HIV infection is a major health problem in Russia. We aimed to assess HIV prevalence in different population groups and to compare the characteristics of 4th generation immunoassays from Abbott, ...Bio-Rad, Vector-Best, Diagnostic Systems, and Medical Biological Unit.
The study included 4452 individuals from the general population (GP), 391 subjects at high risk of HIV infection (HR) and 699 with potentially interfering conditions. HIV positivity was confirmed by immunoblot and by HIV RNA, seroconversion and virus diversity panels were also used. HIV avidity was employed to assess recent infections.
The prevalence in GP was 0.40%, higher in males (0.62%) and in people aged < 40 years (0.58%). Patients attending dermo-venereal centers and drug users had a high prevalence (34.1 and 58.8%). Recent infections were diagnosed in 20% of GP and in 4.2% of HR. Assay sensitivity was 100% except for one false negative (99,54%, MBU). Specificity was 99.58-99.89% overall, but as low as 93.26% on HR (Vector-Best). Small differences on early seroconversion were recorded. Only the Abbott assay detected all samples on the viral diversity panel.
HIV infection rate in the high-risk groups suggests that awareness and screening campaigns should be enhanced. Fourth generation assays are adequate but performance differences must be considered.
Humanized Mouse Model of HIV Infection Leontyev, D. S.; Glazkova, D. V.; Bezborodova, O. A. ...
Bulletin of experimental biology and medicine,
05/2023, Letnik:
175, Številka:
1
Journal Article
Recenzirano
The development of new drugs for the treatment of HIV infection requires testing of their efficacy in a relevant animal model, such as humanized mice, which, unfortunately, are not yet available in ...Russia. In the present study, we have developed conditions for the humanization of immunodeficient NSG mice with human hematopoietic stem cells. Humanized animals generated during the study showed a high degree of chimerism and harbored repopulation of the entire range of human lymphocytes required for HIV replication in the blood and organs. Inoculation of these mice with HIV-1 virus led to stable viremia, which was confirmed by the presence of viral RNA in blood plasma throughout the entire period of observation and proviral DNA in the organs of animals 4 weeks after HIV infection.
Influenza virus is one of the most rapidly evolving human pathogens and causes significant morbidity and mortality worldwide. This feature enables the virus to avoid natural or vaccine-induced ...immunity. For this reason, there is an intensive search for new approaches to create a universal influenza vaccine. Here, we propose pipelines based on modern prediction algorithms that allowed us to select 10 B-cell epitopes, 10 CD8+ T-cell epitopes and 6 CD4+ T-cell epitopes from influenza viruses that were characterized by high conservation and antigenicity. These epitopes could be used to create universal vaccines against influenza viruses. In addition, the scripts used in these pipelines are universal and can be used to select epitopes from other pathogens.
Influenza, Universal vaccine, T- and B-cell epitopes, Computational approaches.
•Novel single-tube real-time PCR to determine a ratio of wild type and rMVA in plaques.•Rapid generation of new pure rMVA in 11 days.•Plaque purification is less effective then end-point dilution as ...the last purification step.•Various marker gene selected plaques differ greatly in proportion of rMVA.
Obtaining a pure recombinant Modified Vaccinia Ankara (MVA) virus is a multistage, time-consuming procedure. We describe a novel single-tube real-time PCR which enables determination of the amount of wild type and recombinant viruses and their ratio in plaques. Use of the real-time PCR significantly reduce the time and efforts needed to obtain purified recombinant MVA. The new approach has been applied to generate recombinant MVAs encoding different SARS-COV-2 antigens.
•The type of nucleic acid and reverse transcription step do not affect the sequencing accuracy.•Accuracy and sensitivity critically depend on the coverage and threshold of sensitivity to minor ...nucleotides.•Sensitivity to minor variants of less than 1% leads to a significant decline in sequencing accuracy.
The accuracy and sensitivity of deep sequencing were assessed using viral standards (pNL4-3 and pLAI.2) of both DNA and RNA. The sequencing accuracy did not depend on the type of nucleic acid, but critically depended on the number of reads and threshold of sensitivity to minor viral populations. With coverage of more than 236 reads, the accuracy of viral RNA sequencing was equal to or exceeded 99.9%, with a sensitivity threshold to minor nucleotides of 20%. When the sensitivity threshold was below 1%, reduced accuracy dynamics were clearly visible even when the coverage was massive (more than 9.000 reads). It was found that the floating sensitivity threshold allowed the sequencing accuracy to be maintained at an acceptable level in cases of low coverage (less than 1.500–2.000) of reads. These results indicate the quality that can be expected with a specific number of reads and sensitivity threshold. Deep sequencing is a very powerful tool that can significantly improve the value of study results, but despite its superior performance, it should be used with caution regarding its sensitivity to minor populations below 1%.
We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput ...sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.
During a 2-year period in 2005–2007, we conducted surveillance of group A rotaviruses and other enteric agents among patients hospitalized with acute gastroenteritis in 8 different cities of the ...Russian Federation. Fecal specimens were gathered from 3208 children (including 2848 children aged <5 years) and 1354 adults who were admitted to hospitals in Moscow, St. Petersburg, Chelyabinsk, Nizhnii Novgorod, Tyumen, Khabarovsk, Makhachkala, and Yakutsk. Polymerase chain reaction was performed to detect rotaviruses of groups A and C, noroviruses of genogroups I and II, astrovirus, sapovirus, and enteric adenoviruses (group F). Group A rotavirus was the most common viral pathogen detected among children aged <5 years (43.6%), followed by norovirus (12.5%), whereas norovirus was the pathogen most commonly detected in adults (11.9%). P and G genotypes were determined for 515 rotavirus specimens, and the most prevalent genotypes were G1P8 (44.9%), G4P8 (40.0%), G2P4 (8.5%), and G3P8 (6.6%). This study is the first multicenter study of rotaviruses in the Russian Federation and documents the important burden of disease caused by this pathogen, which soon may be preventable by vaccination
The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses.
In 2020, a new variant ...of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world.
To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions.
It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х103 copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1–100% for Omicron and 91.3–100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2–100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022.
Highlights • Two cases of rabies among humans were detected using a broad-range PCR analysis followed by high throughput sequencing. • Diagnoses were subsequently confirmed using a fluorescent ...antibody test, an enzyme-linked immunosorbent assay (ELISA) and a mouse inoculation test. • Two strains of rabies virus were isolated and characterized using virological methods. • The entire genome of each strain was sequenced.
Rabies virus is endemic to Russia, among other countries. It is therefore critical to develop a high-quality and high-precision diagnostic procedure for the control and prevention of infection.
The ...main objective of the research presented here was to develop a reliable RT-qPCR assay for rabies diagnostics.
For this purpose, a RABV strains from various biological and geographical origins were used. In addition, rabies-positive and rabies-negative samples, as well as nucleic acids from other viruses and DNA extracted from the brain tissues of mice, dogs, cats, bats and humans, were studied using the developed assay.
The analytical sensitivity of the assay, as assessed using armored recombinant positive control dilutions, was 103 copies/ml, and the sensitivity measured using characterized strains was between 0.1 LD50/ml and 1.0 LD50/ml. A broad range of RNA from RABV strains circulating in different regions of Russia, as well as RNA from RABV-positive primary brain samples from 81 animals and two humans, was detected using the developed assay. No false-positive or false-negative results were obtained.
Given that high analytical and diagnostic sensitivities and a high specificity were verified for this assay, it has high potential as a screening test that may be suitable for the epizootiological monitoring of animals and for the fast postmortem diagnosis of rabies.
•Reliable qRT-PCR assay for RABV detection was developed and evaluated•Analytical sensitivity of the assay was 103 copies/ml, and the sensitivity measured using characterized strains was between 0.1 LD50/1ml and 1.0 LD50/1ml.•Diagnostic sensitivity and specificity were both 100%
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