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1.
Nat Commun ; 13(1): 4054, 2022 07 13.
Article in English | MEDLINE | ID: covidwho-1931408

ABSTRACT

Establishment of zoonotic viruses, causing pandemics like the Spanish flu and Covid-19, requires adaptation to human receptors. Pandemic influenza A viruses (IAV) that crossed the avian-human species barrier switched from binding avian-type α2-3-linked sialic acid (2-3Sia) to human-type 2-6Sia receptors. Here, we show that this specificity switch is however less dichotomous as generally assumed. Binding and entry specificity were compared using mixed synthetic glycan gradients of 2-3Sia and 2-6Sia and by employing a genetically remodeled Sia repertoire on the surface of a Sia-free cell line and on a sialoglycoprotein secreted from these cells. Expression of a range of (mixed) 2-3Sia and 2-6Sia densities shows that non-binding human-type receptors efficiently enhanced avian IAV binding and entry provided the presence of a low density of high affinity avian-type receptors, and vice versa. Considering the heterogeneity of sialoglycan receptors encountered in vivo, hetero-multivalent binding is physiologically relevant and will impact evolutionary pathways leading to host adaptation.


Subject(s)
COVID-19 , Influenza A virus , Influenza Pandemic, 1918-1919 , Influenza, Human , Animals , Hemagglutinin Glycoproteins, Influenza Virus/metabolism , Humans , Influenza A virus/metabolism , N-Acetylneuraminic Acid/metabolism , Receptors, Cell Surface/genetics , Receptors, Cell Surface/metabolism , Receptors, Virus/metabolism
2.
Int J Environ Res Public Health ; 19(10)2022 05 12.
Article in English | MEDLINE | ID: covidwho-1875623

ABSTRACT

Acquired immune deficiency syndrome (AIDS) is a serious public health problem. This study aims to establish a combined model of seasonal autoregressive integrated moving average (SARIMA) and Prophet models based on an L1-norm to predict the incidence of AIDS in Henan province, China. The monthly incidences of AIDS in Henan province from 2012 to 2020 were obtained from the Health Commission of Henan Province. A SARIMA model, a Prophet model, and two combined models were adopted to fit the monthly incidence of AIDS using the data from January 2012 to December 2019. The data from January 2020 to December 2020 was used to verify. The mean square error (MSE), mean absolute error (MAE), and mean absolute percentage error (MAPE) were used to compare the prediction effect among the models. The results showed that the monthly incidence fluctuated from 0.05 to 0.50 per 100,000 individuals, and the monthly incidence of AIDS had a certain periodicity in Henan province. In addition, the prediction effect of the Prophet model was better than SARIMA model, the combined model was better than the single models, and the combined model based on the L1-norm had the best effect values (MSE = 0.0056, MAE = 0.0553, MAPE = 43.5337). This indicated that, compared with the L2-norm, the L1-norm improved the prediction accuracy of the combined model. The combined model of SARIMA and Prophet based on the L1-norm is a suitable method to predict the incidence of AIDS in Henan. Our findings can provide theoretical evidence for the government to formulate policies regarding AIDS prevention.


Subject(s)
Acquired Immunodeficiency Syndrome , Acquired Immunodeficiency Syndrome/epidemiology , China/epidemiology , Forecasting , Humans , Incidence , Models, Statistical
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318389

ABSTRACT

This protocol presents the Variant Nucleotide Guard (VaNGuard) assay, which is robust towards viral mutations and can be performed on purified RNA or directly on nasopharyngeal (NP) swab samples. The procedure typically comprises three parts, namely sample preparation, RT-LAMP reaction, and Cas12a-based detection via fluorescence or lateral flow assay. Sample preparation from NP swabs involves Proteinase K digestion followed by heat inactivation. Purified RNA or digested NP swab samples are then added as templates into RT-LAMP reactions and incubated at 65ºC for 22 minutes. Next, enAsCas12a and ssDNA-probes are added and the reactions are incubated at 60ºC for another 5 minutes. End-point fluorescence can be detected by a plate reader or a real-time PCR machine. Alternatively, a lateral flow strip can be inserted into each reaction tube for equipment-free read-out. The VaNGuard assay is a rapid and convenient point-of-care test for SARS-CoV-2 and is applicable to resource poor settings.

4.
ACS Synth Biol ; 11(1): 448-463, 2022 01 21.
Article in English | MEDLINE | ID: covidwho-1606986

ABSTRACT

The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because it can be performed with simple instrumentation. However, isothermal amplification methods frequently yield spurious amplicons even in the absence of a template. Consequently, RT-LAMP assays can produce false positive results when they are based on generic intercalating dyes or pH-sensitive indicators. Here, we report the development of a sensitive RT-LAMP assay that leverages on a novel sequence-specific probe to guard against spurious amplicons. We show that our optimized fluorescent assay, termed LANTERN, takes only 30 min to complete and can be applied directly on swab or saliva samples. Furthermore, utilizing clinical RNA samples from 52 patients with COVID-19 infection and 21 healthy individuals, we demonstrate that our diagnostic test exhibits a specificity and positive predictive value of 95% with a sensitivity of 8 copies per reaction. Hence, our new probe-based RT-LAMP assay can serve as an inexpensive method for point-of-need diagnosis of COVID-19 and other infectious diseases.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/genetics , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , RNA, Viral/genetics , SARS-CoV-2/genetics , Humans
5.
Chinese Journal of Viral Diseases ; 11(2):87-90, 2021.
Article in Chinese | CAB Abstracts | ID: covidwho-1318573

ABSTRACT

As the original source of the SARS-CoV-2 and the pathogen of the coronavirus disease 2019. SARS-CoV-2 samples are important basic materials for clinical treatment, scientific research, drug screening, and vaccine research and development. They are important national strategic resources and should be preserved. In order to do a good job in the management of the collection of SARS-CoV-2 samples and provide technical support for relevant institutions, China CDC took the lead in formulationg and issuing the group standard of the Chinese Preventive Medicine Association, the Requirements for preservation of SARS-CoV-2 samples (T/CPMA 019-2020). Under the framework of the basic requirements, the standard includes two parts: the preservation information and preservation conditions of SARS-CoV-2 samples. The preservation information describes the necessary and non-essential information items required for the preservation of SARS-CoV-2 samples in the form of a table. The preservation conditions describes the safety and other requirements of SARS-CoV-2 samples container, and also show the optimal preservation conditions and requirements of SARS-CoV-2 samples in the form of a table. It is very important to do a good job in the management of SARS-CoV-2 strains and samples, regulate the preservation of strains and samples, and ensure biosafety and resource securirty.

6.
Trends Microbiol ; 29(11): 983-992, 2021 11.
Article in English | MEDLINE | ID: covidwho-1187873

ABSTRACT

Efficient penetration of the mucus layer is needed for respiratory viruses to avoid mucociliary clearance prior to infection. Many respiratory viruses bind to glycans on the heavily glycosylated mucins that give mucus its gel-like characteristics. Influenza viruses, some paramyxoviruses, and coronaviruses avoid becoming trapped in the mucus by releasing themselves by means of their envelope-embedded enzymes that destroy glycan receptors. For efficient infection, receptor binding and destruction need to be in balance with the host receptor repertoire. Establishment in a novel host species requires resetting of the balance to adapt to the different glycan repertoire encountered. Growing understanding of species-specific mucosal glycosylation patterns and the dynamic interaction with respiratory viruses identifies the mucus layer as a major host-range determinant and barrier for zoonotic transfer.


Subject(s)
Host Specificity , Viruses , Glycosylation , Mucins/metabolism , Mucus/metabolism , Polysaccharides/metabolism , Viruses/metabolism
7.
Nat Commun ; 12(1): 1739, 2021 03 19.
Article in English | MEDLINE | ID: covidwho-1142438

ABSTRACT

Extensive testing is essential to break the transmission of SARS-CoV-2, which causes the ongoing COVID-19 pandemic. Here, we present a CRISPR-based diagnostic assay that is robust to viral genome mutations and temperature, produces results fast, can be applied directly on nasopharyngeal (NP) specimens without RNA purification, and incorporates a human internal control within the same reaction. Specifically, we show that the use of an engineered AsCas12a enzyme enables detection of wildtype and mutated SARS-CoV-2 and allows us to perform the detection step with loop-mediated isothermal amplification (LAMP) at 60-65 °C. We also find that the use of hybrid DNA-RNA guides increases the rate of reaction, enabling our test to be completed within 30 minutes. Utilizing clinical samples from 72 patients with COVID-19 infection and 57 healthy individuals, we demonstrate that our test exhibits a specificity and positive predictive value of 100% with a sensitivity of 50 and 1000 copies per reaction (or 2 and 40 copies per microliter) for purified RNA samples and unpurified NP specimens respectively.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , RNA, Guide , SARS-CoV-2/genetics , Bacterial Proteins/genetics , COVID-19/virology , CRISPR-Associated Proteins/genetics , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Endodeoxyribonucleases/genetics , Humans , Molecular Diagnostic Techniques/methods , Mutation , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , RNA, Viral/genetics , Sensitivity and Specificity
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