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1.
Viruses ; 13(7)2021 07 11.
Artículo en Inglés | MEDLINE | ID: mdl-34372544

RESUMEN

Porcine deltacoronavirus (PDCoV), a highly transmissible intestinal pathogen, causes mild to severe clinical symptoms, such as anorexia, vomiting and watery diarrhea, in piglets and/or sows. Since the first report of PDCoV infection in Hong Kong in 2012, the virus has readily disseminated to North America and several countries in Asia. However, to date, no unified phylogenetic classification system has been developed. To fill this gap, we classified historical PDCoV reference strains into two major genogroups (G-I and G-II) and three subgroups (G-II-a, G-II-b and G-II-c). In addition, no genetic research on the whole PDCoV genome or spike gene has been conducted on isolates from Taiwan so far. To delineate the genetic characteristics of Taiwanese PDCoV, we performed whole-genome sequencing to decode the viral sequence. The PDCoV/104-553/TW-2015 strain is closely related to the G-II-b group, which is mainly composed of PDCoV variants from China. Additionally, various mutations in the Taiwanese PDCoV (104-553/TW-2015) strain might be linked to the probability of recombination with other genogroups of PDCoVs or other porcine coronaviruses. These results represent a pioneering phylogenetic characterization of the whole genome of a PDCoV strain isolated in Taiwan in 2015 and will potentially facilitate the development of applicable preventive strategies against this problematic virus.


Asunto(s)
Deltacoronavirus/clasificación , Deltacoronavirus/genética , Porcinos/virología , Animales , Coronavirus/genética , Infecciones por Coronavirus/virología , Diarrea/genética , Diarrea/virología , Heces/virología , Filogenia , Enfermedades de los Porcinos/virología , Taiwán , Secuenciación Completa del Genoma/métodos
2.
Avian Dis ; 65(3): 364-372, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34427409

RESUMEN

We previously reported that recombinant Newcastle disease virus LaSota (rLS) expressing infectious bronchitis virus (IBV) Arkansas (Ark)-type trimeric spike (S) ectodomain (Se; rLS/ArkSe) provides suboptimal protection against IBV challenge. We have now developed rLS expressing chicken granulocyte-macrophage colony-stimulating factor (GMCSF) and IBV Ark Se in an attempt to enhance vaccine effectiveness. In the current study, we first compared protection conferred by vaccination with rLS/ArkSe and rLS/ArkSe.GMCSF. Vaccinated chickens were challenged with virulent Ark, and protection was determined by clinical signs, viral load, and tracheal histomorphometry. Results showed that coexpression of GMCSF and the Se from rLS significantly reduced tracheal viral load and tracheal lesions compared with chickens vaccinated with rLS/ArkSe. In a second experiment, we evaluated enhancement of cross-protection of a Massachusetts (Mass) attenuated vaccine by priming or boosting with rLS/ArkSe.GMCSF. Vaccinated chickens were challenged with Ark, and protection was evaluated. Results show that priming or boosting with the recombinant virus significantly increased cross-protection conferred by Mass against Ark virulent challenge. Greater reductions of viral loads in both trachea and lachrymal fluids were observed in chickens primed with rLS/ArkSe.GMCSF and boosted with Mass. Consistently, Ark Se antibody levels measured with recombinant Ark Se protein-coated ELISA plates 14 days after boost were significantly higher in these chickens. Unexpectedly, the inverse vaccination scheme, that is, priming with Mass and boosting with the recombinant vaccine, proved somewhat less effective. We concluded that a prime and boost strategy by using rLS/ArkSe.GMCSF and the worldwide ubiquitous Mass attenuated vaccine provides enhanced cross-protection. Thus, rLS/GMCSF coexpressing the Se of regionally relevant IBV serotypes could be used in combination with live Mass to protect against regionally circulating IBV variant strains.


Asunto(s)
Infecciones por Coronavirus/veterinaria , Factor Estimulante de Colonias de Granulocitos y Macrófagos/inmunología , Virus de la Bronquitis Infecciosa/inmunología , Virus de la Enfermedad de Newcastle/genética , Enfermedades de las Aves de Corral/prevención & control , Glicoproteína de la Espiga del Coronavirus/inmunología , Animales , Anticuerpos Antivirales/inmunología , Pollos/genética , Pollos/inmunología , Pollos/virología , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/prevención & control , Infecciones por Coronavirus/virología , Protección Cruzada , Expresión Génica , Factor Estimulante de Colonias de Granulocitos y Macrófagos/administración & dosificación , Factor Estimulante de Colonias de Granulocitos y Macrófagos/genética , Virus de la Bronquitis Infecciosa/química , Virus de la Bronquitis Infecciosa/genética , Virus de la Bronquitis Infecciosa/fisiología , Virus de la Enfermedad de Newcastle/metabolismo , Enfermedades de las Aves de Corral/inmunología , Enfermedades de las Aves de Corral/virología , Dominios Proteicos , Glicoproteína de la Espiga del Coronavirus/administración & dosificación , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/genética , Tráquea/inmunología , Tráquea/virología , Vacunación , Vacunas Atenuadas/administración & dosificación , Vacunas Atenuadas/genética , Vacunas Atenuadas/inmunología , Carga Viral
3.
Biosensors (Basel) ; 11(8)2021 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-34436052

RESUMEN

Cell-based assays are a valuable tool for examination of virus-host cell interactions and drug discovery processes, allowing for a more physiological setting compared to biochemical assays. Despite the fact that cell-based SPR assays are label-free and thus provide all the associated benefits, they have never been used to study viral growth kinetics and to predict drug antiviral response in cells. In this study, we prove the concept that the cell-based SPR assay can be applied in the kinetic analysis of the early stages of viral infection of cells and the antiviral drug activity in the infected cells. For this purpose, cells immobilized on the SPR slides were infected with human coronavirus HCov-229E and treated with hydroxychloroquine. The SPR response was measured at different time intervals within the early stages of infection. Methyl Thiazolyl Tetrazolium (MTT) assay was used to provide the reference data. We found that the results of the SPR and MTT assays were consistent, and SPR is a reliable tool in investigating virus-host cell interaction and the mechanism of action of viral inhibitors. SPR assay was more sensitive and accurate in the first hours of infection within the first replication cycle, whereas the MTT assay was not so effective. After the second replication cycle, noise was generated by the destruction of the cell layer and by the remnants of dead cells, and masks useful SPR signals.


Asunto(s)
Antivirales/uso terapéutico , Coronavirus Humano 229E/fisiología , Infecciones por Coronavirus/tratamiento farmacológico , Hidroxicloroquina/uso terapéutico , Resonancia por Plasmón de Superficie/métodos , Animales , Antivirales/farmacología , Chlorocebus aethiops , Coronavirus Humano 229E/efectos de los fármacos , Coronavirus Humano 229E/aislamiento & purificación , Infecciones por Coronavirus/patología , Infecciones por Coronavirus/virología , Humanos , Hidroxicloroquina/farmacología , Cinética , Índice de Severidad de la Enfermedad , Células Vero
4.
Avian Dis ; 65(1): 40-45, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-34339120

RESUMEN

We performed viral metagenomics analysis of Japanese quail affected with enteritis to elucidate the viral etiology. Metagenomics generated 21,066,442 sequence reads via high-throughput sequencing, with a mean length of 136 nt. Enrichment in viral sequences suggested that at least three viruses were present in quail samples. Coronavirus and picornavirus were identified and are known as pathogens causing quail enteritis that match the observed morphology. Abundant reads of coronavirus from quail samples yielded four fragment sequences exhibiting six genomes of avian coronavirus. Sequence analysis showed that this quail coronavirus was related to turkey coronavirus and chicken infectious bronchitis virus. Quail picornavirus 8177 bp in size was identified and was similar to the QPV1/HUN/01 virus detected in quails without clinical symptoms in Hungary with 84.6% nucleotide and 94.6% amino acid identity. Our results are useful for understanding the genetic diversity of quail viruses. Further studies must be performed to determine whether quail coronavirus and quail picornavirus are pathogens of the digestive tract of quails.


Asunto(s)
Infecciones por Coronavirus/veterinaria , Coronavirus/genética , Coturnix/virología , Enteritis/veterinaria , Metagenómica/métodos , Enfermedades de las Aves de Corral/virología , Animales , Coronavirus/aislamiento & purificación , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Enteritis/epidemiología , Enteritis/virología , Genoma Viral , Picornaviridae/aislamiento & purificación , Infecciones por Picornaviridae/epidemiología , Infecciones por Picornaviridae/veterinaria , Infecciones por Picornaviridae/virología , Enfermedades de las Aves de Corral/epidemiología , República de Corea/epidemiología
5.
Avian Dis ; 65(1): 188-197, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-34339139

RESUMEN

Infectious bronchitis virus (IBV) causes significant losses in the poultry industry throughout the world. Here we characterize the lesions of infectious bronchitis (IB) and IBV prevalence and identify the circulating strains in small flocks in California. Backyard chickens (BYCs) submitted to the Davis (Northern California; NorCal) and San Bernardino (Southern California; SoCal) branches of the California Animal Health and Food Safety Laboratory System from January through March 2019 were included in the study. Trachea, kidney, and cecal tonsils were collected for real-time reverse transcriptase (qRT)-PCR, histology, immunohistochemistry (IHC), and sequence analysis. A total of 50 chickens out of 169 submissions tested positive for IBV by qRT-PCR. Of these, 16% (20/123) were from NorCal and 65% (30/46) from SoCal laboratory. The cecal tonsil was the most frequently positive tissue by qRT-PCR and IHC. Lymphoplasmacytic tracheitis was the most frequent histopathologic finding in 24 of 39 birds, while the kidney showed interstitial nephritis, tubular necrosis, tubular dilation, and/or gout in 14 of 43 chickens. Infectious bronchitis virus played a primary role or a synergistic effect in the mortality of chickens that succumbed to other infectious diseases. The sequences of IBV detected in 22 birds were analyzed, and 14 strains were most similar to CA1737. One strain each matched Conn46, Cal99, and ArkDPI, and the remaining five did not have a substantial match to any available reference strains. The findings in this study indicate that small flocks can be reservoirs of IBV and might facilitate evolution of new variants as well as reversion of attenuated strains to virulence.


Asunto(s)
Pollos , Infecciones por Coronavirus/veterinaria , Virus de la Bronquitis Infecciosa/aislamiento & purificación , Enfermedades de las Aves de Corral/virología , Animales , California/epidemiología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Virus de la Bronquitis Infecciosa/clasificación , Enfermedades de las Aves de Corral/epidemiología
6.
Nat Commun ; 12(1): 5148, 2021 08 26.
Artículo en Inglés | MEDLINE | ID: mdl-34446714

RESUMEN

Coronavirus infection in humans is usually associated to respiratory tract illnesses, ranging in severity from mild to life-threatening respiratory failure. The aryl hydrocarbon receptor (AHR) was recently identified as a host factor for Zika and dengue viruses; AHR antagonists boost antiviral immunity, decrease viral titers and ameliorate Zika-induced pathology in vivo. Here we report that AHR is activated by infection with different coronaviruses, potentially impacting antiviral immunity and lung epithelial cells. Indeed, the analysis of single-cell RNA-seq from lung tissue detected increased expression of AHR and AHR transcriptional targets, suggesting AHR signaling activation in SARS-CoV-2-infected epithelial cells from COVID-19 patients. Moreover, we detected an association between AHR expression and viral load in SARS-CoV-2 infected patients. Finally, we found that the pharmacological inhibition of AHR suppressed the replication in vitro of one of the causative agents of the common cold, HCoV-229E, and the causative agent of the COVID-19 pandemic, SARS-CoV-2. Taken together, these findings suggest that AHR activation is a common strategy used by coronaviruses to evade antiviral immunity and promote viral replication, which may also contribute to lung pathology. Future studies should further evaluate the potential of AHR as a target for host-directed antiviral therapy.


Asunto(s)
Infecciones por Coronavirus/metabolismo , Coronavirus/fisiología , Receptores de Hidrocarburo de Aril/metabolismo , Transducción de Señal , COVID-19/genética , COVID-19/metabolismo , COVID-19/virología , Infecciones por Coronavirus/genética , Infecciones por Coronavirus/virología , Células Epiteliales/metabolismo , Células Epiteliales/virología , Femenino , Humanos , Masculino , Receptores de Hidrocarburo de Aril/genética , SARS-CoV-2/fisiología
7.
Viruses ; 13(8)2021 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-34452482

RESUMEN

The COVID-19 pandemic has highlighted the importance of understanding the immune response to seasonal human coronavirus (HCoV) infections such as HCoV-NL63, how existing neutralising antibodies to HCoV may modulate responses to SARS-CoV-2 infection, and the utility of seasonal HCoV as human challenge models. Therefore, in this study we quantified HCoV-NL63 neutralising antibody titres in a healthy adult population using plasma from 100 blood donors in Australia. A microneutralisation assay was performed with plasma diluted from 1:10 to 1:160 and tested with the HCoV-NL63 Amsterdam-1 strain. Neutralising antibodies were detected in 71% of the plasma samples, with a median geometric mean titre of 14. This titre was similar to those reported in convalescent sera taken from individuals 3-7 months following asymptomatic SARS-CoV-2 infection, and 2-3 years post-infection from symptomatic SARS-CoV-1 patients. HCoV-NL63 neutralising antibody titres decreased with increasing age (R2 = 0.042, p = 0.038), but did not differ by sex. Overall, this study demonstrates that neutralising antibody to HCoV-NL63 is detectable in approximately 71% of the healthy adult population of Australia. Similar titres did not impede the use of another seasonal human coronavirus (HCoV-229E) in a human challenge model, thus, HCoV-NL63 may be useful as a human challenge model for more pathogenic coronaviruses.


Asunto(s)
Anticuerpos Neutralizantes/sangre , Anticuerpos Antivirales/sangre , Infecciones por Coronavirus/epidemiología , Coronavirus Humano NL63/inmunología , Adulto , Factores de Edad , Anciano , Australia/epidemiología , COVID-19/inmunología , Prueba Serológica para COVID-19 , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/virología , Estudios Transversales , Femenino , Humanos , Masculino , Persona de Mediana Edad , SARS-CoV-2/inmunología , Estudios Seroepidemiológicos , Adulto Joven
8.
Int J Mol Sci ; 22(15)2021 Jul 29.
Artículo en Inglés | MEDLINE | ID: mdl-34360898

RESUMEN

Previous studies have shown that microRNAs (miRNAs) are closely related to many viral infections. However, the molecular mechanism of how miRNAs regulate porcine epidemic diarrhea virus (PEDV) infection remains unclear. In this study, we first constructed a PEDV-infected IPEC-J2 cytopathic model to validate the relationship between miR-129a-3p expression levels and PEDV resistance. Secondly, we explored the effect of miR-129a-3p on PEDV infection by targeting the 3'UTR region of the ligand ectodysplasin (EDA) gene. Finally, transcriptome sequencing was used to analyze the downstream regulatory mechanism of EDA. The results showed that after 48 h of PEDV infection, IPEC-J2 cells showed obvious pathological changes, and miR-129a-3p expression was significantly downregulated (p < 0.01). Overexpression of miR-129a-3p mimics inhibited PEDV replication in IPEC-J2 cells; silencing endogenous miR-129a-3p can promote viral replication. A dual luciferase assay showed that miR-129a-3p could bind to the 3'UTR region of the EDA gene, which significantly reduced the expression level of EDA (p < 0.01). Functional verification showed that upregulation of EDA gene expression significantly promoted PEDV replication in IPEC-J2 cells. Overexpression of miR-129a-3p can activate the caspase activation and recruitment domain 11 (CARD11) mediated NF-κB pathway, thus inhibiting PEDV replication. The above results suggest that miR-129a-3p inhibits PEDV replication in IPEC-J2 cells by activating the NF-κB pathway by binding to the EDA 3'UTR region. Our results have laid the foundation for in-depth study of the mechanism of miR-129a-3p resistance and its application in porcine epidemic diarrhea disease-resistance breeding.


Asunto(s)
Infecciones por Coronavirus/metabolismo , Ectodisplasinas/metabolismo , Enterocitos/metabolismo , MicroARNs/metabolismo , FN-kappa B/metabolismo , Virus de la Diarrea Epidémica Porcina/fisiología , Transducción de Señal/genética , Replicación Viral/genética , Regiones no Traducidas 3' , Animales , Chlorocebus aethiops , Infecciones por Coronavirus/virología , Regulación hacia Abajo/genética , Ectodisplasinas/genética , Enterocitos/virología , Células HEK293 , Humanos , MicroARNs/genética , Porcinos , Transfección , Regulación hacia Arriba/genética , Células Vero , Secuenciación del Exoma Completo/métodos
9.
Viruses ; 13(8)2021 07 23.
Artículo en Inglés | MEDLINE | ID: mdl-34452302

RESUMEN

Transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs through respiratory droplets passed directly from person to person or indirectly through fomites, such as common use surfaces or objects. The aim of this study was to determine the virucidal efficacy of blue LED (405 nm) and far-UVC (222 nm) light in comparison to standard UVC (254 nm) irradiation for the inactivation of feline infectious peritonitis virus (FIPV) on different matrices as a model for SARS-CoV-2. Wet or dried FIPV on stainless steel, plastic, or paper discs, in the presence or absence of artificial saliva, were exposed to various wavelengths of light for different time periods (1-90 min). Dual activity of blue LED and far-UVC lights were virucidal for most wet and dried FIPV within 4 to 16 min on all matrices. Individual action of blue LED and far-UVC lights were virucidal for wet FIPV but required longer irradiation times (8-90 min) to reach a 4-log reduction. In comparison, LED (265 nm) and germicidal UVC (254 nm) were virucidal on almost all matrices for both wet and dried FIPV within 1 min exposure. UVC was more effective for the disinfection of surfaces as compared to blue LED and far-UVC individually or together. However, dual action of blue LED and far-UVC was virucidal. This combination of lights could be used as a safer alternative to traditional UVC.


Asunto(s)
COVID-19/virología , Coronavirus Felino/efectos de la radiación , Desinfección/métodos , SARS-CoV-2/efectos de la radiación , Animales , COVID-19/prevención & control , Gatos , Infecciones por Coronavirus/virología , Coronavirus Felino/crecimiento & desarrollo , Coronavirus Felino/fisiología , Desinfección/instrumentación , Humanos , SARS-CoV-2/crecimiento & desarrollo , SARS-CoV-2/fisiología , Rayos Ultravioleta , Inactivación de Virus/efectos de la radiación
10.
Viruses ; 13(8)2021 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-34452323

RESUMEN

Over the past 18 years, three highly pathogenic human (h) coronaviruses (CoVs) have caused severe outbreaks, the most recent causative agent, SARS-CoV-2, being the first to cause a pandemic. Although much progress has been made since the COVID-19 pandemic started, much about SARS-CoV-2 and its disease, COVID-19, is still poorly understood. The highly pathogenic hCoVs differ in some respects, but also share some similarities in clinical presentation, the risk factors associated with severe disease, and the characteristic immunopathology associated with the progression to severe disease. This review aims to highlight these overlapping aspects of the highly pathogenic hCoVs-SARS-CoV, MERS-CoV, and SARS-CoV-2-briefly discussing the importance of an appropriately regulated immune response; how the immune response to these highly pathogenic hCoVs might be dysregulated through interferon (IFN) inhibition, antibody-dependent enhancement (ADE), and long non-coding RNA (lncRNA); and how these could link to the ensuing cytokine storm. The treatment approaches to highly pathogenic hCoV infections are discussed and it is suggested that a greater focus be placed on T-cell vaccines that elicit a cell-mediated immune response, using rapamycin as a potential agent to improve vaccine responses in the elderly and obese, and the potential of stapled peptides as antiviral agents.


Asunto(s)
COVID-19/inmunología , Infecciones por Coronavirus/inmunología , Síndrome Respiratorio Agudo Grave/inmunología , Animales , COVID-19/epidemiología , COVID-19/virología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Citocinas/inmunología , Humanos , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Coronavirus del Síndrome Respiratorio de Oriente Medio/fisiología , Pandemias , Virus del SRAS/genética , Virus del SRAS/fisiología , SARS-CoV-2/genética , SARS-CoV-2/fisiología , Síndrome Respiratorio Agudo Grave/epidemiología , Síndrome Respiratorio Agudo Grave/virología
11.
Viruses ; 13(8)2021 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-34452362

RESUMEN

The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct "pigeon-like" group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.


Asunto(s)
Animales Salvajes/virología , Biodiversidad , Enfermedades de las Aves/virología , Infecciones por Coronavirus/veterinaria , Gammacoronavirus/aislamiento & purificación , Animales , Animales Salvajes/clasificación , Anseriformes/virología , Charadriiformes/virología , Columbiformes/virología , Infecciones por Coronavirus/virología , Patos/virología , Galliformes/virología , Gammacoronavirus/clasificación , Gammacoronavirus/genética , Filogenia , Polonia
12.
Viruses ; 13(8)2021 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-34452372

RESUMEN

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus in humans, has expanded globally over the past year. COVID-19 remains an important subject of intensive research owing to its huge impact on economic and public health globally. Based on historical archives, the first coronavirus-related disease recorded was possibly animal-related, a case of feline infectious peritonitis described as early as 1912. Despite over a century of documented coronaviruses in animals, the global animal industry still suffers from outbreaks. Knowledge and experience handling animal coronaviruses provide a valuable tool to complement our understanding of the ongoing COVID-19 pandemic. In this review, we present an overview of coronaviruses, clinical signs, COVID-19 in animals, genome organization and recombination, immunopathogenesis, transmission, viral shedding, diagnosis, treatment, and prevention. By drawing parallels between COVID-19 in animals and humans, we provide perspectives on the pathophysiological mechanisms by which coronaviruses cause diseases in both animals and humans, providing a critical basis for the development of effective vaccines and therapeutics against these deadly viruses.


Asunto(s)
Enfermedades de los Animales/virología , Infecciones por Coronavirus/veterinaria , Infecciones por Coronavirus/virología , Coronavirus/fisiología , Enfermedades de los Animales/epidemiología , Animales , COVID-19/epidemiología , COVID-19/virología , Coronavirus/genética , Infecciones por Coronavirus/epidemiología , Humanos , Salud Pública , SARS-CoV-2/genética , SARS-CoV-2/fisiología
13.
Viruses ; 13(8)2021 07 31.
Artículo en Inglés | MEDLINE | ID: mdl-34452378

RESUMEN

Endemic human coronaviruses (HCoV) are capable of causing a range of diseases from the common cold to pneumonia. We evaluated the epidemiology and seasonality of endemic HCoVs in children hospitalized with clinical pneumonia and among community controls living in countries with a high HIV burden, namely South Africa and Zambia, between August 2011 to October 2013. Nasopharyngeal/oropharyngeal swabs were collected from all cases and controls and tested for endemic HCoV species and 12 other respiratory viruses using a multiplex real-time PCR assay. We found that the likelihood of detecting endemic HCoV species was higher among asymptomatic controls than cases (11% vs. 7.2%; 95% CI: 1.2-2.0). This was however only observed among children > 6 months and was mainly driven by the Betacoronavirus endemic species (HCoV-OC43 and -HKU1). Endemic HCoV species were detected through the year; however, in Zambia, the endemic Betacoronavirus species tended to peak during the winter months (May-August). There was no association between HIV status and endemic HCoV detection.


Asunto(s)
Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Coronavirus/fisiología , Estudios de Casos y Controles , Niño , Preescolar , Coronavirus/clasificación , Coronavirus/genética , Coronavirus/aislamiento & purificación , Infecciones por Coronavirus/terapia , Hospitalización , Humanos , Lactante , Masculino , Nasofaringe/virología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Estaciones del Año , Sudáfrica/epidemiología , Zambia/epidemiología
14.
Emerg Microbes Infect ; 10(1): 1660-1668, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34350810

RESUMEN

The coronavirus disease (COVID-19) pandemic is a major challenge worldwide. However, the epidemic potential of common human coronaviruses (HCoVs) remains unclear. This study aimed to determine the epidemiological and co-infection characteristics of common HCoVs in individuals with influenza-like illness (ILI) and severe acute respiratory infection (SARI). This retrospective, observational, multicentre study used data collected from patients admitted to nine sentinel hospitals with ILI and SARI from January 2015 through December 2020 in Shanghai, China. We prospectively tested patients for a total of 22 respiratory pathogens using multi-real-time polymerase chain reaction. Of the 4541 patients tested, 40.37% (1833/4541) tested positive for respiratory pathogens and 3.59% (163/4541) tested positive for common HCoVs. HCoV infection was more common in the non-endemic season for respiratory pathogens (odds ratio: 2.33, 95% confidence interval: 1.64-3.31). HCoV-OC43 (41.72%, 68/163) was the most common type of HCoV detected. The co-infection rate was 31.29% (51/163) among 163 HCoV-positive cases, with HCoV-229E (53.13%, 17/32), the HCoV type that was most frequently associated with co-infection. Respiratory pathogens responsible for co-infections with HCoVs included parainfluenza virus, rhinovirus/enterovirus, influenza A virus, and adenovirus. Furthermore, we identified one patient co-infected with HCoV-OC43 and HCoV-NL63/HKU1. The prevalence of common HCoVs remains low in ILI/SARI cases, in Shanghai. However, the seasonal pattern of HCoVs may be opposite to that of other respiratory pathogens. Moreover, HCoVs are likely to co-exist with specific respiratory pathogens. The potential role of co-infections with HCoVs and other pathogenic microorganisms in infection and pathogenesis of ILI and SARI warrants further study.


Asunto(s)
Alphacoronavirus , COVID-19/epidemiología , COVID-19/virología , Coinfección/epidemiología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , SARS-CoV-2 , Adulto , Anciano , Anciano de 80 o más Años , Alphacoronavirus/clasificación , Alphacoronavirus/genética , COVID-19/diagnóstico , COVID-19/historia , China/epidemiología , Infecciones por Coronavirus/diagnóstico , Infecciones por Coronavirus/historia , Femenino , Historia del Siglo XXI , Humanos , Masculino , Persona de Mediana Edad , Prevalencia , Vigilancia en Salud Pública , Estudios Retrospectivos , SARS-CoV-2/clasificación , SARS-CoV-2/genética , Estaciones del Año
15.
Arch Virol ; 166(9): 2461-2468, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-34212242

RESUMEN

Bovine coronavirus (BCoV) can be spread by animal activity. Although cattle farming is widespread in Turkey, there are few studies of BCoV. The aim of this study was to evaluate the current situation regarding BCoV in Turkey. This is the first study reporting the full-length nucleotide sequences of BCoV spike (S) genes in Turkey. Samples were collected from 119 cattle with clinical signs of respiratory (n = 78) or digestive tract (n = 41) infection on different farms located across widely separated provinces in Turkey. The samples were screened for BCoV using RT-nested PCR targeting the N gene, which identified BCoV in 35 samples (9 faeces and 26 nasal discharge). RT-PCR analysis of the S gene produced partial/full-length S gene sequences from 11 samples (8 faeces and 3 nasal discharge samples). A phylogenetic tree of the S gene sequences was made to analyze the genetic relationships among BCoVs from Turkey and other countries. The results showed that the local strains present in faeces and nasal discharge samples had many different amino acid changes. Some of these changes were shown in previous studies to be critical for tropism. This study provides new data on BCoV in Turkey that will be valuable in designing effective vaccine approaches and control strategies.


Asunto(s)
Enfermedades de los Bovinos/epidemiología , Infecciones por Coronavirus/veterinaria , Coronavirus Bovino/genética , Diarrea/veterinaria , ARN Viral/genética , Infecciones del Sistema Respiratorio/veterinaria , Glicoproteína de la Espiga del Coronavirus/genética , Agricultura , Sustitución de Aminoácidos , Animales , Bovinos , Enfermedades de los Bovinos/virología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Coronavirus Bovino/clasificación , Diarrea/epidemiología , Diarrea/virología , Monitoreo Epidemiológico/veterinaria , Evolución Molecular , Heces/virología , Humanos , Mutación , Cavidad Nasal/virología , Filogenia , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Turquia/epidemiología
16.
mSphere ; 6(4): e0021921, 2021 08 25.
Artículo en Inglés | MEDLINE | ID: mdl-34287009

RESUMEN

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.


Asunto(s)
Infecciones por Coronavirus/virología , Microbiota/genética , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Anciano , Animales , COVID-19/virología , Femenino , Humanos , Masculino , Persona de Mediana Edad , SARS-CoV-2/genética
17.
Virus Res ; 302: 198497, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34217778

RESUMEN

Porcine deltacoronavirus (PDCoV) is an emerging coronavirus that causes vomiting, diarrhea, dehydration, and even death of piglets, resulting in significant losses to the pig industry worldwide. However, the epitopes of PDCoV remain largely unknown. In this study, a monoclonal antibody (mAb) against the PDCoV nucleocapsid (N) protein, termed 9G1, was prepared using the lymphocyte hybridoma technique, and was identified as a type IgG1 with a κ light chain and reacted with the native N protein of PDCoV. Furthermore, the epitope recognized by the 9G1 mAb was subjected to western blot and an ELISA using truncated recombinant proteins and synthetic polypeptides of the PDCoV N protein. The results indicate that 9G1 mAb recognized the epitope, G59TPIPPSYAFYY70 (EP-9G1), a novel linear B cell epitope of the PDCoV N protein. A comparison analysis revealed that the EP-9G1 epitope was highly conserved among PDCoV strains, in which four residues (G59-F68YY70) were observed among different coronavirus genera. These data demonstrate that the EP-9G1 epitope identified in this study provides some basic information for further characterization of the antigenic structure of the PDCoV N protein and has potential use for developing diagnostic reagents for PDCoV.


Asunto(s)
Anticuerpos Monoclonales/inmunología , Infecciones por Coronavirus/veterinaria , Deltacoronavirus/inmunología , Epítopos de Linfocito B/inmunología , Proteínas de la Nucleocápside/inmunología , Secuencia de Aminoácidos , Animales , Infecciones por Coronavirus/diagnóstico , Infecciones por Coronavirus/inmunología , Infecciones por Coronavirus/virología , Deltacoronavirus/genética , Ensayo de Inmunoadsorción Enzimática/veterinaria , Femenino , Inmunoglobulina G/inmunología , Ratones Endogámicos BALB C , Proteínas de la Nucleocápside/genética , Proteínas Recombinantes , Alineación de Secuencia , Porcinos
18.
Viruses ; 13(7)2021 06 25.
Artículo en Inglés | MEDLINE | ID: mdl-34201926

RESUMEN

The SARS-CoV-2 coronavirus is the focus of attention as it has caused more than three million human deaths globally. This and other coronaviruses, such as MERS-CoV, have been suggested to be related to coronaviruses that are hosted in bats. This work shows, through a bibliographic review, the frequency of detection of coronavirus in bats species of the Americas. The presence of coronavirus in bats has been examined in 25 investigations in 11 countries of the Americas between 2007 and 2020. Coronaviruses have been explored in 9371 individuals from 160 species of bats, and 187 coronavirus sequences have been deposited in GenBank distributed in 43 species of bats. While 91% of the coronaviruses sequences identified infect a single species of bat, the remainder show a change of host, dominating the intragenera change. So far, only Mex-CoV-6 is related to MERS-CoV, a coronavirus pathogenic for humans, so further coronavirus research effort in yet unexplored bat species is warranted.


Asunto(s)
Quirópteros/virología , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/veterinaria , Coronavirus/clasificación , Coronavirus/genética , Américas/epidemiología , Animales , COVID-19/epidemiología , Coronavirus/aislamiento & purificación , Infecciones por Coronavirus/virología , Humanos , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Coronavirus del Síndrome Respiratorio de Oriente Medio/aislamiento & purificación , Filogenia , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación
19.
Viruses ; 13(7)2021 06 29.
Artículo en Inglés | MEDLINE | ID: mdl-34209881

RESUMEN

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.


Asunto(s)
Coronavirus/clasificación , Coronavirus/genética , Evolución Molecular , Variación Genética , Genoma Viral , Recombinación Genética , Animales , Aves/virología , Infecciones por Coronavirus/virología , Filogenia , Proteínas Virales/genética
20.
Sci Rep ; 11(1): 14961, 2021 07 22.
Artículo en Inglés | MEDLINE | ID: mdl-34294757

RESUMEN

Influenza and other respiratory viruses present a significant threat to public health, national security, and the world economy, and can lead to the emergence of global pandemics such as from COVID-19. A barrier to the development of effective therapeutics is the absence of a robust and predictive preclinical model, with most studies relying on a combination of in vitro screening with immortalized cell lines and low-throughput animal models. Here, we integrate human primary airway epithelial cells into a custom-engineered 96-device platform (PREDICT96-ALI) in which tissues are cultured in an array of microchannel-based culture chambers at an air-liquid interface, in a configuration compatible with high resolution in-situ imaging and real-time sensing. We apply this platform to influenza A virus and coronavirus infections, evaluating viral infection kinetics and antiviral agent dosing across multiple strains and donor populations of human primary cells. Human coronaviruses HCoV-NL63 and SARS-CoV-2 enter host cells via ACE2 and utilize the protease TMPRSS2 for spike protein priming, and we confirm their expression, demonstrate infection across a range of multiplicities of infection, and evaluate the efficacy of camostat mesylate, a known inhibitor of HCoV-NL63 infection. This new capability can be used to address a major gap in the rapid assessment of therapeutic efficacy of small molecules and antiviral agents against influenza and other respiratory viruses including coronaviruses.


Asunto(s)
Antivirales/farmacología , Infecciones por Coronavirus/virología , Gripe Humana/virología , Pruebas de Sensibilidad Microbiana/instrumentación , Técnicas Analíticas Microfluídicas/instrumentación , Mucosa Respiratoria/citología , Bronquios/citología , Bronquios/virología , COVID-19/tratamiento farmacológico , COVID-19/virología , Técnicas de Cultivo de Célula/instrumentación , Línea Celular , Coronavirus/efectos de los fármacos , Infecciones por Coronavirus/tratamiento farmacológico , Diseño de Equipo , Ensayos Analíticos de Alto Rendimiento/instrumentación , Humanos , Virus de la Influenza A/efectos de los fármacos , Gripe Humana/tratamiento farmacológico , Mucosa Respiratoria/virología , Infecciones del Sistema Respiratorio/tratamiento farmacológico , Infecciones del Sistema Respiratorio/virología , SARS-CoV-2/efectos de los fármacos
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