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1.
Virus Evolution ; 8(veac080), 2022.
Article in English | CAB Abstracts | ID: covidwho-2051563

ABSTRACT

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

2.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(11):1373-1378, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040499

ABSTRACT

In order to build a specific, sensitive and rapid detection method for PAstV3 detection, the PAstVB gene sequences in Genbank were used and the conserved region in ORFlb was selected to design specific primers and TaqMan probe. Clinical stool samples were collected and preliminary detected by this newly established real-time RT-PCR method after reaction systems and conditions optimization. This detection method established in this study has a good linear relationship with the standard curve, with R2 value up to 0.9971. The sensitivity is 100 times higher than conventional PCR method, The variation co-efficient of in-batch and inter-batch repeatability test is less than 2.0%, indicating good repeatability. The detection results of Clinical samples showed that the positive rate of this method is higher than conventional PCR method. The establishment of this method provides a rapid detection means for PAstV3 laboratory diagnosis and epidemiological investigation.

3.
Zhongguo Yufang Shouyi Xuebao / Chinese Journal of Preventive Veterinary Medicine ; 44(1):108-108, 2022.
Article in English, Chinese | CAB Abstracts | ID: covidwho-2034138

ABSTRACT

Avian infectious bronchitis (IB) is one of the acute and highly contagious upper respiratory tract infectious diseases in poultry caused by the Infectious bronchitis virus (IBV), which significantly affects the health and development of world poultry farming industry. IBV RNA polymerase lacks a complete correctional function and is prone to gene mutation and RNA-RNA recombination during the replication process, resulting in the emergence of new serotypes, genotypes and mutant strains. The continuous generation of recombinant strains through homologous recombination between strains also complicates the prevention and control of IB. Therefore, monitoring the genetic evolutionary characteristics of circulating strains and evaluating the protective effect of commonly used vaccines against local circulating strains of IBV are the keys to preventing and controlling this disease.

4.
American Journal of Primatology ; 84(4/5), 2022.
Article in English | CAB Abstracts | ID: covidwho-2033684

ABSTRACT

This special issue consists of 17 papers dealing with issues animal health (captive and wild primates), environmental health (rain forests and mountain areas), and human health (the role of religion in One Health, lessons from the Hanuman langur (Semnopithecus entellus) and other human-non-human primate interactions,and Covid-19).

5.
Archives of Razi Institute ; 77(5):1611-1619, 2022.
Article in English | CAB Abstracts | ID: covidwho-2002783

ABSTRACT

Infectious bronchitis (IB) disease, avian Infectious Bronchitis disease in one of the major cause of respiratory problems and economic loss in poultry industry, even in developed countries with good biosecurity practice. Since the first isolation of the virus in 1931, a lot of serotypes and genotypes of the virus have been reported around the world. The GI-1 lineage, including Massachusetts (Mass) serotype viruses, is one of the most widely spread types worldwide. Moreover, the GI-23 lineage with a growing incidence rate was reported approximately 20 years ago in the Middle East, with no or little homologues vaccine use. The genotype was previously restricted to the Middle East;now, there is evidence that it has spread to European countries, raising concerns regarding potential outbreaks. In the present study, our attempt was to phylogenetically analyze the S1 gene of six isolates from Massachusetts and variant 2 genotypes, which were isolated from broiler and broiler breeder flocks in Iran. The variant 2 viruses were compared to other reported variant 2 viruses from neighboring countries and they had more than 98% identity with the latest reported Iranian variant 2. In addition, Three Mass type viruses were similar to vaccine strains which may be shows continuous circulation of vaccine viruses in the field. This event can cause increasing the risk of their mutation or even reversion to virulence after several passages in natural host, furthermore circulating viruses may recombinant with virulent field viruses and cause emergence of new variants. Considering the variable nature of IB viruses in which few changes lead to important differences, continuous epidemiological surveillance along with clinical studies of new isolates, are crucial to a better understanding of their pathogenicity and subsequent disease control.

6.
Zycie Weterynaryjne ; 95(7):405-413, 2020.
Article in Polish | CAB Abstracts | ID: covidwho-1998970

ABSTRACT

This paper presents a review of most important zoonotic diseases that are threatening human World population in the first 20 years of XXI century. Zoonoses diseases naturally transmitted through several modes from vertebrate animal hosts to humans. SARS-CoV-Z - severe acute respiratory syndrome coronavirus 2, was identified as the cause of an outbreak of COVID-2 pandemic in humans in 2019/2020. Coronavirus positive Chinese bats and an unrecognized yet natural reservoir of emerging SARS-Z, are indicated as a primary source of infection. So far, there is no evidence that companion or farm animals can become infected by contact with a sick/infected person, so SARS-2 virus strains isolated from humans are not zoonotic. This review contains a description of SARS-2 virus structure, genetic diversity, structure and function of viral proteins, including class I viral fusion protein S. The review also includes an assessment of epidemiology of SARS-2 infection, criteria and epidemiological interactions, perspectives on emerging zoonoti'c disease research in contact with public health service. More closed cooperation between different services, including Veterinary Services, with WHO and OIE international standards, as eg. One Health partnership, is essential to avoid or minimize risk of new infections in future.

7.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(9):1147-1158, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-1994654

ABSTRACT

To understand the genetic diversity of porcine deltacoronavirus(PDCo V) in Guangxi Province, clinical diarrhea samples were collected from suspected piglets in Guangxi Province from2017 to 2019, detected by RT-PCR for PDCoV, and the positive samples were used for amplification and sequence of S, M, N genes. Finally, 16 S, M and N gene sequences of PDCoV were obtained. Homology analysis showed that the S, M, N gene nucleotide identity among Guangxi strains were 95.8% -99.9%, 95.9%-100% and 97.9%-99.9%, respectively. The nucleotide identity of S, M and N genes among Guangxi strains and other reference strains were 95.1%-100%, 95.0%-100%and 96.3%-99.9%, respectively. Sequence alignment showed that S1 protein existed amino acid mutations and insertions, and there were some variations among different epidemic strains. Phylogenetic trees based on S, M and N genes obtained similar topological diagram and all strains could be divided into Group I, Group II and GroupIII, of which Group I came from USA, Japan and Korea, Group II came from China, and Group III came from China, Vietnam, Laos and Thailand. Most strains from Guangxi Province distributed in Group II, individual strain distributed in Group III and some strains formed a single small branch. The evolutionary rates of S, M and N genes of Guangxi strains and other reference strains were 2.57 x 10-4, 2.07 x 10-4, 1.70 x 10-4 substitutions/site/year, respectively, showing that the evolutionary rate of S gene was the fastest. The results indicated that the S, M, N genes of PDCo V strains from Guangxi Province had some variations and existed genetic diversity.

8.
Indian Journal of Animal Sciences ; 92(6):693-700, 2022.
Article in English | CAB Abstracts | ID: covidwho-1975927

ABSTRACT

Emergence of avian infectious bronchitis virus (IBV) variants with altered tissue tropism and host range has been reported from different parts of the world. Little is known about the different IBV variants existing and emerging in India. To explore the same, an IBV isolate, namely B17 isolated from backyard chicken in Tamil Nadu was used in the present study. The complete genome of B17 was sequenced and its phylogenetic relationship with the existing vaccine strain genotypes was analysed. The phylogenetic analysis of both S1 gene and complete genome sequence grouped B17 under Mass41 genotype comprising of M41, Beaudette, H120 and H120 variant with bootstrap value of 95-100%. Further, genomic analysis of B17 revealed the possibilities of emergence of the same from H120 vaccine strain through mutations at various genes.

9.
Journal of Drug Delivery and Therapeutics ; 12(3):138-157, 2022.
Article in English | CAB Abstracts | ID: covidwho-1975615

ABSTRACT

Revitalization of local health traditions (RLHT) has become an inevitable aspect of human wellbeing in the post COVID era. An ethnobotanical survey was carried out to collect information on local health traditions and cultural reflections associate with the age old use of wild edible fruits (WEFs) from common plants in Melur Region of Madurai district, TamilNadu, India as the habit of consuming WEFs is quite common among people in this region and has not been completely abandoned in particular among the age old people. Information presented in this paper has been gathered from local people using an integrated approach of botanical collections, group discussions and interviews with questionnaires during the period from Apr 2021 to Mar 2022. As much as 29 informants were interviewed, among the informants 6 were local health-care practitioners (Vidiyars). Studies on the use of WEFs from common plants in Melur resulted in collection and documentation of information on a total of 34 ethnomedicinal plant species distributed across 20 families. Medicinal plants used by local people are listed with scientific name, family, local name, plant part(s) used, mode of consumption and preparation and medicinal uses. Data collected during the study clearly indicates that fresh parts of the plant (Fruit (Ripe/ Unripe)) were more preferred in general for the preparation of medicinal formulations by the local health practitioners. Documented ethnomedicinal plants were mostly used to cure long term complications associated with diabetics, gastrointestinal disorders, skin diseases, poison bites and nervous disorders. Howsoever, results of this study is clear record to the claim that the local people still depend on medicinal plants to overcome situations like COVID pandemic as fruits from most of the plants documented serve as natural source of immune boosters. Further, in-depth studies (both In-silico and Pre Clinical trials) are expected to bring to limelight the hidden quantum of bioactive compounds in the fruits these medicinal plants and their therapeutic potential.

10.
Bonplandia ; 31(2), 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-1934961

ABSTRACT

The normal management of plant germplasm conservation laboratories involves carrying out numerous and diverse activities, which were affected by the coronavirus pandemic (COVID-19). The objective of this publication was to review the evolution of the cassava in vitro germplasm bank at the FCA-UNNE and IBONE (CONICET-UNNE) and to tell about usual management practices and the procedures to preserve living plant material and the personnel's life involved in pre-pandemic and COVID-19 pandemic times. Teachers, researchers, undergraduate and graduate students carried out, for almost 40 years, the in vitro conservation of 56 cassava cultivars from different countries. Before March 2020, the bank management consisted mainly in scientific-technological activities for the conservation of the material and the search for parameters to establish an order of subcultures. Having decreed Social, Preventive and Compulsory Isolation in Argentina, conservation activities continued applying the usual practices by following political-institutional sanitary measures. To face the new sanitary scenarios, methodologies must be adjusted so that they are effective at maintaining viability of the plant material and at prolonging conservation time.

11.
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.

12.
Pakistan Journal of Zoology ; 54(4):1899-1904, 2022.
Article in English | CAB Abstracts | ID: covidwho-1904009

ABSTRACT

Coronavirus consists of single-stranded, enveloped and RNA virus, largest genome among all RNA viruses and has 4 proteins i.e. envelope, spike, nucleocapsid and membrane. Coronaviruses are classified into 4 genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Betacoronavirus most probably originated from bats and the virus may have jumped to avian species and evolved as Deltacoronavirus group. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavirus from Deltacoronavirus, while Betacoronavirus may have given rise to Alphacoronavirus. It is known that SARS-CoV-2 belongs to Betacoronavirus. This most similar virus is verified in bat and Malayan Pangolin. Analysis showed that SARS-CoV-2 most probably originated by recombination of both bat and pangolin viruses. Viral protein seroconversion and viral specific nucleotide positive documented in all COVID-19 patients tested provides confirmation of a link between the presence of this virus and the disease.

13.
NAVC Clinician's Brief ; 29, 2022.
Article in English | CAB Abstracts | ID: covidwho-1898327
14.
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.

15.
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.

16.
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.

17.
Chinese Journal of Zoonoses ; 38(1):42-47, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-1789499

ABSTRACT

Since the end of December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to global public health security. Many coronaviruses, including SARS-CoV-2, are of animal origin. Therefore, monitoring of animal coronavirus must be strengthened. Herein, the common sample types, cell types used for viral isolation and culture, viral molecular detection methods, and immunological detection of animal coronaviruses are reviewed to provide a reference for follow-up studies of animal coronaviruses.

18.
Journal of Medical Microbiology and Infectious Diseases ; 10(1):1-9, 2022.
Article in English | CAB Abstracts | ID: covidwho-1787279

ABSTRACT

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) spilled over to humans via wild mammals, entering the host cell using angiotensin-converting enzyme 2 (ACE2) as receptor through Spike (S) protein binding. While SARS-CoV-2 became fully adapted to humans and globally spread, some mammal species were infected back. The present study evaluated the potential risk of mammals becoming hosts for SARS-CoV-2 through bioinformatics prediction based on ACE2 receptors.

19.
Uttar Pradesh Journal of Zoology ; 42(19):69-72, 2021.
Article in English | CAB Abstracts | ID: covidwho-1652250

ABSTRACT

The growing awareness that biodiversity is a precious global asset to present and future generation and that species's survival and the integrity of habitats and ecosystems are at serious risk, has increased significantly the importance of biodiversity related research. Biodiversity can be defined as the variability among living organism from all sources, including terrestrial, marine and other aquatic ecosystem and the ecological complexes of which they are part;this includes diversity within species between species and of ecosystems. The diversity of life on earth is nearly unimaginable. There is such a wealth of organism that it's a continuous need to keep trace of the diversity and there is always a provision for the discovery of new ones as it is a well-known fact that changing environmental conditions, habitat food and other ecological factors are more than enough to bring out certain definite changes and the accumulation of small changes give rise to a new species. With covid-19 we have seen the damage the diseases can do not only to human health but also to the global economy.By protecting biodiversity in Earth's ecosystem, countries could save lives and money while helping to prevent future pandemics. The present findings add one new species of an acanthocephalan parasite i.e. Raosentis cavasii from fresh water fish Mystus cavasius. It differs from R.thapari in presence of 20 rows of trunk spines instead of 9 rows, in having unequal lemnisci instead of being equal and in their extension upto proboscis receptacle and in the number of hypodermic nuclei 2-3 pairs dorsal and 1 ventral instead of 3 pairs on both sides.

20.
Kurdistan Journal of Applied Research ; - (ICHMS):137-144, 2020.
Article in English | CAB Abstracts | ID: covidwho-1573683

ABSTRACT

Coronavirus Disease 19 (COVID-19) emergence reveals globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV;moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade.

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