Characterization Of Coronavirus Research Articles

Design of customized coronavirus receptors.

Although coronaviruses use diverse receptors, the characterization of coronaviruses with unknown receptors has been impeded by a lack of infection models1,2. Here we introduce a strategy to engineer functional customized viral receptors (CVRs). The modular design relies on building artificial receptor scaffolds comprising various modules and generating specific virus-binding domains. We identify key factors for CVRs to functionally mimic native receptors by facilitating spike proteolytic cleavage, membrane fusion, pseudovirus entry and propagation for various coronaviruses. We delineate functional SARS-CoV-2 spike receptor-binding sites for CVR design and reveal the mechanism of cell entry promoted by the N-terminal domain-targeting S2L20-CVR. We generated CVR-expressing cells for 12 representative coronaviruses from 6 subgenera, most of which lack known receptors, and show that a pan-sarbecovirus CVR supports propagation of a propagation-competent HKU3 pseudovirus and of authentic RsHuB2019A3. Using an HKU5-specific CVR, we successfully rescued wild-type and ZsGreen-HiBiT-incorporated HKU5-1 (LMH03f) and isolated a HKU5 strain from bat samples. Our study demonstrates the potential of the CVR strategy for establishing native receptor-independent infection models, providing a tool for studying viruses that lack known susceptible target cells.

Molecular Detection and Characterization of Coronaviruses in Migratory Ducks from Portugal Show the Circulation of Gammacoronavirus and Deltacoronavirus.

Coronaviruses (CoVs) are part of the Coronaviridae family, and the genera Gamma (γ) and Delta (δ) are found mostly in birds. Migratory birds have an enormous potential for dispersing pathogenic microorganisms. Ducks (order Anseriformes) can host CoVs from birds, with pathogenic expression and high economic impact. This study aimed to identify and characterize the diversity of CoVs in migratory ducks from Portugal. Duck stool samples were collected using cloacal swabs from 72 individuals (Anas platyrhynchos, Anas acuta, and Anas crecca). Among the 72 samples tested, 24 showed amplicons of the expected size. Twenty-three were characterized as Gammacoronavirus and one as Deltacoronavirus (accession numbers ON368935-ON368954; ON721380-ON721383). The Gammacoronaviruses sequences showed greater similarities to those obtained in ducks (Anas platyrhynchos) from Finland and Poland, Anas crecca duck from the USA, and mute swans from Poland. Birds can occupy many habitats and therefore play diverse ecological roles in various ecosystems, especially given their ability to migrate exceptional distances, facilitating the dispersal of microorganisms with animal and/or human impact. There are a considerable number of studies that have detected CoVs in ducks, but none in Portugal. The present study assessed the circulation of CoVs in wild ducks from Portugal, being the first description of CoVs for these animals in Portugal.

A Literature Review on the Epidemiology, Virology, Clinical Characteristics, Prevention and Treatment of Novel Coronavirus (2019-nCoV)

The World Health Organization (WHO) has issued a public health emergency of international concern for the outbreak of the novel coronavirus (2019-nCoV). This study aimed to review the findings of recent published literature to provide researchers with information regarding the current biggest global health threat of 2019-nCoV pandemic on the basis of previous coronaviruses. To do so, this study attempted to review the available online data on biological nature of 2019-nCoV compared to previous coronaviruses. Additionally, the epidemiology, susceptible population, transmission routes, clinical characteristics, and medications for 2019-nCoV were reviewed. In this article, after an introduction to the subject and characterization of coronavirus, we considered the experiences and lessons learned from previous outbreaks to review the epidemiology, clinical characteristics, prevention, and medications of 2019-nCov disease. There are three main routes for transmission of 2019-nCoV including close contact to infected cases, aerosol, and touch transmissions. This newfound virus can be transmitted from asymptomatic patients or from infected cases with symptoms ranging from a flu-like to severe respiratory syndrome. Currently, there are no 100% approved therapeutic drugs and vaccination for this disease. In conclusion, given that development of vaccine for 2019-nCoV requires close collaboration of vaccine manufacturers and biotechnology companies, which takes a long period for production of vaccine, implementation of prevention and controlling measures based on the current available information about the subject is the best measure to control the spread of the virus.

Clinical Application of Chest Computed Tomography (CT) in Detection and Characterization of Coronavirus (Covid-19) Pneumonia in Adults.

To analyze diagnostic accuracy of chest computed tomography (CT) and RT-PCR (real-time polymerase chain reaction) for COVID-19 (coronavirus disease 19) pneumonia in early and progressive stages. To evaluate if combination of chest CT with RT-PCR can supplement the shortage of RT-PCR in diagnosis of COVID-19 pneumonia. We conducted a prospective study on 103 male patients. The study population were divided into two groups; early COVID-19 stage (number = 50 patients, with positive RT-PCR but mild symptoms) and progressive COVID-19 stage (number = 53, positive RT-PCR and sever symptoms including fever > 37.5 °C, cough, and shortness of breath). All patients underwent CT imaging. The early stage included typical category; 34% (17 out of 50 cases), 6% indeterminate category (3 cases), 10% atypical category (5 cases) and 50% (25 cases) were normal CT imaging. The progressive stage included typical category that was further divided to five subgroups; (i) peripheral bilateral lower lobe ground-glass opacity (GGO) in (37.7%), (ii) peripheral bilateral lower lobes GGO with peribronchovascular consolidation and bronchiolar dilatation in (18.8%), (iii) peripheral bilateral lower lobes GGO with crazy paving appearance in (15%), (iv) bilateral diffuse GGO in (18.8%), and (v) peripheral bilateral GGO with mediastinal lymph node enlargement (9.4%). Chest CT imaging could aid to supplement the shortages of PCR for clinically suspected patients of COVID-19 in the epidemic area as CT was positive in 50% of patients. Chest CT is very effective in detecting pulmonary parenchymal abnormalities in the progressive stage of COVID-19 patients in 100%.

Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2

Coronavirus disease 2019 (COVID-19) pandemic has been a catastrophic burden to global healthcare systems. The fast spread of the etiologic agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need to identify unknown coronaviruses rapidly for prompt clinical and public health decision making. Moreover, owing to the high mutation rate of RNA viruses, periodic surveillance on emerging variants of key virus components is essential for evaluating the efficacy of antiviral drugs, diagnostic assays and vaccines. These 2 knowledge gaps formed the basis of this study. In the first place, we evaluated the feasibility of characterizing coronaviruses directly from respiratory specimens. We amplified partial RdRP gene, a stable genetic marker of coronaviruses, from a collection of 57 clinical specimens positive for SARS-CoV-2 or other human coronaviruses, and sequenced the amplicons with Nanopore Flongle and MinION, the fastest and the most scalable massively-parallel sequencing platforms to-date. Partial RdRP sequences were successfully amplified and sequenced from 82.46% (47/57) of specimens, ranging from 75 to 100% by virus type, with consensus accuracy of 100% compared with Sanger sequences available (n = 40). In the second part, we further compared 19 SARS-CoV-2 RdRP sequences collected from the first to third waves of COVID-19 outbreak in Hong Kong with 22,173 genomes from GISAID EpiCoV™ database. No single nucleotide variants (SNVs) were found in our sequences, and 125 SNVs were observed from global data, with 56.8% being low-frequency (n = 1–47) missense mutations affecting the rear part of RNA polymerase. Among the 9 SNVs found on 4 conserved domains, the frequency of 15438G > T was highest (n = 34) and was predominantly found in Europe. Our data provided a glimpse into the sequence diversity of a primary antiviral drug and diagnostic target. Further studies are warranted to investigate the significance of these mutations.

Molecular epidemiology of coronavirus in faeces of Brazilian calves and Peruvian camelid herds.

The enteric disorders represent a serious hazard for bovine and camelid breeding. The aim of this study was to examine the frequency of detection and molecular characteristics of enteric coronavirus (CoV) infections in cattle, alpaca, and llama herds bred in family-based farms in Brazil and Peru. Stool samples were collected from calves from Brazil and camelids from Peru for detection and characterization of CoV by reverse transcription polymerase chain reaction (RT-PCR) and sequence analysis. 46.5% (47/101) samples from calves and 26.8% (70/261) from alpaca tested positive for CoV. All strains belong to lineage A1 of the Betacoronavirus genus. Phylogenetic analysis showed high identity between CoV strains detected in calves and alpacas. This study characterised CoV strains from dairy cattle herds in the state of Rio de Janeiro, Brazil, and indicated that this virus is spread among the state herds. The results also indicate widespread circulation of CoV among the alpacas of Cuzco, Peru.

Functional Transcriptional Regulatory Sequence (TRS) RNA Binding and Helix Destabilizing Determinants of Murine Hepatitis Virus (MHV) Nucleocapsid (N) Protein

Coronavirus (CoV) nucleocapsid (N) protein contains two structurally independent RNA binding domains. These are denoted N-terminal domain (NTD) and C-terminal domain and are joined by a charged linker region rich in serine and arginine residues (SR linker). In mouse hepatitis virus (MHV), the NTD binds the transcriptional regulatory sequence (TRS) RNA, a conserved hexanucleotide sequence required for subgenomic RNA synthesis. The NTD is also capable of disrupting a short RNA duplex. We show here that three residues on the β3 (Arg-125 and Tyr-127) and β5 (Tyr-190) strands play key roles in TRS RNA binding and helix destabilization with Ala substitutions of these residues lethal to the virus. NMR studies of the MHV NTD·TRS complex revealed that this region defines a major RNA binding interface in MHV with site-directed spin labeling studies consistent with a model in which the adenosine-rich 3'-region of TRS is anchored by Arg-125, Tyr-127, and Tyr-190 in a way that is critical for efficient subgenomic RNA synthesis in MHV. Characterization of CoV N NTDs from infectious bronchitis virus and from severe acute respiratory syndrome CoV revealed that, although detailed NTD-TRS determinants are distinct from those of MHV NTD, rapid helix destabilization activity of CoV N NTDs is most strongly correlated with CoV function and virus viability.

Neutralizing Antibody to Calf Diarrhea Coronavirus in Various Animal Species in Japan

Neutralizing Antibody to Calf Diarrhea Coronavirus in Various Animal Species in Japan