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1.
Acta Agriculturae Jiangxi ; 34(2):160-165, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-1964892

ABSTRACT

In this study, 650 tissue samples which were collected from 16 pig farms in Hubei Province, were used to detect porcine circovirus (PCV) and Porcine epidemic diarrhea virus (PEDV). The results showed that the positive rates of PCV1, PCV2, PCV3 and PEDV single infection were 1.08%, 4.15%, 2.46% and 6.46%, respectively. In the double infections, PEDV+PCV2 had the highest positive rate of 3.54%, followed by PCV2+PCV3, with a positive rate of 1.54%. In multiple infections, PEDV+PCV2+PCV3 had the highest positive rate of 2.00%. The results indicated that the positive rates of PEDV and PCV were decreased compared with the previous studies, but the prevalence of PEDV and PCV was still wide in Hubei Province, and most of which were co-infection.

2.
Journal of Yangzhou University, Agricultural and Life Sciences Edition ; 42(6):48-53, 2021.
Article in English, Chinese | CAB Abstracts | ID: covidwho-1964809

ABSTRACT

As a member of the family Picornaviridae, porcine sapelovirus (PSV) is often infected with porcine epidemic diarrhea virus, teschovirus and so on. In recent years, PSV has been isolated from porcine in many provinces of China. It suggests that it is necessary to strengthen the research on PSV. In this study, according to the sequence of PSV HuN2 strain, VP1 gene was inserted into the pGEX-6 P-1 vector, and expressed the recombinant protein. BALB/c mice aged 6-8 weeks were immunized according to the standard procedure. After the third immunization, the mouse orbital blood was collected to identify the antibody level. The highly positive mouse spleen cells were selected for cell fusion. The positive hybridoma cells and two subclones were screened by IFA method, and then a PSV VP1 monoclonal antibody was obtained, named as 33-2 A. The results of IFA showed that PSV could be recognized by 33-2 A MAb, and specific green fluorescence appeared in the cytoplasm;The results of WB and IP showed that PSV infected porcine cell could specifically bind to 33-2 A, and there was a specific band at 32 ku. We also identified the B-cell antigen epitope of 33-2 A, it was at amino acids 40-46 of PSV VP1 protein, and the polypeptide sequence was 40PALTAAE46. The results showed that the monoclonal antibody can react with PSV VP1 protein. The epitope was analyzed with the PSV sequences uploaded in NCBI, 33-2 A antibody can react with most PSV strains and has a certain universal to PSV. This study laid a foundation for the study of the etiology and pathogenesis of PSV.

3.
Animal Husbandry and Feed Science ; 43(4):109-115, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-1964619

ABSTRACT

Objective: To gather information on the research status and the hot spots of zoonosis and zoonotic microorganisms worldwide, and to provide references for the prevention and control of zoonotic diseases in China. Method: COOC 12.6 and Citespace 5.8 R1 software were used to carry out frequency statistics, co-occurrence analysis, cluster analysis, timeline analysis and burst analysis on the keywords associated with zoonosis and zoonotic microorganisms in PubMed database. Result: According to the keywords frequency statistics and co-occurrence analysis results from the year of 2001 to 2021 in pubMed database, the zoonosis and zoonotic microorganisms arousing high international attentions were classified into the following three categories: the first category was commonly observed zoonotic microorganisms such as Brucella, hepatitis E virus, Streptococcus, Escherichia coli (E. coli) and Salmonella, to which continuous public attentions were still needed to be paid;the second category was the zoonotic microorganisms worldwide concerned in recent years such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza A virus, which were worthy of more in-depth research to control the spread of these diseases as soon as possible;the third category was the zoonosis that had massively prevailed in specific regions abroad such as Q fever and middle east respiratory syndrome (MERS), and these diseases were expected to be noticed in terms of imported risks to avoid their outbreaks in China. In addition to the above mentioned zoonosis and zoonotic microorganisms, some keywords associated with detection and diagnosis such as phylogeny and PCR were also of high interests. The cluster analysis generated a total of 10 clusters, in which the tick-borne infectious disease cluster suggested the role of ticks in the transmission of zoonotic diseases;the results of timeline and burst analysis demonstrated that among the zoonotic microorganisms, the attentions being paid to influenza A virus and SARS-CoV-2 were gradually increasing. At the same time, the detection technology of zoonotic microorganisms was evolving from specific sequence detection to whole genome sequencing. These fields were likely to be the research direction and trend in the future.

4.
Journal of Applied Biological Sciences ; 16(1):89-101, 2022.
Article in English | CAB Abstracts | ID: covidwho-1964344

ABSTRACT

COVID-19 outbreak is still threatening the public health. Therefore, in the middle of the pandemic, all kind of knowledge on SARS-CoV-2 may help us to find the solution. Determining the 3D structures of the proteins involved in host-pathogen interactions are of great importance in the fight against infection. Besides, post-translational modifications of the protein on 3D structure should be revealed in order to understand the protein function since these modifications are responsible for the host-pathogen interaction. Based on these, we predicted O-glycosylation and phosphorylation positions using full amino acid sequence of S1 protein. Candidate positions were further analyzed with enzyme binding activity, solvent accessibility, surface area parameters and the positions determined with high accuracy rate were used to design 3D O-glycoprotein structure of the S1 protein using carbohydrate force field. In addition, the interaction between the C-type lectin CD209L and a-mannose residues was examined and carbohydrate recognition positions were predicted. We suggest these positions as a potential target for the inhibition of the initial binding of SARS-CoV-2 S1 protein to the host cell.

5.
Biomedica ; 42(Suppl. 2), 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-1957852

ABSTRACT

Introduction: The severe acute respiratory syndrome of the new coronavirus (SARS-CoV-2) is the causal agent of the health emergency due to the COVID-19 pandemic. Although humans are the main susceptible host, experimental studies and reported cases of natural infection have evidenced scenarios of SARS-CoV-2 reverse zoonosis in animals.

6.
Veteriner Hekimler Dernegi Dergisi / Journal of the Turkish Veterinary Medical Society ; 93(2):124-132, 2022.
Article in Turkish | CAB Abstracts | ID: covidwho-1924975

ABSTRACT

Coronaviruses in the family Coronaviridae cause digestive and respiratory system infections in humans and animals. There are two subtypes of canine coronaviruses (CCoV), which are included in the alfacoronavirus, as CCoV I and CCoV II. CCoV-II is divided into two genotypes, CCoV-IIa and IIb. Although CCoV affects dogs of all ages and all diets, newborn puppies can be particularly susceptible and severely affected. According to the literature research, no molecular studies have been found in our country for the detection of canine coronavirus, especially in lower respiratory tract infections. In this study, it was aimed to detect and molecular characterization of CCoV un shelter dogs with lower respiratory tract infection. For this purpose, Bronchoalveolar Lavage (BAL) fluids taken from 40 shelter dogs with lower respiratory tract infections were examined. CCoV was detected in 3 of the BAL fluids of 40 dogs tested. A phylogenetic tree was constructed with the sequences obtained after the sequence analysis. It was determined that 2 of the 3 positive samples in the phylogenetic tree were CCoV-I and one sample was CCoV-II. In conclusion, this study revealed that CCoV-I and CCoV-II may play a role in lower respiratory system disorders of shelter dogs. In addition, the detection of two different CCoVs in different animals in the same shelter has been considered as an important data, and the detection of both types in dogs housed in crowded environments such as shelter conditions shows that the possibility of new variants or subtypes that may occur in the future should not be ignored.

7.
Studies in Mycology ; 101:417-564, 2022.
Article in English | CAB Abstracts | ID: covidwho-1902874

ABSTRACT

This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names.

8.
NAVC Clinician's Brief ; 29, 2022.
Article in English | CAB Abstracts | ID: covidwho-1898327
9.
Zhongguo Yufang Shouyi Xuebao / Chinese Journal of Preventive Veterinary Medicine ; 44(3):320-324, 2022.
Article in English, Chinese | CAB Abstracts | ID: covidwho-1898320

ABSTRACT

Chicken infectious bronchitis (IB) is one of the epidemic diseases that cause severe economic loss to poultry industry and induced by the infection of infectious bronchitis virus (IBV). IBV was prone to mutation and recombination due to its genomic characteristics, resulting in new antigenic variants. In order to understand the prevalence and variation of IBV in Shanxi province and provide reference for IB epidemic prevention and control in this area, tissues of a broiler flock suspected of respiratory virus infection were collected in Jinzhong city, Shanxi province. Through PCR identification, chicken embryo inoculation, and sequencing verification, an IBV strain was isolated and named CK/Shanxi-01/2021. On the basis of S1 gene sequencing, the sequence was compared with those of the representative IBV strains of different genotypes deposited in NCBI database, and the phylogenetic tree was constructed. The results of genetic evolution analysis showed that the IBV strain isolated in this study was belonged to GI-19 genotype. The sequence alignment of CK/Shanxi-01/2021 with common IBV vaccine strains H120, M41, H52, 4/91, and LDT3-A showed that the nucleotide homology between the isolated strain and the current common vaccine strain was 78.1%-85.2%, and the amino acid homology was only 75.2%-78.4%. Compared with the sequences of GI-19 genotype strains, some new mutations, including V68I, S120A, A271T, N282T, and N291S, were identified in the S1 protein hypervariable region(HVR). Therefore, it is of great significance for the prevention and control of IB epidemic to strengthen the epidemiological monitoring of IBV and timely grasp the current epidemic IBV genotype and its variation characteristics.

10.
Peer Community Journal ; 1(e45), 2021.
Article in English | CAB Abstracts | ID: covidwho-1893604

ABSTRACT

France was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration and Rt are in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.

11.
Jiangsu Journal of Agricultural Sciences ; 38(2):422-428, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-1893038

ABSTRACT

In this study, we detected the viral load and protein expression of porcine epidemic diarrhea virus (PEDV) after overexpression and inhibition of integrin avbeta1 on the surface of Vero cells, and then cleared the role of integrin avbeta1 in the PEDV infection process. The results showed that the viral load and protein expression were significantly increased in the Vero cells which overexpressed integrin avbeta1, and the viral load and protein expression were significantly reduced in the Vero cells with silent integrin avbeta1 gene. Integrin avbeta1 promotes PEDV to infect Vero cells.

12.
Journal of Communicable Diseases ; 54(1):141-149, 2022.
Article in English | CAB Abstracts | ID: covidwho-1865707

ABSTRACT

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in December 2019, scientists have tracked five variants of concern (VOC) of SARS-CoV-2. The variants such as B.1.1.7 and B.1.617.2 primarily originated independently from the United Kingdom and India, respectively, and subsequently became dominant across the globe. The adaptability of these variants depends on their relative survival fitness to the positive selection pressure acting on them. Antiviral drugs and vaccine usage might act as a selective environment, thus, facilitating the positive selection resulting in the rapid emergence of new variants with higher fitness and survival value. The recently emerged VOC, the omicron variant (B.1.1.529), was first reported from South African samples, and it has a large number of mutations some of which are concerning as per the preliminary evidence. Owing to the dynamism of mutations in the SARS-CoV-2 genome, we may expect many unexpected events as far as the emergence of variants, virulence, and transmissibility is concerned. However, as an evolutionary trade-off strategy, the virulence of SARS-CoV-2 might get reduced with an increase in the transmissibility to attain a wider host range. The intermingling of vaccinated and unvaccinated individuals provides the virus opportunity to amplify by infecting the unvaccinated individuals and causing breakthrough infections. Moreover, the prevalence of different variants of SARS-CoV-2 has been different in different geographic zones as far as the cases and causalities are concerned. Sustained viral surveillance and monitoring with region-wise variant-specific preventive strategies are required to prevent and contain the outbreak of emerging variants of SARS-CoV-2.

13.
Livestock and Animal Research ; 20(1):83-90, 2022.
Article in Indonesian | CAB Abstracts | ID: covidwho-1865689

ABSTRACT

Objective: To obtain information about the presence of coronavirus in bats to find potential of new disease reservoir as well as not yet reported disease reservoir in Lamongan District. This research can be used by the government as a basis for planning and evaluating disease control programs and for researchers it can be used for vaccine and drug design, viral phylogenetic, analysis of viral distribution, and viral databases.

14.
Indian Journal of Poultry Science ; 56(2):173-179, 2021.
Article in English | CAB Abstracts | ID: covidwho-1865636

ABSTRACT

Poultry enteritis is an important multifactorial disease. Avian coronavirus (ACV) is one of many viruses related to enteric diseases and infectious bronchitis. Aim of this study was to find out the occurrence of ACV in enteritis affected broiler, molecular detection, phylogenetic analysis of avian corona virus and to examine intestine and liver for gross and microscopic lesions. Dead poultry birds (N=604) affected with enteritis were examined for presence of ACV. Intestinal samples of four birds were pooled to make one biological sample enteric ACV as the causative agent of enteritis in commercial poultry sector in and around four major districts of Rajasthan by RT-PCR. Molecular characterization was carried out by partial gene sequencing. Liver and intestine were examined grossly during post-mortem and by histopathology. Out of 151 pooled samples tested 51 (35.10%) were found positive for ACV. Prevalence of enteric ACV was highest in Ajmer (45.94%) and lowest in Dungarpur (23.07%) districts. 0-1 weeks age chicken flocks were found more susceptible for enteric ACV with 33.80% prevalence. Comparison of ACV sequence of this study revealed nucleotide (nt) identities from 99.44% among themselves, 99.44% with ACV from abroad. The amino acid (aa) identities of ACV of this study among themselves and with abroad sequences was 47.06 to 100%. Further severe congestion in intestine and necrotic patches on liver were recorded. Histopathology showed severe villous atrophy, congestion and cystic glands in sub-mucosa in intestine and severe congestion and haemorrhages along with infiltration of inflammatory cells in liver parenchyma.

15.
Journal of the Japan Veterinary Medical Association ; 75(4):e62-e68, 2022.
Article in Japanese | CAB Abstracts | ID: covidwho-1856346

ABSTRACT

A 12-year-old indoor cat showed severe respiratory symptoms such as sneezing, nasal discharge and cough. On Day 5 after disease onset, an oral swab was collected and a real-time RT-PCR test was performed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), indicating that the sample from the cat was positive for SARS-CoV-2 genes. Since the symptoms worsened on Day 8, a general physical examination, blood tests, chest x-rays and treatment were carried out and oral, nasal and rectal swabs were collected. Mild bronchitis and increased serum amyloid A (SAA) were observed, but it did not lead to pneumonia. In addition, whole-genome analysis revealed that it was the delta variant of SARS-CoV-2. Then the cat recovered, and a significant increase of virus-neutralizing antibody titer was observed in the convalescent serum. In conclusion, this is the first report on a cat with respiratory symptoms caused by SARS-CoV-2 infection in Japan.

16.
PLoS Global Public Health ; 2(2), 2022.
Article in English | CAB Abstracts | ID: covidwho-1854956

ABSTRACT

Despite considerable progress being made on vaccine roll out, practicing proper hand hygiene has been advocated as a consistent precautionary intervention against the circulating and emerging variants of SARS-CoV-2. Two variants of concern, namely beta and delta, have been shown to exhibit enhanced transmissibility, high viral load, and ability to escape antibody-mediated neutralization. In this report we have empirically determined the efficacy of selected personal care formulations from Unilever in inactivating the beta and delta variants of SARS-CoV-2 under simulated real-life conditions. All the formulations demonstrated greater than 99.9% reduction in viral infective titres which is comparable to inactivation of the original strain of SARS-CoV-2 virus tested under the same conditions. Therefore, it can be concluded that well-designed personal care formulations when tested under consumer-centric conditions, and with proven efficacy against the parent strain of SARS-CoV-2 will continue to be effective against extant and emerging variants of SARS-CoV-2.

17.
Journal of Veterinary Clinical Pathology ; 15(59), 2021.
Article in Persian | CAB Abstracts | ID: covidwho-1841817

ABSTRACT

Avian infectious bronchitis (IB) is an acute and highly contagious disease of the upper-respiratory tract caused by the infectious bronchitis virus (IBV). The virus is a member of the Coronaviridae family and has numerous serotypes and strains. Rapid replication combined with high mutation rate and recombination are the main causes of the observed high diversity. Feed conversion and average daily gain are affected in broilers, and infection is often followed by secondary bacterial infections. In layers, IBV causes a reduction in egg production. Today, IB is one of the most economically important diseases in the poultry industry. Transcriptional profiles of trachea tissue of the infected group (IBV) were studied with control group to evaluate changes in transcriptome profile at the early stages of infection. After the challenge of SPF chickens with IBV IS-1494 like (GI-23), the trachea tissue was used for RNA extraction, and changes in the transcriptome were investigated by Illumina RNA-seq technique. Up-regulated and down-regulated differentially expressed genes (DEGs) in the transcriptome of trachea were identified. Gene ontology category, KEGG pathway were analyzed to identify relationships among differentially expressed genes. In general, the numbers of up-regulated genes were higher than of down-regulated genes in experimental group. In the experimental group, a more severe immune response occurred;an important up-regulated genes in this group's was Toll-like receptor signaling pathway, apoptotic pathway, MAPK signaling pathway. Results of this study could provide a general overview of transcriptome changes in the trachea at the early stage of infection with avian infectious bronchitis (IBV) virus.

18.
Sel'skokhozyaistvennaya Biologiya ; 56(6):1079-1098, 2021.
Article in Russian | CAB Abstracts | ID: covidwho-1841718

ABSTRACT

The wide spread of viral infections and the ease of overcoming the species-specific barriers require the identification of critical stages in the virus interaction with multicellular organisms of mammals and the analysis of key molecular genetic systems involved. To date, a large amount of data has already been accumulated on the diversity and complexity of such systems, as well as the involvement in them the wide range of metabolic pathways. In this regard, attempts to identify some common elements that are implemented in different infectious processes are of particular relevance. This paper is such attempt made on the example of the analysis of the main events of cattle infection by bovine leukemia virus (BLV). Systems involved in the entry of BLV genetic material into the cytoplasm of host cells, the suppression of innate and adaptive immunity, as well as interactions between the genomes of the BLV provirus and the host genome are the identified critical stages. The direct participants in the reception of viral proteins are parts of some host tansmembrane systems (G.Yu. Kosovsky et al., 2017;V.I. Glazko et al., 2018;L. Bai et al., 2019;H. Sato et al., 2020). During virus reproduction in host cells, host enzymes modify virus envelope proteins by (A. De Brogniez et al., 2016;W. Assi et al., 2020). Importantly, modifications of SARS-CoV-2 spike proteins, as well as BLV envelope proteins, have a significant impact on their pathogenicity (M. Hoffmann et al., 2020). Pathogenicity and depressing effect of both BLV and SARS-CoV-2 on innate and adaptive immunity is realized in part through the activation of T regulatory cells and an increase in the expression of the growth transforming factor TGF-b (L.Y. Chang et al., 2015;G.Yu. Kosovsky et al., 2017;W. Chen et al., 2020). Intracellular mechanisms of protection against retrotranspositions, recombinations between viruses and host retrotransposons, the formation of new elements of host regulatory networks such as microRNAs, and the integration of proviral DNA into the host genome are closely related and controlled by interfering RNA (RNAi) systems with the key gene dicer1 (P.V. Maillard et al., 2019;E.Z. Poirier et al., 2021;G.Y. Kosovsky et al., 2020). These systems can provide a certain left-pointing-double-angle resistance right-pointing-double-angle of the host genome both to the integration of exogenous genetic material and to transpositions of own mobile genetic elements. Apparently, it is the polygenicity of the control of these critical stages of viral infection that leads to difficulties in predicting their development and developing methods for their prevention.

19.
Arab Gulf Journal of Scientific Research ; 39(Special Issue (2):79-137, 2021.
Article in English | CAB Abstracts | ID: covidwho-1837421

ABSTRACT

Purpose: Evolving technologies allow us to measure human molecular data in a wide reach. Those data are extensively used by researchers in many studies and help in advancements of medical field. Transcriptome, proteome, metabolome, and epigenome are few such molecular data. This study utilizes the transcriptome data of COVID-19 patients to uncover the dysregulated genes in the SARS-COV-2. Method: Selected genes are used in machine learning models to predict various phenotypes of those patients. Ten different phenotypes are studied here such as time since onset, COVID-19 status, connection between age and COVID-19, hospitalization status and ICU status, using classification models. Further, this study compares molecular characterization of COVID-19 patients with other respiratory diseases.

20.
Journal of Genetics and Genomics ; 48(9):755-866, 2021.
Article in English | CAB Abstracts | ID: covidwho-1823474

ABSTRACT

This special issue includes 13 articles focusing on innate lymphoid cells and gastrointestinal disease;microbiota-gut-brain axis in autism spectrum disorder;characteristic dysbiosis in gout and the impact of a uric acid-lowering treatment, febuxostat on the gut microbiota;gut microbiota, inflammation, and molecular signatures of host response to infection;the rice histone methylation regulates hub species of the root microbiota;a powerful adaptive microbiome-based association test for microbial association signals with diverse sparsity levels;an efficient metatranscriptomic approach for capturing RNA virome and its application to SARS-CoV-2;easy to create repeatable and editable Venn diagrams and Venn networks online.

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