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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.
Boletin de Malariologia y Salud Ambiental ; 62(1):24-31, 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-2040758

ABSTRACT

During the COVID-19 pandemic, doctors faced an unprecedented mass admission of patients with viral atypical pneumonia. The objective of the study was to compare the clinical characteristics of the first and second waves of the pandemic. An analytical observational study was carried out on patients with COVID-19 pneumonia who were admitted to Hospital Carrion de Huancayo, Peru located at more than 3000 meters above sea level. Two study periods were determined, group one represented by the first wave characterized by massive restriction and strict quarantine and the second wave where productive activities had already normalized to a great extent. Of a total of 252 patients with COVID-19, the average age was 56 years in the first wave and 52 years in the second wave, the male sex was more frequent in both 74% and 57%, mortality was 27% and 23%, the time of illness was 8 days and 10 days, respectively. On the other hand, the percentage of use of antibiotics, ivermectin and hydroxychloroquine was higher in the first wave. The use of corticosteroids and prolonged hospital stay was more frequent in the second wave. Comparison of both waves shows differences in age, mortality and time of illness, which may be due to the new molecular variants of SARS-COV-2.

3.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(12):1500-1508, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040500

ABSTRACT

Based on the M gene sequence of TGEV and PEDV and VP2 gene sequence of PoRV, the optimal reaction system and amplification procedure were established by optimizing primer, probe concentration and annealing temperature, and the Quantitative PCR method of TaqMan probes for three viruses is successfully established. On this basis, after further optimization of conditions, a triple real-time fluorescent quantitative PCR method for detecting TGEV, PEDV, and PoRV was established. The detection sensitivity of this method for TGEV, PEDV, and PoRV were 2.49 copies/ L, 4.36 copies/ L, and 4.96 copies/ L respectively. The maximum value of CV in repeated trials detected by TGEV, PEDV and PoRV were 2.5%, 3.8%, 4.3%, and the maximum value of CV in repeated trials between groups were 3.7%, 3.4%, 3.2%, which are no more than 5%.indicating that the established method has good reproducibility. Using this method to detect PRV, PCV1, and PRRSV virus samples, there is no cross-reaction, indicating that the method is specific. Using the established method to detect 40 clinical diseases, the samples were tested, and the positive rates of TGEV, PEDV, and PoRV were 5%, 30%, and 12.5%respectively. The mixed infection rate of TGEV and PEDV was 2.5%, the mixed infection rate of PEDV and PoRV was 5%. The results of the multiple fluorescence quantitative PCR method are consistent with those of the detection of a single fluorescent RT-PCR method, indicating that the established method has good clinical application value.

4.
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.

5.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(11):1421-1427, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040498

ABSTRACT

Recently, the variation and isolation of porcine epidemic diarrhea Virus (PEDV) has been a focus of industry research. Whether porcine aminopeptidase (pAPN) is a functional receptor of PEDV infection is still controversial. Therefore, this article aims to review the latest progress on pAPN as a receptor of PEDV and its role during infection, to clarify whether pAPN is a functional receptor and to provide a reference for isolation and subsequent study of PEDV.

6.
Zhongguo Bingyuan Shengwuxue Zazhi / Journal of Pathogen Biology ; 15(9):997-1004, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040442

ABSTRACT

Objective: To investigate the molecular mechanism of the action by which the MERS-CoV E proxein induces autophagy in 293T cells.

7.
Sri Lankan Journal of Infectious Diseases ; 12(2), 2022.
Article in English | CAB Abstracts | ID: covidwho-2040070

ABSTRACT

Real time RT-PCR is considered as the gold standard test to detect COVID-19. The use of sample pooling strategy increases testing capacity and spares resources. However, the effectiveness of sample pooling should be evaluated in the setting before being implemented. Forty five samples including 20 high positives (Ct<20), 20 low positives (Ct 20-40) and 05 negative samples were used to prepare 1:1, 1:3 and 1:5 simulated sample pools which were then subjected to viral RNA extraction followed by real time RT-PCR. Sensitivity and specificity of sample pooling technique in the detection of SARS-CoV-2 RNA was 100% without significant variation of Ct values. According to our results, pooling of up to 6 samples will not have an effect on the final result in clinical samples and hence can be adopted in the given context for the diagnosis of COVID-19 by RT-PCR.

8.
Chinese Journal of Nosocomiology ; 32(12):1880-1884, 2022.
Article in English, Chinese | CAB Abstracts | ID: covidwho-2034518

ABSTRACT

OBJECTIVE: To explore a new method for detecting respiratory viruses by extracting residual virus on mask, and verify its reliability and sensitivity. METHODS: The novel coronavirus analogs-s La Sota strains of chicken Newcastle disease virus and H120 strains of infectious bronchitis virus with different diluted concentrations were sprayed onto surgical masks and N95 masks through a respiratory simulator, and they were left standing at room temperature for 2 hours and 12 hours, respectively. The cDNA and its amplification cycle(CT) values of the nucleoocapsid protein(N) of chicken Newcastle disease virus and the nucleoprotein(NP) genes of infectious bronchitis virus were detected by ordinary polymerase chain reaction(PCR) and quantitative real-time PCR(qRT-PCR). The minimum detectable virus concentration and viral content in masks under different retention times were compared. RESULTS: The gene bands of the Newcastle disease virus La Sota strains and the infectious bronchitis virus H120 strains were detected on the masks stored for different times, and the total RNA of the virus had good amplification curves in the range of 10 pg-10 ng. The mean CT values of N gene and NP gene of the residual virus on the general medical surgical mask and N95 masks placed for 2 h were 22.547+or-0.342,23.698+or-0.501 and 22.855+or-0.308,24.036+or-0.338, respectively. However, only part of them could be detected after 12 h. respectively, and there was no significant difference in CT values between the two masks during the same period of time(P2 h=0.452, P12 h=0.355). The minimum detectable concentration of virus in the masks was 1:800, and the number of residual viruses on the mask that can be detected was 6.75x10~3. CONCLUSION: The method of screening coronavirus by detecting virus residues on masks within 2 hours was feasible and suitable for medical surgical masks and N95 masks, which can be used for preliminary screening of respiratory viruses.

9.
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.

10.
Zycie Weterynaryjne ; 96(1):42-49, 2021.
Article in Polish | CAB Abstracts | ID: covidwho-2034018

ABSTRACT

Poultry industry is dynamically developing worldwide, and the threat from infectious viral diseases also increases. One of them is an acute, highly contagious avian infectious bronchitis (IB), caused by infectious bronchitis virus (IBV), the coronavirus of the fowl. IBV is characterized by extensive variations in the surface spike protein gene. Those genetic variations lead to rapid changes in IBV serotypes that need to be constantly monitored to assess the epidemiological situation in the field. The aim of this article was to present current knowledge and recent epidemiology, based on IBV field strains circulation. Several serotypes can be simultaneously present in a region and as they cross-protect poorly, broiler chickens can be infected more than once within their short period of life. Careful, constant monitoring is necessary to respond fast in case of new genetic IBV variants development. Some of these strains have global range, while the prevalence of others is limited to some geographical areas. Thus, the understanding the IB epidemiology, virus spread and the occurrence of individual strains allows to use the optimal vaccination schedule to limit the disease and improve the poultry production. Finaily, a good recognition of the IB problem in Central and Eastern Europe on the example of Poland as the largest European poultry producer, can be a key factor in the quickest response to emerging new IBV variants. Some practical solutions may help to introduce the similar and effective procedures also in other regions of the world with high intensity of poultry production.

11.
Zoonoses ; 1(13), 2021.
Article in English | CAB Abstracts | ID: covidwho-2025746

ABSTRACT

As the novel coronavirus SARS-CoV-2 spread around the world, multiple waves of variants emerged, thus leading to local or global population shifts during the pandemic. A new variant named Omicron (PANGO lineage B.1.1.529), which was first discovered in southern Africa, has recently been proposed by the World Health Organization to be a Variant of Concern. This variant carries an unusually large number of mutations, particularly on the spike protein and receptor binding domain, in contrast to other known major variants. Some mutation sites are associated with enhanced viral transmission, infectivity, and pathogenicity, thus enabling the virus to evade the immune protective barrier. Given that the emergence of the Omicron variant was accompanied by a sharp increase in infection cases in South Africa, the variant has the potential to trigger a new global epidemic peak. Therefore, continual attention and a rapid response are required to decrease the possible risks to public health.

12.
Acta Veterinaria et Zootechnica Sinica ; 53(6):2024-2028, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-2025545

ABSTRACT

This study aimed to analyze the proliferation characteristics of porcine deltacoronavirus (PDCoV) in suspension cultured porcine kidney cells LLC-PK1, so as to provide Candidate cell for large-scale production of PDCoV inactivated vaccine. LLC-PK1 cells were suspended by gradually decreasing serum method. PDCoV adaptive monoclonal cell lines were screened by limited dilution method. Indirect immunofluorescence method was used to identify the infectivity of PDCoV. The initial cell density, MOI, time of receiving virus collection and TPCK pancreatin concentration were screened to determine the best suspension culture conditions. The suspension cell strain LLC-PK1Sa which can proliferate PDCoV efficiently was screened out;PDCoV can specifically infect LLC-PK1 cells;PDCoV inoculated LLC-PK1Sa cells with a density of 2 x 106 cells.mL-1 according to the MOI of 10-3, When the final concentration of TPCK pancreatin reached 7.5 g.mL-1, the titer of virus solution harvested 48 h after inoculation was the highest. In this study, the efficient proliferation of PDCoV in LLC-PK1Sa suspension cells was realized for the first time, and the suspension culture conditions were preliminarily optimized, which could provide theoretical reference for large-scale production of PDCoV inactivated vaccine.

13.
PLoS Global Public Health ; 2(7), 2022.
Article in English | CAB Abstracts | ID: covidwho-2021498

ABSTRACT

Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.

14.
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.

15.
Zycie Weterynaryjne ; 95(7):398-405, 2020.
Article in Polish | CAB Abstracts | ID: covidwho-1999285

ABSTRACT

Family Coronaviridae (coronaviruses, CoVs), comprises enveloped, positive sense RNA viruses. They are largest RNA viruses identified so far. CoVs are known for over half a century as agents causing respiratory, alimentary or systemic infections in domestic and wild birds and mammals. Feline (FcoV) and canine coronaviruses (CCoV) are common in the populations of these animals and fetine infectious peritonitis virus (FIPV), infection may often be fatal. The new human coronavirus, SARS-CoV-Z, causing COVID-19 (coronavirus disease-IQ), identified in 2019 and responsible for the ongoing pandemics, has raised concerns about its zoonotic potential. Since cats and dogs live in close contact with owners it is important to establish their possible role in COVlD-19 epidemiology. There have been reports of SAHS-Covo2 positive dogs and cats in the literature and on various websites, including OIE website. However, considering that despite that millions of people are infected and the virus is still spreading worldwide, while only few cases of SARS-CoV-19 in dogs and cats have been confirmed, these companion animals do not play a role as virus reservoirs, thus are not important in COVlD-19 pandemics.

16.
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.

17.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(7):825-832, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-1994655

ABSTRACT

In order to establish a method for rapid differential identification of Senecavirus A (SVA) and en-cephalomyocarditis virus (EMCV), two pairs of corresponding specific primers were designed based on the highly conserved 3D genes of SVA and EMCV. And two different fluorescent labeled TaqMan probes were used to establish a dual TaqMan real-time PCR method for simultaneous detection of these two viruses, and we also optimize the reaction conditions. The results showed that the minimum detection of the method was 760 copies/ micro L and 98 copies/ micro L for SVA and EMCV. respectively, and it can specifically detect SVA and EMCV, and there was no cross reaction with CSFV, PRRSV and PEDV. The established standard curves showed good linear relationship. Repeated experimental group and inter-group coefficient of variation were less than 5%. The results indicated that the dual-quantitative PCR established in this study has the advantages of convenience, rapidity, good specificity. high sensitivity and good repeatability .and can be used for simultaneous detection of SVA and EMCV.

18.
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.

19.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(9):1112-1118, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-1994653

ABSTRACT

The effects of heat shock protein HSPQOABl on the replication of avian infectious bronchitis virus(AIBV) were confirmed by using over expression and RNA interference methods. The results showed that over expression of HSPQOABI inhibited AIBV replication, whereas knockdown of HSPQOABl in- creased AIBV replication. These results indicated that HSPQOABI is a potential anti-viral host factor. These findings provide the basis for further study of the pathogenic mechanism of AIBV and anti-coronavirus infection.

20.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(5):537-544, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-1994651

ABSTRACT

Long noncoding RNA (lncRNA) is a type of non-coding RNA molecule longer than 200 nt, which plays vital roles in biological events. Our previous results demonstrated that the host's lncRNA expression profile was significantly changed after porcine epidemic diarrhea virus (PEDV) infection. In this study, one of the lncRNAs, lncRNA9606, was selected to investigate its impact on PEDV replication. First, the kinetics of lncRNA9606 expression in IPEC-J2 cells were examined at different time points after PEDV infection. The results confirmed that PEDV infection significantly upregulated the expression of lncRNA9606. The lncRNA9606 expression levels in different cells or tissues were evaluated and the results showed that the amount of lncRNA9606 in Peyer's patches and peripheral blood mononuclear cells were significantly higher than that in small intestinal epithelial cell lines. It was mainly localized in the nucleus. Further investigations indicated that over expression of lncRNA in LLC-PK1 cells significantly inhibited PEDV replication. In conclusion, lncRNA9606 can suppress the PEDV replication in LLC-PK1 cells.

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