scholarly journals Isolation and Identification of a Rare Spike Gene Double-Deletion SARS-CoV-2 Variant From the Patient With High Cycle Threshold Value

2022 ◽  
Vol 8 ◽  
Author(s):  
Li-Teh Liu ◽  
Jih-Jin Tsai ◽  
Chun-Hong Chen ◽  
Ping-Chang Lin ◽  
Ching-Yi Tsai ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cultured Cells ◽  
Nucleic Acid Amplification ◽  
Post Inoculation ◽  
Rt Pcr ◽  
Isolation And Identification ◽  
Spike Gene ◽  
Double Deletion ◽  
Blind Passage ◽  
The Impact

Coronavirus disease 2019 (COVID-19) is an emerging life-threatening pulmonary disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, Hubei Province, China, in December 2019. COVID-19 develops after close contact via inhalation of respiratory droplets containing SARS-CoV-2 during talking, coughing, or sneezing by asymptomatic, presymptomatic, and symptomatic carriers. This virus evolved over time, and numerous genetic variants have been reported to have increased disease severity, mortality, and transmissibility. Variants have also developed resistance to antivirals and vaccination and can escape the immune response of humans. Reverse transcription polymerase chain reaction (RT–PCR) is the method of choice among diagnostic techniques, including nucleic acid amplification tests (NAATs), serological tests, and diagnostic imaging, such as computed tomography (CT). The limitation of RT–PCR is that it cannot distinguish fragmented RNA genomes from live transmissible viruses. Thus, SARS-CoV-2 isolation by using cell culture has been developed and makes important contributions in the field of diagnosis, development of antivirals, vaccines, and SARS-CoV-2 virology research. In this research, two SARS-CoV-2 strains were isolated from four RT–PCR-positive nasopharyngeal swabs using VERO E6 cell culture. One isolate was cultured successfully with a blind passage on day 3 post inoculation from a swab with a Ct > 35, while the cells did not develop cytopathic effects without a blind passage until day 14 post inoculation. Our results indicated that infectious SARS-CoV-2 virus particles existed, even with a Ct > 35. Cultivable viruses could provide additional consideration for releasing the patient from quarantine. The results of the whole genome sequencing and bioinformatic analysis suggested that these two isolates contain a spike 68-76del+spike 675-679del double-deletion variation. The double deletion was confirmed by amplification of the regions spanning the spike gene deletion using Sanger sequencing. Phylogenetic analysis revealed that this double-deletion variant was rare (one per million in public databases, including GenBank and GISAID). The impact of this double deletion in the spike gene on the SARS-CoV-2 virus itself as well as on cultured cells and/or humans remains to be further elucidated.

Transition from Antigenemia to Quantitative Nucleic Acid Amplification Testing in Kidney Transplant Recipients Receiving Preemptive Therapy for Cytomegalovirus Infection.

2021 ◽  
Author(s):  
Mônica Rika Nakamura ◽  
Lúcio R. Requião-Moura ◽  
Roberto Mayer Gallo ◽  
Camila Botelho ◽  
Júlia Taddeo ◽  
...  
Keyword(s):  
Glomerular Filtration Rate ◽  
Nucleic Acid ◽  
Acute Rejection ◽  
Glomerular Filtration ◽  
Filtration Rate ◽  
Nucleic Acid Amplification ◽  
Rt Pcr ◽  
Cmv Infection ◽  
Preemptive Treatment ◽  
The Impact

Abstract Due to the high costs, the strategy to reduce the impact of cytomegalovirus (CMV) after kidney transplant (KT) involves preemptive treatment in low and middle-income countries. Thus, this retrospective cohort study compared the performance of antigenemia transitioned to quantitative nucleic acid amplification testing, RT-PCR, in KT recipients receiving preemptive treatment as a strategy to prevent CMV infection. Between 2016 and 2018, 363 patients were enrolled and received preemptive treatment based on antigenemia (n=177) or RT-PCR (n=186). The primary outcome was CMV infection or disease. There were no differences in one-year cumulative incidence of CMV-related events (50.8% vs. 44.1%, P=0.20), neither in time to diagnosis (47.0 vs. 47.0 days) among patients conducted by antigenemia vs. RT-PCR, respectively. The length of CMV first treatment was longer with RT-PCR (20.0 vs. 27.5 days, P<0.001), while the rate of retreatment was not different (14.7% vs. 11.8%, P=0.48). In the Cox regression, the variables associated with CMV-related events were acute rejection within 30 days (HR=2.05, p=0.01) and 30-day glomerular filtration rate (HR=0.98, p<0.001). In conclusion, acute rejection and glomerular filtration rate are risk factors for CMV infection and disease, showing comparable performance in the impact of CMV-related events between antigenemia and RT-PCR for preemptive treatment.

Development of a Molecular Method for the Detection of Enteric Viruses in Oysters

1995 ◽  
Vol 58 (12) ◽  
pp. 1357-1362 ◽  
Author(s):  
LEE-ANN JAYKUS ◽  
RICARDO DE LEON ◽  
MARK D. SOBSEY
Keyword(s):  
Cell Culture ◽  
Nucleic Acid ◽  
Hepatitis A Virus ◽  
Enteric Virus ◽  
Nucleic Acid Amplification ◽  
Detection Methods ◽  
Ammonium Bromide ◽  
Rt Pcr ◽  
Initial Inoculum ◽  
Ctab Precipitation

Detection of enteric virus contamination of shellfish is limited by current methodology, which is time-consuming, tedious, and lacking in sensitivity due to reliance on cell culture infectivity. Alternative detection methods based on nucleic acid amplification have been hampered by high sample volumes and the presence of enzymatic inhibitors. The goal of this study was to develop methods to purify and concentrate intact virions from oyster extracts to a volume and quality compatible with viral genomic nucleic acid amplification by reverse transcriptase-polymerase chain reaction (RT-PCR). Fifty-gram oyster samples were homogenized and processed by standard adsorption-elution precipitation methodology and then seeded with 105 PFU of poliovirus 1 (PV1) or hepatitis A virus (HAV). Seeded viruses were concentrated by fluorocarbon extraction, polyethylene glycol (PEG) precipitation, chloroform extraction, and cetyltrimethyl ammonium bromide (CTAB) precipitation to a volume of 100 μl with removal of RT-PCR inhibitors. Virus recovery after elution of PEG precipitates was 50% for PVI and IS to 20% for HAV as evaluted by cell culture infectivity. The CTAB precipitation step yielded a concentrated sample which was directly compatible with RT-PCR reactions and capable of detecting about 100 placque=forming units (PFU) of PVl or HAV. When 50-g oyster extracts were seeded and processed by the entire concentration and purification scheme, direct RT-PCR detection of viral genomic RNA was possible at initial inoculum levels of 104 PFU of HAV and 103 PFU of PV1, with recoveries of 1 to 5% of seeded viruses.

scholarly journals Construction of an infectious cDNA clone of hepatitis E virus strain JE03-1760F that can propagate efficiently in cultured cells

2009 ◽  
Vol 90 (2) ◽  
pp. 457-462 ◽  
Author(s):  
Kentaro Yamada ◽  
Masaharu Takahashi ◽  
Yu Hoshino ◽  
Hideyuki Takahashi ◽  
Koji Ichiyama ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cdna Clone ◽  
Hepatitis E Virus ◽  
Culture Supernatant ◽  
Cultured Cells ◽  
A549 Cells ◽  
Hepatitis E ◽  
Infectious Cdna Clone ◽  
Post Inoculation ◽  
Genotype 3

A full-length infectious cDNA clone (pJE03-1760F/wt) of a genotype 3 hepatitis E virus (HEV) (strain JE03-1760F) obtained from a faecal specimen was constructed in this study. Upon transfection of the capped in vitro transcripts of pJE03-1760F/wt into PLC/PRF/5 cells, the viral RNA levels in the culture supernatant started to increase on day 6 post-transfection (p.t.) and reached 107 copies ml−1 on day 28 p.t. Detection of increasing numbers of cells with ORF2 protein expression by immunofluorescence assay at 5, 7, 11 and 15 days p.t. indicated the spread of HEV infection in cell culture. When the cDNA-derived virus in culture supernatant was inoculated into PLC/PRF/5 or A549 cells, it grew as efficiently as the faeces-derived virus in both cells, reaching 106 copies ml−1 at 30 days post-inoculation. Our reverse genetics system for HEV that is usable in a robust cell-culture system will be useful for elucidation of the mechanism of HEV replication and functional roles of HEV proteins.

scholarly journals Fatty Acyl Availability Modulates Cardiolipin Composition and Alters Mitochondrial Function in HeLa Cells

2020 ◽  
Author(s):  
Gregor Oemer ◽  
Marie-Luise Edenhofer ◽  
Katharina Lackner ◽  
Geraldine Leman ◽  
Jakob Koch ◽  
...  
Keyword(s):  
Cell Culture ◽  
Growth Medium ◽  
Mammalian Cells ◽  
Cultured Cells ◽  
Citrate Synthase ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Fatty Acyl ◽  
Membrane Composition ◽  
The Impact

The molecular assembly of cells depends not only on their balance between anabolism and catabolism, but to a large degree also on the building blocks available in the environment. For cultivated mammalian cells, this is largely determined by the composition of the growth medium used. Here we study the impact of medium lipids on mitochondrial membrane architecture and function by combining LC-MS/MS lipidomics and functional tests with lipid supplementation experiments in an otherwise serum- and lipid-free cell culture model. We demonstrate that the composition of mitochondrial cardiolipins (CL) strongly depends on the lipid environment in cultured cells and prefers the incorporation of essential linoleic acid over other fatty acids. Simultaneously, the mitochondrial respiratory complex I activity was altered, whereas the matrix-localized enzyme citrate synthase was unaffected. This suggests a link between membrane composition and respiratory capacity. In summary, we find a strong dependency of central mitochondrial features on the type of lipids contained in the growth medium. Thus, this underlines the importance of considering these factors when using and establishing cell culture models in biomedical research.

scholarly journals Isolation and identification of Newcastle disease viruses from field outbreaks in chickens and pigeons

2013 ◽  
Vol 29 (2) ◽  
pp. 41-48 ◽  
Author(s):  
AC Mazumder ◽  
S Khatun ◽  
M Nooruzzaman ◽  
EH Chowdhury ◽  
PM Das ◽  
...  
Keyword(s):  
Cell Culture ◽  
Newcastle Disease ◽  
Chicken Embryo Fibroblast ◽  
Haemagglutination Inhibition ◽  
Rt Pcr ◽  
Isolation And Identification ◽  
Cytopathic Effects ◽  
History Of ◽  
Chicken Eggs ◽  
Embryonated Chicken

Eleven dead or sick birds submitted from farms in the year 2010 with a history of sudden death with respiratory and/or diarrhoeal signs were used for isolation and identification of Newcastle disease virus (NDV). All samples were subjected to routine necropsy. Pooled respiratory tissues were inoculated in embryonated chicken eggs and chicken embryo fibroblast (CEF) cell culture. The growth of NDV was confirmed by embryo mortality, cytopathic effects (CPE) in cell culture, haemagglutination (HA) and haemagglutination inhibition (HI) test. The presence of NDV was confirmed by reverse transcriptionpolymerase chain reaction (RT-PCR). At necropsy seven cases were tentatively diagnosed as Newcastle disease (ND). Out of seven ND-suspected samples, four yielded virus in both embryos and cell culture, while one was positive only in embryos, one only in cell culture and one sample was negative in both embryos and cell culture. RT-PCR successfully amplified a 766 bp fragment covering parts of Matrix and Fusion protein genes of NDV from the samples that were positive either in embryos or in cell culture. It is suggested that RT-PCR could be a rapid and sensitive tool for the detection of NDV. DOI: http://dx.doi.org/10.3329/bvet.v29i2.14341 Bangl. vet. 2012. Vol. 29, No. 2, 41-48

scholarly journals In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains

2021 ◽  
Author(s):  
Michael Diamond ◽  
Rita Chen ◽  
Emma Winkler ◽  
James Case ◽  
Ishmael Aziati ◽  
...  
Keyword(s):  
Cell Culture ◽  
South African ◽  
Neutralizing Antibodies ◽  
Partial Loss ◽  
Spike Gene ◽  
Immunocompetent Mice ◽  
The Impact ◽  
Emergence Of Resistance ◽  
Higher Doses

Abstract Rapidly-emerging variants jeopardize antibody-based countermeasures against SARS-CoV-2. While recent cell culture experiments have demonstrated loss of potency of several anti-spike neutralizing antibodies against SARS-CoV-2 variant strains1-3, the in vivo significance of these results remains uncertain. Here, using a panel of monoclonal antibodies (mAbs) corresponding to many in advanced clinical development by Vir Biotechnology, AbbVie, AstraZeneca, Regeneron, and Lilly we report the impact on protection in animals against authentic SARS-CoV-2 variants including WA1/2020 strains, a B.1.1.7 isolate, and chimeric strains with South African (B.1.351) or Brazilian (B.1.1.28) spike genes. Although some individual mAbs showed reduced or abrogated neutralizing activity against B.1.351 and B.1.1.28 viruses with E484K spike protein mutations in cell culture, low prophylactic doses of mAb combinations protected against infection in K18-hACE2 transgenic mice, 129S2 immunocompetent mice, and hamsters without emergence of resistance. Two exceptions were mAb LY-CoV555 monotherapy which lost all protective activity in vivo, and AbbVie 2B04/47D11, which showed partial loss of activity. When administered after infection as therapy, higher doses of mAb cocktails protected in vivo against viruses displaying a B.1.351 spike gene. Thus, many, but not all, of the antibody products with Emergency Use Authorization should retain substantial efficacy against the prevailing SARS-CoV-2 variant strains.

IN VITRO METHODS FOR THE STUDY OF THE ADENOHYPOPHYSIAL FUNCTIONS TO SECRETE GONADOTROPHIN

1971 ◽  
Vol 68 (1_Suppl) ◽  
pp. S27-S40 ◽  
Author(s):  
T. Kobayashi ◽  
T. Kigawa ◽  
M. Mizuno ◽  
T. Watanabe
Keyword(s):  
Cell Culture ◽  
Organ Culture ◽  
Cultured Cells ◽  
Cell Sheet ◽  
Short Term ◽  
Hypothalamic Extract ◽  
Numerous Cell ◽  
Single Cell Culture ◽  
Almost All

ABSTRACT There are several in vitro methods to analyse the function of the adenohypophysis or the mechanisms of its regulation. The present paper deals with single cell culture, organ culture and short term incubation techniques by which the morphology and gonadotrophin-secreting function of the adenohypophysis were studied. In trypsin-dispersed cell culture, the adenohypophysial cells showed extensive propagation to form numerous cell colonies and finally develop into a confluent monolayer cell sheet covering completely the surface of culture vessels. Almost all of the cultured cells, however, became chromophobic, at least at the end of the first week of cultivation, when gonadotrophin was detectable neither in the culture medium nor in the cells themselves. After the addition of the hypothalamic extract, gonadotrophin became detectable again, and basophilic or PAS-positive granules also reappeared within the cells, suggesting that the gonadotrophs were stimulated by the extract to produce gonadotrophin. In organ culture and short term incubation, the incorporation of [3H] leucine into the adenohypophysial cells in relation to the addition of hypothalamic extract was examined. It was obvious that the ability to incorporate [3H] leucine into the gonadotrophs in vitro was highly dependent upon the presence of the hypothalamic extract.

Detection of enteroviruses in marine waters by direct RT-PCR and cell culture

1995 ◽  
Vol 31 (5-6) ◽  
pp. 323-328 ◽  
Author(s):  
K. A. Reynolds ◽  
C. P. Gerba ◽  
I. L. Pepper
Keyword(s):  
Cell Culture ◽  
Polymerase Chain Reaction Amplification ◽  
Cost Effective ◽  
The United States ◽  
Water Runoff ◽  
Rt Pcr ◽  
Marine Waters ◽  
Storm Water Runoff ◽  
Routine Monitoring ◽  
Reaction Amplification

Sewage outfalls and storm water runoff introduces pathogenic human enteric viruses into marine coastal waters, which may pose a potential public health risk. Although members of the enterovirus group have been suggested as possible indicators of sewage pollution in marine waters, the lack of rapid, sensitive and cost effective methods have prevented routine monitoring in the United States. This study compared traditional cell culture and direct RT-PCR (reverse transcriptase-polymerase chain reaction) amplification for detection of an enterovirus. Poliovirus could be recovered from 100 L of artificial seawater with an average efficiency of 77%, using adsorption and elution from electronegative filters. Viruses were eluted from the filters with 1.5% beef extract for viruses (BEV) adjusted to pH 9.5 and reconcentrated by organic flocculation to a volume of 30 mL. Substances which interfered with detection by RT-PCR were removed by treatment of the concentrates with sephadex and chelex resins. Direct RT-PCR could detect 2.5 and 0.025 PFU (plaque forming units) for single (25 cycles) and double PCR (2 × 25 cycles) in 10 μL of pure culture poliovirus samples, respectively. These methods are currently being applied to assess the occurrence of enteroviruses at marine bathing beaches influenced by sewage discharges.

Change in mutation frequency at a TP53 hotspot during culture of ENU-mutagenised human lymphoblastoid cells

Mutagenesis ◽  
2019 ◽  
Author(s):  
Masahiko Watanabe ◽  
Masae Toudou ◽  
Taeko Uchida ◽  
Misato Yoshikawa ◽  
Hiroaki Aso ◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Growth ◽  
Mutation Frequency ◽  
Cultured Cells ◽  
Tp53 Gene ◽  
Tumour Suppressor Genes ◽  
Restriction Sites ◽  
Mutation Spectra ◽  
Risk Of Cancer ◽  
Assay Conditions

Abstract Mutations in oncogenes or tumour suppressor genes cause increases in cell growth capacity. In some cases, fully malignant cancer cells develop after additional mutations occur in initially mutated cells. In such instances, the risk of cancer would increase in response to growth of these initially mutated cells. To ascertain whether such a situation might occur in cultured cells, three independent cultures of human lymphoblastoid GM00130 cells were treated with N-ethyl-N-nitrosourea to induce mutations, and the cells were maintained for 12 weeks. Mutant frequencies and spectra of the cells at the MspI and HaeIII restriction sites located at codons 247–250 of the TP53 gene were examined. Mutant frequencies at both sites in the gene exhibited a declining trend during cell culture and reached background levels after 12 weeks; this was also supported by mutation spectra findings. These results indicate that the mutations detected under our assay conditions are disadvantageous to cell growth.

scholarly journals PC12 and THP-1 Cell Lines as Neuronal and Microglia Model in Neurobiological Research

2021 ◽  
Vol 11 (9) ◽  
pp. 3729
Author(s):  
Katarzyna Balon ◽  
Benita Wiatrak
Keyword(s):  
Cell Culture ◽  
Dna Damage ◽  
Cell Lines ◽  
Inflammatory Factor ◽  
Research Model ◽  
Differentiated Cells ◽  
Undifferentiated Cells ◽  
Primary Cell Lines ◽  
Neurobiological Research ◽  
The Impact

Models based on cell cultures have become a useful tool in modern scientific research. Since primary cell lines are difficult to obtain and handle, neoplasm-derived lines like PC12 and THP-1 offer a cheap and flexible solution for neurobiological studies but require prior differentiation to serve as a neuronal or microglia model. PC12 cells constitute a suitable research model only after differentiation by incubation with nerve growth factor (NGF) and THP-1 cells after administering a differentiation factor such as phorbol 12-myristate-13-acetate (PMA). Still, quite often, studies are performed on these cancer cells without differentiation. The study aimed to assess the impact of PC12 or THP-1 cell differentiation on sensitivity to harmful factors such as Aβ25-35 (0.001–5 µM) (considered as one of the major detrimental factors in the pathophysiology of Alzheimer’s disease) or lipopolysaccharide (1–100 µM) (LPS; a pro-inflammatory factor of bacterial origin). Results showed that in most of the tests performed, the response of PC12 and THP-1 cells induced to differentiation varied significantly from the effect in undifferentiated cells. In general, differentiated cells showed greater sensitivity to harmful factors in terms of metabolic activity and DNA damage, while in the case of the free radicals, the results were heterogeneous. Obtained data emphasize the importance of proper differentiation of cell lines of neoplastic origin in neurobiological research and standardization of cell culture handling protocols to ensure reliable results.

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