred between viral and their host RNAs. Our data reveal that the virions can package detectable amounts of multivariate recombinant RNAs, contributing to the flexible nature of the viral genomes.

Rapid, Multispecies Detection of SARS-CoV-2 Antibodies via a Meta-Surface Plasmon Resonance Biosensor

Public health concerns have been raised by numerous reports of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and its variations infecting a range of animals. Wildlife reservoirs may facilitate the evolution of viral types capable of causing human infection in the future. Therefore, epidemiological monitoring of animals in close contact with humans is necessary. Yet, infection symptoms are not obvious in most animals, which leads to a short nucleic acid test-detection period and limits the application of this method in animals. The use of virus- and pseudovirus-based neutralizing antibody detection techniques is restricted to establishments with elevated biosafety standards. Traditional enzyme-linked immunosorbent assays (ELISA) do not offer multispecies detection and are time-consuming and labor-intensive. This work developed a polyethyleneimine-gold nanoparticle meta-surface plasmon resonance biosensor system-based multispecies SARS-CoV-2 antibody detection platform that is fast, sensitive, has a high throughput, and is fully automated. The test can be done in 30 min and specificity is up to 100% for detection in cats, dogs, and minks. Moreover, the coincidence rate was up to 99.36% (313/315) for the detection of pseudovirus in clinical and immune sera. Additionally, this method's detection sensitivity in cat, dog, and mink serum is 2,048, 1,024, and 4,096 times, which is much better than indirect ELISA and comparable to indirect immunofluorescence assays. An efficient method for COVID-19 epidemiology screening in animal serum will be made available by this platform.

Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2

SARS-CoV-2 can infect human cells through the recognition of the human angiotensin-converting enzyme 2 receptor. This affinity is given by six amino acid residues located in the variable loop of the receptor binding domain (RBD) within the Spike protein. Genetic recombination involving bat and pangolin Sarbecoviruses, and natural selection have been proposed as possible explanations for the acquisition of the variable loop and these amino acid residues. In this study we employed Bayesian phylogenetics to jointly reconstruct the phylogeny of the RBD among human, bat and pangolin Sarbecoviruses and detect recombination events affecting this region of the genome. A recombination event involving RaTG13, the closest relative of SARS-CoV-2 that lacks five of the six residues, and an unsampled Sarbecovirus lineage was detected. This result suggests that the variable loop of the RBD didn't have a recombinant origin and the key amino acid residues were likely present in the common ancestor of SARS-CoV-2 and RaTG13, with the latter losing five of them probably as the result of recombination.

Virus-Receptor Interactions and Receptor-Mediated Virus Entry into Host Cells

The virus particles described in the previous chapters of this book are vehicles that transmit the viral genome and the infection from cell to cell. To initiate the infective cycle, the viral genome must therefore translocate from the viral particle to the cell cytoplasm. Via distinct proteins or motifs in their outermost shell, the particles of animal viruses or bacteriophages attach initially to specific receptors on the host cell surface. These viral receptors thus mediate penetration of the viral genome inside the cell, where the intracellular infective cycle starts. The presence of these receptors on the cell surface is a principal determinant of virus-host tropism. Viruses can use diverse types of molecules to attach to and enter into cells. In addition, virus-receptor recognition can evolve over the course of an infection, and viral variants with distinct receptor-binding specificities and tropism can appear. The identification of viral receptors and the characterization of virus-receptor interactions have been major research goals in virology. In this chapter, we will describe, from a structural perspective, several virus-receptor interactions and the active role of receptor molecules in virus cell entry.

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

BACKGROUND

The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell entry, immunoevasion, and pathological progression.

METHODS

This in silico study is focused on designing sequence specific siRNA molecules as a tool for silencing the non-structural and accessory genes of the virus. The gene sequences of NSP3, 4, and 6 along with ORF3a, 6, 7a, 8, and 10 were retrieved for conservation, phylogenetic, and sequence logo analyses. siRNA candidates were predicted using siDirect 2.0 targeting these genes. The GC content, melting temperatures, and various validation scores were calculated. Secondary structures of the guide strands and siRNA-target duplexes were predicted. Finally, tertiary structures were predicted and subjected to structural validations.

RESULTS

This study revealed that NSP3, 4, and 6 and accessory genes ORF3a, 6, 7a, 8, and 10 have high levels of conservation across globally circulating SARS-CoV-2 strains. A total of 71 siRNA molecules were predicted against the selected genes. Following rigorous screening including binary validations and minimum free energies, final siRNAs with high therapeutic potential were identified, including 7, 2, and 1 against NSP3, NSP4, and NSP6, as well as 3, 1, 2, and 1 targeting ORF3a, ORF7a, ORF8, and ORF10, respectively.

CONCLUSION

Our novel in silico pipeline integrates effective methods from previous studies to predict and validate siRNA molecules, having the potential to inhibit viral replication pathway in vitro. In total, this study identified 17 highly specific siRNA molecules targeting NSP3, 4, and 6 and accessory genes ORF3a, 7a, 8, and 10 of SARS-CoV-2, which might be used as an additional antiviral treatment option especially in the cases of life-threatening urgencies.

Genomic Mutations in SARS-CoV-2 Genome following Infection in Syrian Golden Hamster and Associated Lung Pathologies

The continuous evolution of the SARS-CoV-2 virus led to constant developments and efforts in understanding the significance and impacts of SARS-CoV-2 variants on human health. Our study aimed to determine the accumulation of genetic mutations and associated lung pathologies in male and female hamsters infected with the ancestral Wuhan strain of SARS-CoV-2. The present study showed no significant difference in the viral load between male and female hamsters and peak infection was found to be on day four post infection in both sexes of the animals. Live virus particles were detected up to 5 days post infection (dpi) through the TCID-50 assay, while qRT-PCR could detect viral RNA up to 14 dpi from all the infected animals. Further, the determination of the neutralizing antibody titer showed the onset of the humoral immune response as early as 4 dpi in both sexes against SARS-CoV-2, and a significant cross-protection against the delta variant of SARS-CoV-2 was observed. Histopathology showed edema, inflammation, inflammatory cell infiltration, necrosis, and degeneration of alveolar and bronchial epithelium cells from 3 dpi to 14 dpi in both sexes. Furthermore, next-generation sequencing (NGS) showed up to 10 single-nucleotide polymorphisms (SNPs) in the SARS-CoV-2 (ancestral Wuhan strain) genome isolated from both male and female hamsters. The mutation observed at the 23014 position (Glu484Asp) in the SARS-CoV-2 genome isolated from both sexes of the hamsters plays a significant role in the antiviral efficacy of small molecules, vaccines, and the Mabs-targeting S protein. The present study shows that either of the genders can be used in the pre-clinical efficacy of antiviral agents against SARS-CoV-2 in hamsters. However, considering the major mutation in the S protein, the understanding of the genetic mutation in SARS-CoV-2 after passing through hamsters is crucial in deciding the efficacy of the antiviral agents targeting the S protein. Importance: Our study findings indicate the accumulation of genomic mutations in SARS-CoV-2 after passing through the Syrian golden hamsters. Understanding the genomic mutations showed that either of the hamster genders can be used in the pre-clinical efficacy of antiviral agents and vaccines.

Menstrual irregularities associated with COVID-19 vaccines among women in Saudi Arabia: A survey during 2022

Some changes appeared in women's menstrual cycle after receiving the coronavirus disease 2019 (COVID-19) vaccine, but the information about the pattern and characteristics of these symptoms was unclear. This study was conducted to estimate the prevalence of menstruation change and evaluate the association between COVID-19 vaccination and the occurrence of such disturbance. An online web-based survey was conducted during March-April 2022 that targeted 729 COVID-19 vaccinated women aged between 18 and 45 years in the Jazan region of Kingdom of Saudi Arabia. The tool collected demographic information, psychological data, and COVID-19 post-vaccination side effects. The overall prevalence of menstrual change among the women was 60.9% (95% CI 57.3-64.4). 66.3% and 64.1% of women, respectively, in the age group of 25-34 and 35-45 years were more affected. Most of the detected abnormalities were related to delayed menstruation and changes in pain intensity. Menstrual disturbances that occur after immunization are transient and have no long-term implications. Menstrual disorders are prevalent before vaccination, but there is a considerable increase following vaccination. Because there is no apparent cause for these post-vaccine disturbances, and their effects are difficult to anticipate, it is preferable to warn those concerned and encourage them to learn more about the biological changes causing these problems.

From Emergence to Endemicity: A Comprehensive Review of COVID-19

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), later renamed coronavirus disease 2019 (COVID-19), was first identified in Wuhan, China, in early December 2019. Initially, the China office of the World Health Organization was informed of numerous cases of pneumonia of unidentified etiology in Wuhan, Hubei Province at the end of 2019. This would subsequently result in a global pandemic with millions of confirmed cases of COVID-19 and millions of deaths reported to the WHO. We have analyzed most of the data published since the beginning of the pandemic to compile this comprehensive review of SARS-CoV-2. We looked at the core ideas, such as the etiology, epidemiology, pathogenesis, clinical symptoms, diagnostics, histopathologic findings, consequences, therapies, and vaccines. We have also included the long-term effects and myths associated with some therapeutics of COVID-19. This study presents a comprehensive assessment of the SARS-CoV-2 virology, vaccines, medicines, and significant variants identified during the course of the pandemic. Our review article is intended to provide medical practitioners with a better understanding of the fundamental sciences, clinical treatment, and prevention of COVID-19. As of May 2023, this paper contains the most recent data made accessible.

Analysis of codon usage patterns of porcine enteric alphacoronavirus and its host adaptability

Porcine enteric alphacoronavirus (PEAV) is a newly emerging swine enteropathogen that poses a threat to the swine industry. To understand the PEAV genome evolution, we performed a comprehensive analysis of the codon usage patterns in fifty-nine PEAV strains currently available. Phylogenetic analysis showed that PEAV can be divided into six lineages. Effective number of codons analysis demonstrated that the PEAV genome exhibits a low codon usage bias (CUB). Nucleotide composition analysis indicated that the PEAV genome has the most abundant nucleotide U content, with GC content (39.37% ± 0.08%) much lower than AU content (60.63% ± 0.08%). Neutrality and effective number of codons plot analyses suggested that natural selection rather than mutation pressure dominates the CUB of PEAV. Host adaptation analysis revealed that PEAV fits the codon usage pattern of non-human primates, humans and mice better than that of pigs. Our data enriches information on PEAV evolution, host adaptability, and cross-species transmission.

History, origin, transmission, genome structure, replication, epidemiology, pathogenesis, clinical features, diagnosis, and treatment of COVID-19: A review

In December, 2019, pneumonia triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surfaced in Wuhan, China. An acute respiratory illness named coronavirus disease 2019 (COVID-19) is caused by a new coronavirus designated as SARS-CoV-2. COVID-19 has surfaced as a major pandemic in the 21st century as yet. The entire world has been affected by this virus. World Health Organization proclaimed COVID-19 pandemic as a public health emergency of international concern on January 30, 2020. SARS-CoV-2 shares the same genome as coronavirus seen in bats. Therefore, bats might be its natural host of this virus. It primarily disseminates by means of the respiratory passage. Evidence revealed human-to-human transmission. Fever, cough, tiredness, and gastrointestinal illness are the manifestations in COVID-19-infected persons. Senior citizens are more vulnerable to infections which can lead to dangerous consequences. Various treatment strategies including antiviral therapies are accessible for the handling of this disease. In this review, we organized the most recent findings on COVID-19 history, origin, transmission, genome structure, replication, epidemiology, pathogenesis, clinical features, diagnosis, and treatment strategies.

Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission

Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.

Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere

Bats, recognized as considerable reservoirs for coronaviruses (CoVs), serve as natural hosts for several highly pathogenic CoVs, including SARS-CoV and SARS-CoV-2. Investigating the bat CoV community provides insights into the origin for highly pathogenic CoVs and highlights bat CoVs with potential spillover risks. This study probes the evolution, recombination, host range, geographical distribution, and cross-species transmission characteristics of bat CoVs across China and its associated CoVs in other regions. Through detailed research on 13,064 bat samples from 14 provinces of China, 1141 CoV strains are found across 10 subgenera and one unclassified Alpha-CoV, generating 399 complete genome sequences. Within bat CoVs, 11 new CoV species are identified and 425 recombination events are detected. Bats in southern China, particularly in Yunnan province, exhibit a pronounced diversity of CoVs. Limited sampling and low detection rates exist for CoVs in Myotacovirus, Nyctacovirus, Hibecovirus, Nobecovirus in China. The genus Myotis is highlighted as a potential ancestral host for Alpha-CoV, with the genus Hipposideros suggested as a likely progenitor host for bat-associated Beta-CoV, indicating the complexity of cross-species transmission dynamics. Through the comprehensive analysis, this study enriches the understanding of bat CoVs and offers a valuable resource for future research.

Secure reversal of immune evasion from refractory NSCLC and highly contagious CoV-2 mutants by using 3D-engineered multifunctional biologics

There is an imperative choice to develop a secure feasible strategy to address evasion dynamics of refractory tumors and SARS-CoV-2-variants, while stem cell-based protocol may be more reliable as its unique ability for resetting multifunctional immunity to address progressive tumor and the constantly-evolving virus. In this study, spheroid-embryonoid stem cells from mature somatic cells were engineered as multifunctional biologics (3D-E/BSC) and inoculated in senile rhesus to identify secure potential against immune-evasion from viral-variants. Meanwhile, a cohort of eligible patients with stage IV NSCLC were approved for phase I clinical trials. Subsequently, long-lasting security and efficacy were validated by primate and clinical trials (p < 0.01) in that it could not only stimulate serological immunity, but also reset core immunity for hosts to address variant evasion after 3D-E/BSC withdrawal. Particularly, illustrated by single-cell evolving trajectory, 3D-E/BSC had securely reset senile thymus of aging hosts to remodel core immunity by rearranging naive rhythm to evolve TRGC2+/JCHAIN+NKT clusters to abolish tumoral and viral evasion dynamics with path-feedbacks of NSCLC and COVID-19 simultaneously activated, leading to continuous blockade of breakthrough infection of viral-mutants and long-term survival in one-third of terminal patients without adjuvant required. Our study may pioneer a practical multifunctional strategy to eliminate evasion of SARS-CoV-2 variants and refractory NSCLC so as for victims to restart a new life-equation.

The mRNA Vaccine Revolution: COVID-19 Has Launched the Future of Vaccinology

During the COVID-19 pandemic, mRNA (mRNA) vaccines emerged as leading vaccine candidates in a record time. Nonreplicating mRNA (NRM) and self-amplifying mRNA (SAM) technologies have been developed into high-performing and clinically viable vaccines against a range of infectious agents, notably SARS-CoV-2. mRNA vaccines demonstrate efficient in vivo delivery, long-lasting stability, and nonexistent risk of infection. The stability and translational efficiency of in vitro transcription (IVT)-mRNA can be further increased by modulating its structural elements. In this review, we present a comprehensive overview of the recent advances, key applications, and future challenges in the field of mRNA-based vaccinology.

Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype

Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.

Identification, Isolation, and Molecular Characterization of Betacoronavirus in Oryx leucoryx

Coronaviruses (CoVs) are enveloped viruses with a large RNA genome (26 to 32 kb) and are classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. CoV infections cause respiratory, enteric, and neurologic disorders in mammalian and avian species. In 2019, Oryx leucoryx animals suffered from severe hemorrhagic diarrhea and high morbidity rates. Upon initial diagnosis, we found that the infected animals were positive for coronavirus by pancoronavirus reverse transcriptase RT-PCR. Next, we detected the presence of CoV particles in these samples by electron microscopy and immunohistochemistry. CoV was isolated and propagated on the HRT-18G cell line, and its full genome was sequenced. Full-genome characterization and amino acid comparisons of this viral agent demonstrated that this virus is an evolutionarily distinct Betacoronavirus belonging to the subgenus Embecovirus and the Betacoronavirus 1 species. Furthermore, we found that it is most similar to the subspecies dromedary camel coronavirus HKU23 by phylogenetic analysis. Here, we present the first report of isolation and characterization of Betacoronavirus associated with enteric disease in Oryx leucoryx. IMPORTANCE CoVs cause enteric and respiratory infections in humans and animal hosts. The ability of CoVs to cross interspecies barriers is well recognized, as emphasized by the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The identification of novel CoV strains and surveillance of CoVs in both humans and animals are relevant and important to global health. In this study, we isolated and characterized a newly identified Betacoronavirus that causes enteric disease in a wild animal, Oryx leucoryx (the Arabian oryx). This work is the first report describing CoV infection in Oryx leucoryx and provides insights into its origin.

Recombination between coronaviruses and synthetic RNAs and biorisk implications motivated by a SARS-CoV-2 FCS origin controversy

The urgent need for improved policy, regulation, and oversight of research with potential pandemic pathogens (PPPs) has been widely acknowledged. A 2022 article in Frontiers in Virology raises questions, reporting on a 100% sequence homology between the SARS-CoV-2 furin cleavage site (FCS) and the negative strand of a 2017 patented sequence. Even though Ambati and collaborators suspect a possible inadvertent or intentional cause leading to the FCS insert, the related underpinnings have not been studied from the perspective of potential biorisk policy gaps. A commentary on their article contests the low coincidence likelihood that was calculated by Ambati et al., arguing that the sequence match could have been a chance occurrence alone. Additionally, it has been suggested that the odds of the recombination event may be low. These considerations seem to have put many speculations related to any implied viral beginnings, notably from a research setting likely outside the Wuhan Institute of Virology, to rest. However, potential implications for future disasters in terms of biosafety and biosecurity have not been addressed. To demonstrate the feasibility of the Ambati et al. postulate, a theoretical framework is developed that substantially extends the research orientations implicated by these authors and the related patent. It is argued that specific experimental conditions, in combination, could significantly increase the implied recombination profile between coronaviruses and synthetic RNAs. Consequently, this article scrutinizes these largely unrecognized vulnerabilities to discuss implications across the spectrum of the biological risk landscape, with special attention to a potential "crime harvest." Focusing on insufficiently understood features of interaction between the natural and man-made world, vulnerabilities related to contaminants, camouflaging, and various misuse potentials fostered by the digitization and computerization of synthetic biology, it highlights novel biorisk gaps not covered by existing PPP policy. Even though this work does not aim to provide proof of the viral origin, it will make the point that, in theory, a convergence of under-appreciated lab experiments and technologies could have led to the SARS-CoV-2 FCS insert, which analogously could be exploited by various threat actors for the clandestine genesis of similar or even worse pathogens.

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection

BACKGROUND

Accessory proteins have diverse roles in coronavirus pathobiology. One of them in SARS-CoV (the causative agent of the severe acute respiratory syndrome outbreak in 2002-2003) is encoded by the open reading frame 8 (ORF8). Among the most dramatic genomic changes observed in SARS-CoV isolated from patients during the peak of the pandemic in 2003 was the acquisition of a characteristic 29-nucleotide deletion in ORF8. This deletion cause splitting of ORF8 into two smaller ORFs, namely ORF8a and ORF8b. Functional consequences of this event are not entirely clear.

RESULTS

Here, we performed evolutionary analyses of ORF8a and ORF8b genes and documented that in both cases the frequency of synonymous mutations was greater than that of nonsynonymous ones. These results suggest that ORF8a and ORF8b are under purifying selection, thus proteins translated from these ORFs are likely to be functionally important. Comparisons with several other SARS-CoV genes revealed that another accessory gene, ORF7a, has a similar ratio of nonsynonymous to synonymous mutations suggesting that ORF8a, ORF8b, and ORF7a are under similar selection pressure.

CONCLUSIONS

Our results for SARS-CoV echo the known excess of deletions in the ORF7a-ORF7b-ORF8 complex of accessory genes in SARS-CoV-2. A high frequency of deletions in this gene complex might reflect recurrent searches in "functional space" of various accessory protein combinations that may eventually produce more advantageous configurations of accessory proteins similar to the fixed deletion in the SARS-CoV ORF8 gene.

The coronavirus recombination pathway

Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.

A Tale of Two Proteases: MPro and TMPRSS2 as Targets for COVID-19 Therapies

Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (MPro) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral MPro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel MPro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.