Seasonal human coronavirus NL63 epidemics in children in Guilin, China, reveal the emergence of a new subgenotype of HCoV-NL63.

Introduction: Seasonal human coronavirus NL63 (HCoV-NL63) is a frequently encountered virus linked to mild upper respiratory infections. However, its potential to cause more severe or widespread disease remains an area of concern. This study aimed to investigate a rare localized epidemic of HCoV-NL63-induced respiratory infections among pediatric patients in Guilin, China, and to understand the viral subtype distribution and genetic characteristics. Methods: In this study, 83 pediatric patients hospitalized with acute respiratory infections and positive for HCoV-NL63 were enrolled. Molecular analysis was conducted to identify the viral subgenotypes and to assess genetic variations in the receptor-binding domain of the spiking protein. Results: Among the 83 HCoV-NL63-positive children, three subgenotypes were identified: C4, C3, and B. Notably, 21 cases exhibited a previously unreported subtype, C4. Analysis of the C4 subtype revealed a unique amino acid mutation (I507L) in the receptor-binding domain of the spiking protein, which was also observed in the previously reported C3 genotype. This mutation may suggest potential increases in viral transmissibility and pathogenicity. Discussion: The findings of this study highlight the rapid mutation dynamics of HCoV-NL63 and its potential for increased virulence and epidemic transmission. The presence of a unique mutation in the C4 subtype, shared with the C3 genotype, raises concerns about the virus's evolving nature and its potential public health implications. This research contributes valuable insights into the understanding of HCoV-NL63's epidemiology and pathogenesis, which is crucial for effective disease prevention and control strategies. Future studies are needed to further investigate the biological significance of the observed mutation and its potential impact on the virus's transmissibility and pathogenicity.

Evidence for cross-species transmission of human coronavirus OC43 through bioinformatics and modeling infections in porcine intestinal organoids.

Cross-species transmission of coronaviruses has been continuously posing a major challenge to public health. Pigs, as the major animal reservoirs for many zoonotic viruses, frequently mediate viral transmission to humans. This study comprehensively mapped the relationship between human and porcine coronaviruses through in-depth bioinformatics analysis. We found that human coronavirus OC43 and porcine coronavirus PHEV share a close phylogenetic relationship, evidenced by high genomic homology, similar codon usage patterns and comparable tertiary structure in spike proteins. Inoculation of infectious OC43 viruses in organoids derived from porcine small and large intestine demonstrated that porcine intestinal organoids (pIOs) are highly susceptible to human coronavirus OC43 infection and support infectious virus production. Using transmission electron microscopy, we visualized OC43 viral particles in both intracellular and extracellular compartments, and observed abnormalities of multiple organelles in infected organoid cells. Robust OC43 infections in pIOs result in a significant reduction of organoids viability and widespread cell death. This study bears essential implications for better understanding the evolutionary origin of human coronavirus OC43, and provides a proof-of-concept for using pIOs as a model to investigate cross-species transmission of human coronavirus.

Covid's cold cousins.

Four largely ignored coronaviruses circulate in humans without causing great harm and may portend the future for SARS-CoV-2.

The role of lysosomes as intermediates in betacoronavirus PHEV egress from nerve cells.

IMPORTANCE: Betacoronaviruses, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and mouse hepatitis virus (MHV), exploit the lysosomal exocytosis pathway for egress. However, whether all betacoronaviruses members use the same pathway to exit cells remains unknown. Here, we demonstrated that porcine hemagglutinating encephalomyelitis virus (PHEV) egress occurs by Arl8b-dependent lysosomal exocytosis, a cellular egress mechanism shared by SARS-CoV-2 and MHV. Notably, PHEV acidifies lysosomes and activates lysosomal degradative enzymes, while SARS-CoV-2 and MHV deacidify lysosomes and limit the activation of lysosomal degradative enzymes. In addition, PHEV release depends on V-ATPase-mediated lysosomal pH. Furthermore, this is the first study to evaluate ßCoV using lysosome for spreading through the body, and we have found that lysosome played a critical role in PHEV neural transmission and brain damage caused by virus infection in the central nervous system. Taken together, different betacoronaviruses could disrupt lysosomal function differently to exit cells.

Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States.

IMPORTANCE: Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.

Global patterns of phylogenetic diversity and transmission of bat coronavirus.

Bats are reservoirs for multiple coronaviruses (CoVs). However, the phylogenetic diversity and transmission of global bat-borne CoVs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat CoV RdRp gene sequences to study the phylogenetic diversity and transmission of bat-borne CoVs and the underlying driving factors. We found that host-switching events occurred more frequently for α-CoVs than for ß-CoVs, and the latter was highly constrained by bat phylogeny. Bat species in the families Molossidae, Rhinolophidae, Miniopteridae, and Vespertilionidae had larger contributions to the cross-species transmission of bat CoVs. Regions of eastern and southern Africa, southern South America, Western Europe, and Southeast Asia were more frequently involved in cross-region transmission events of bat CoVs than other regions. Phylogenetic and geographic distances were the most important factors limiting CoV transmission. Bat taxa and global geographic hotspots associated with bat CoV phylogenetic diversity were identified, and bat species richness, mean annual temperature, global agricultural cropland, and human population density were strongly correlated with the phylogenetic diversity of bat CoVs. These findings provide insight into bat CoV evolution and ecological transmission among bat taxa. The identified hotspots of bat CoV evolution and transmission will guide early warnings of bat-borne CoV zoonotic diseases.

Perfil epidemiológico de óbitos decorrentes da Covid-19 em um município do sudoeste do Paraná / Epidemiological profile of death resulting from Covid-19 in a municipality in southwest of Paraná / Perfil epidemiológico de las muertes por Covid-19 en un municipio del suroeste de Paraná

Introdução: No final do ano de 2019 surgiu na China uma doença infectocontagiosa de característica respiratória e alto grau de disseminação até então desconhecida. No Brasil o primeiro caso de Covid-19 foi confirmado no final de fevereiro de 2020 e a primeira morte em meados de março. Segundo dados da plataforma Coronavírus Brasil, em 17 de março de 2021, houve registro de 11.603.535 casos confirmados e 282.127 óbitos. Objetivo: Descrever o perfil de pessoas que morreram tendo como causa básica do óbito a Covid-19, em um município do Sudoeste do Paraná, entre os anos de 2020 e 2021. Metodologia: Trata-se de um estudo transversal, descritivo, documental de caráter quantitativo que foi realizado na prefeitura municipal de Francisco Beltrão. Resultados: Houve prevalência de óbitos em pacientes do sexo masculino, idosos, com presença de alguma comorbidade associada, sendo hipertensão a mais citada (50,8%). Os sintomas mais prevalentes foram tosse (74,4%), dispneia (56,3%) e saturação < 95% (48,3%), necessitando ainda de hospitalização em algum período da doença (94,1%), sendo os leitos de Sistema Único de Saúde os mais procurados (74,4%). Quanto à taxa de ocupação 49,6% dos casos necessitou apenas de leitos de enfermaria e 42% unidades de terapia intensiva. Discussão: Diversas pesquisas apontam que o sexo masculino é o mais acometido por condições graves de saúde, devido à demora na busca de assistência médica. No que se refere à idade, neste estudo, a prevalência de óbitos se deu entre 71 e 75 anos (15,1%) o que justifica que o envelhecimento é um fator de risco elevado para complicações da doença. Durante a análise dos dados, notou- se que grande parte dos pacientes que tiveram como desfecho o óbito, possuíam algum fator associado, dentre os mais citados, verificou-se a Hipertensão Arterial Sistêmica (50,8%) Diabetes Mellitus (24,8%), doenças cardiovasculares (23,9%) e obesidade (14,7%). No que diz respeito à hospitalização, nesse estudo notou-se que 74,4% da amostra foram hospitalizadas em leitos de SUS, 18,5% em hospitais particulares e 7,1% não possuíam essa informação. Conclusão: É possível observar a importância do estudo epidemiológico para identificar o perfil da população em risco, podendo auxiliar no planejamento do atendimento, rastreamento e controle da doença, além de conhecer a evolução da patologia, a fim de buscar ações adequadas para seu enfrentamento.

Introduction: At the end of 2019, a previously unknown infectious disease with respiratory characteristics and a high degree of dissemination emerged in China. In Brazil the first case of Covid-19 was confirmed in late February 2020 and the first death in mid-March. According to data from the Coronavirus Brazil platform, as of March 17, 2021, 11,603,535 confirmed cases and 282,127 deaths were recorded. Objective: To describe the profile of people who died with Covid-19 as the underlying cause of death in a city in southwestern Paraná between the years 2020 and 2021. Methodology: This is a cross-sectional, descriptive, documental, quantitative study carried out at the Francisco Beltrão City Hall. Results: There was a prevalence of deaths in male patients, elderly, with the presence of some associated comorbidity, hypertension being the most cited (50.8%). The most prevalent symptoms were cough (74.4%), dyspnea (56.3%) and saturation < 95% (48.3%), requiring hospitalization in some period of the disease (94.1%), and the Unified Health System beds were the most sought (74.4%). As for the occupancy rate, 49.6% of the cases required only ward beds and 42% intensive care units. Discussion: Several studies show that men are the most affected by serious health conditions, due to the delay in seeking medical assistance. Regarding age, in this study, the prevalence of deaths was between 71 and 75 years (15.1%), which justifies that aging is a high risk factor for disease complications. During data analysis, it was noted that most patients who died had some associated factor, among the most cited were systemic arterial hypertension (50.8%), diabetes mellitus (24.8%), cardiovascular diseases (23.9%) and obesity (14.7%). Regarding hospitalization, in this study it was noted that 74.4% of the sample were hospitalized in SUS beds, 18.5% in private hospitals, and 7.1% did not have this information. Conclusion: It is possible to observe the importance of the epidemiological study to identify the profile of the population at risk, which can help in planning care, tracking and control of the disease, besides knowing the evolution of the pathology in order to seek appropriate actions for its confrontation

Introducción: A finales del año 2019 apareció en China una enfermedad infecto- contagiosa de característica respiratoria y alto grado de diseminación desconocida hasta entonces. En Brasil se confirmó el primer caso de Covid-19 a finales de febrero de 2020 y la primera muerte a mediados de marzo. Según los datos de la plataforma Coronavirus Brasil, hasta el 17 de marzo de 2021, había 11.603.535 casos confirmados y 282.127 muertes. Objetivo: Describir el perfil de las personas fallecidas con Covid-19 como causa subyacente de muerte en una ciudad del sudoeste de Paraná entre los años 2020 y 2021. Metodología: Se trata de un estudio transversal, descriptivo, documental de carácter cuantitativo que se realizó en la prefectura municipal de Francisco Beltrão. Resultados: Hubo una prevalencia de muertes en pacientes masculinos, de edad avanzada, con presencia de alguna comorbilidad asociada, siendo la hipertensión la más citada (50,8%). Los síntomas más prevalentes fueron la tos (74,4%), la disnea (56,3%) y la saturación < 95% (48,3%), requiriendo hospitalización en algún periodo de la enfermedad (94,1%), siendo las camas del Sistema Único de Salud las más solicitadas (74,4%). En cuanto a la tasa de ocupación, el 49,6% de los casos sólo necesitaban camas de sala y el 42% unidades de cuidados intensivos. Discusión: Varias investigaciones señalan que el género masculino es el más afectado por las condiciones de salud graves, debido al retraso en la búsqueda de asistencia médica. En cuanto a la edad, en este estudio, la prevalencia de muertes se produjo entre los 71 y los 75 años (15,1%), lo que justifica que el envejecimiento sea un factor de riesgo elevado para las complicaciones de la enfermedad. Durante el análisis de los datos, se observó que la mayoría de los pacientes que fallecieron tenían algún factor asociado, entre los más citados estaban la Hipertensión Arterial Sistémica (50,8%), la Diabetes Mellitus (24,8%), las enfermedades cardiovasculares (23,9%) y la obesidad (14,7%). En lo que respecta a la hospitalización, en este estudio se observó que el 74,4% de la muestra estaba hospitalizada en camas del SUS, el 18,5% en hospitales privados y el 7,1% no tenía esta información. Conclusión: Es posible observar la importancia del estudio epidemiológico para identificar el perfil de la población en riesgo, pudiendo ayudar en la planificación de la atención, el rastreo y el control de la enfermedad, además de conocer la evolución de la patología, con el fin de buscar las acciones adecuadas para su enfrentamiento.

Wildlife susceptibility to infectious diseases at global scales.

Disease transmission prediction across wildlife is crucial for risk assessment of emerging infectious diseases. Susceptibility of host species to pathogens is influenced by the geographic, environmental, and phylogenetic context of the specific system under study. We used machine learning to analyze how such variables influence pathogen incidence for multihost pathogen assemblages, including one of direct transmission (coronaviruses and bats) and two vector-borne systems (West Nile Virus [WNV] and birds, and malaria and birds). Here we show that this methodology is able to provide reliable global spatial susceptibility predictions for the studied host-pathogen systems, even when using a small amount of incidence information (i.e., [Formula: see text] of information in a database). We found that avian malaria was mostly affected by environmental factors and by an interaction between phylogeny and geography, and WNV susceptibility was mostly influenced by phylogeny and by the interaction between geographic and environmental distances, whereas coronavirus susceptibility was mostly affected by geography. This approach will help to direct surveillance and field efforts providing cost-effective decisions on where to invest limited resources.

A Novel Pathway for Porcine Epidemic Diarrhea Virus Transmission from Sows to Neonatal Piglets Mediated by Colostrum.

The mechanisms of colostrum-mediated virus transmission are difficult to elucidate because of the absence of experimental animal models and the difficulties in tissue sample collection from mothers in the peripartum period. Porcine epidemic diarrhea virus (PEDV) is a reemerging enteropathogenic coronavirus that has catastrophic impacts on the global pig industry. PEDV primarily infects neonatal piglets by multiple routes, especially 1- to 2-day-old neonatal piglets. Here, our epidemiological investigation and animal challenge experiments revealed that PEDV could be vertically transmitted from sows to neonatal piglets via colostrum, and CD3+ T cells in the colostrum play an important role in this process. The results showed that PEDV colonizing the intestinal epithelial cells (IECs) of orally immunized infected sows could be transferred to CD3+ T cells located just beneath the IECs. Next, PEDV-carrying CD3+ T cells, with the expression of integrin α4ß7 and CCR10, migrate from the intestine to the mammary gland through blood circulation. Arriving in the mammary gland, PEDV-carrying CD3+ T cells could be transported across mammary epithelial cells (MECs) into the lumen (colostrum), as illustrated by an autotransfusion assay and an MECs/T coculture system. The PEDV-carrying CD3+ T cells in colostrum could be interspersed between IECs of neonatal piglets, causing intestinal infection via cell-to-cell contact. Our study demonstrates for the first time that colostrum-derived CD3+ T cells comprise a potential route for the vertical transmission of PEDV. IMPORTANCE The colostrum represents an important infection route for many viruses. Here, we demonstrate the vertical transmission of porcine epidemic diarrhea virus (PEDV) from sows to neonatal piglets via colostrum. PEDV colonizing the intestinal epithelial cells could transfer the virus to CD3+ T cells located in the sow intestine. The PEDV-carrying CD3+ T cells in the sow intestine, with the expression of integrin α4ß7 and CCR10, arrive at the mammary gland through blood circulation and are transported across mammary epithelial cells into the lumen, finally leading to intestinal infection via cell-to-cell contact in neonatal piglets. Our study not only demonstrates an alternative route of PEDV infection but also provides an animal model of vertical transmission of human infectious disease.

Porcine Epidemic Diarrhea Virus Infection Disrupts the Nasal Endothelial Barrier To Favor Viral Dissemination.

Crossing the endothelium from the entry site and spreading in the bloodstream are crucial but obscure steps in the pathogenesis of many emerging viruses. Previous studies confirmed that porcine epidemic diarrhea virus (PEDV) caused intestinal infection by intranasal inoculation. However, the role of the nasal endothelial barrier in PEDV translocation remains unclear. Here, we demonstrated that PEDV infection causes nasal endothelial dysfunction to favor viral dissemination. Intranasal inoculation with PEDV compromised the integrity of endothelial cells (ECs) in nasal microvessels. The matrix metalloproteinase 7 (MMP-7) released from the PEDV-infected nasal epithelial cells (NECs) contributed to the destruction of endothelial integrity by degrading the tight junctions, rather than direct PEDV infection. Moreover, the proinflammatory cytokines released from PEDV-infected NECs activated ECs to upregulate ICAM-1 expression, which favored peripheral blood mononuclear cells (PBMCs) migration. PEDV could further exploit migrated cells to favor viral dissemination. Together, our results reveal the mechanism by which PEDV manipulates the endothelial dysfunction to favor viral dissemination and provide novel insights into how coronavirus interacts with the endothelium. IMPORTANCE The endothelial barrier is the last but vital defense against systemic viral transmission. Porcine epidemic diarrhea virus (PEDV) can cause severe atrophic enteritis and acute viremia. However, the mechanisms by which the virus crosses the endothelial barrier and causes viremia are poorly understood. In this study, we revealed the mechanisms of endothelial dysfunction in PEDV infection. The viral infection activates NECs and causes the upregulation of MMP-7 and proinflammatory cytokines. Using NECs, ECs, and PBMCs as in vitro models, we determined that the released MMP-7 contributed to the destruction of endothelial barrier, and the released proinflammatory cytokines activated ECs to facilitate PBMCs migration. Moreover, the virus further exploited the migrated cells to promote viral dissemination. Thus, our results provide new insights into the mechanisms underlying endothelial dysfunction induced by coronavirus infection.

Two novel human coronavirus OC43 genotypes circulating in hospitalized children with pneumonia in China.

HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.

Feed or feed transport as a potential route for a porcine epidemic diarrhoea outbreak in a 10,000-sow breeding herd in Mexico.

Porcine epidemic diarrhoea virus (PEDV) infects pigs of all ages causing vomiting and diarrhoea. PEDV is transmitted via the oral-faecal route, and a very low dose is enough to infect susceptible pigs, resulting in significant production losses. This short communication aims to describe the introduction of PEDV into a 10,000-sow farrow-to-wean farm located in northwest Mexico. Following the onset of clinical signs, an outbreak investigation was conducted to determine the most probable route of introduction. Based on data collected from interviews, construction of a timeline of events, and the detection of PEDV RNA in feed samples and samples collected from various surfaces of feed transport vehicles, it was concluded that the most probable route for PEDV incursion into this breeding herd was contaminated feed or a contaminated feed transport vehicle. This paper describes how feed or feed transport could serve as potential routes of PEDV infection to a farm and highlights the importance of establishing biosecurity programs to mitigate these risks.

How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology.

We hypothesized that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, including generating reduced susceptibility in children. To determine what the prepandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 y of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.8 y (95% CI 6.3 to 8.1) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.

Interspecies Jumping of Bat Coronaviruses.

In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.

SDAV, the Rat Coronavirus-How Much Do We Know about It in the Light of Potential Zoonoses.

Sialodacryoadenitis virus (SDAV) is known to be an etiological agent, causing infections in laboratory rats. Until now, its role has only been considered in studies on respiratory and salivary gland infections. The scant literature data, consisting mainly of papers from the last century, do not sufficiently address the topic of SDAV infections. The ongoing pandemic has demonstrated, once again, the role of the Coronaviridae family as extremely dangerous etiological agents of human zoonoses. The ability of coronaviruses to cross the species barrier and change to hosts commonly found in close proximity to humans highlights the need to characterize SDAV infections. The main host of the infection is the rat, as mentioned above. Rats inhabit large urban agglomerations, carrying a vast epidemic threat. Of the 2277 existing rodent species, 217 are reservoirs for 66 zoonotic diseases caused by viruses, bacteria, fungi, and protozoa. This review provides insight into the current state of knowledge of SDAV characteristics and its likely zoonotic potential.

Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5.

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential.