ABSTRACT
Background: In 2018 we reported the emergence of the new HIV-1 recombinant CRF94-02BF2 involved in a large transmission cluster of 49 French MSM mostly infected in 2016-2017. This CRF94 raised concerns of enhanced virulence. Prevention actions were undertaken in the area and population affected. This study reported the molecular and epidemiological evolution of this CRF94 until June 2022. Method(s): In 2021-2022, French sequence databases were screened for patients infected with HIV-1 subtype CRF94 or similar strain. HIV subtyping was confirmed by phylogenetic analysis of genes encoding both protease and reverse transcriptase (1070bps), and integrase (696bps) using IQ-Tree. Five whole genomes, related but distinct from CRF94, were obtained with the DeepChek assay Whole Genome kits. Recombination breakpoints were estimated using RDP4 and SimPlot. Mann-Whitney and LogRank tests were used for statistical analyses to compare patients' characteristics. Result(s): In June 2022, 49 new HIV-1 sequences were collected: 14 clustered with the 49 previous CRF94, 32 formed a new cluster next to but distinct from CRF94, and 3 strains could not be classified. Analysis of 5 whole genomes from the new cluster revealed a new recombinant, the CRF132-94B, mainly consisting of CRF94 which recombined with subtype B in the POL and accessory genes. Vif gene changed from the F2 to the B subtype. Both CRF94 and 132 clusters involved >95% of MSM, mostly infected < 1 year before diagnosis. However, there were differences: 97% were diagnosed in 2013-2019 for CRF94 vs 90% in 2020-2022 for CRF132. At time of diagnosis, 33% of patients infected with CRF94 knew the Prep vs 95% for CRF132. In the cluster CRF94, patients were older (34 vs 30 years, p=0.02), had higher viral loads (5.42 vs 4.42 log10 copies/Ml;p< 0.001), a lower CD4 cell counts (358 vs 508 /mm3, p=0.002). On treatment, the patients with the CRF94 reached viremia < 50 copies/Ml significantly later than those infected with CRF132 (p=0.0002). The prevention activities targeting the CRF94 cluster could explained the few patients infected with this strain after 2018. The CRF132 is mainly located in another Paris region area, but no specific transmission place has been identified. Conclusion(s): After 2019, the CRF94 spread seems greatly slowed down but the very close CRF132-94B has given birth to a new highly active cluster in 2020- 2022, despite the COVID social-distancing and a strong knowledge of the Prep. CRF132 appears to be less virulent perhaps due to the Vif gene change. Identified breakpoints positions of the new HIV-1 CRF132-94B. GenBank accession numbers of the five references : ON901787 to ON901791.
ABSTRACT
Background: Despite increased social vulnerability and barriers to care, there has been a paucity of data on SARS-CoV-2 incidence among key populations in sub-Saharan Africa. We seek to characterize active infections and define transmission dynamics of SARS-CoV-2 among people who inject drugs (PWID) and their sexual and injecting partners from Nairobi and the coastal region in Kenya. Method(s): This was a nested cross-sectional study of SARS-CoV-2 infection from April to July 2021 within a cohort study of assisted partner services for PWID in Kenya. A total of 1000 PWID and their partners (500 living with and 500 living without HIV) were recruited for SARS-CoV-2 antibody testing, of whom 440 were randomly selected to provide self-collected nasal swabs for real-time PCR testing. Whole genome sequencing (WGS) was completed on a limited subset of samples (N=23) with cycle threshold values 32.0. Phylogenetic tree construction and analysis was performed using the Nextstrain pipeline and compared with publicly available SARS-CoV-2 sequences from GenBank. Result(s): A total of 438 (99.5%) participants provided samples for SARS-CoV-2 PCR testing. Median age was 37 (IQR 32-42);128 (29.2%) were female;and 222 (50.7%) were living with HIV. The overall prevalence of SARS-CoV-2 infection identified by RT-PCR was 86 (19.6%). In univariate analyses, there was no increased relative risk of SARSCoV- 2 infection related to positive HIV status, frequenting an injection den, methadone treatment, unstable housing, report of any high-risk exposure, or having a sexual or injecting partner diagnosed with COVID-19 or who died from COVID-19 or flu-like illness. Eight samples were successfully sequenced via WGS and classified as WHO variants of concern: 3 Delta, 3 Alpha, and 2 Beta. Seven were classified into clades predominantly circulating in Kenya during 2021. Notably, two sequences were identical and matched identically to another Kenyan sequence, which is consistent with, though not indictive of, a transmission linkage. Conclusion(s): Overall, the risk of SARS-CoV-2 infection in this population of PWID and their partners was not significantly associated with risk factors related to injection drug use. At a genomic level, the SARS-CoV-2 strains in this study were consistent with contemporary Kenyan lineages circulating during the time and not unique to PWID. Prevention efforts, therefore, must also focus on marginalized groups for control given the substantial amount of mixing that likely occurs between populations.
ABSTRACT
BACKGROUND: Nirsevimab is an extended half-life monoclonal antibody to the respiratory syncytial virus (RSV) fusion protein that has been developed to protect infants for an entire RSV season. Previous studies have shown that the nirsevimab binding site is highly conserved. However, investigations of the geotemporal evolution of potential escape variants in recent (ie, 2015-2021) RSV seasons have been minimal. Here, we examine prospective RSV surveillance data to assess the geotemporal prevalence of RSV A and B, and functionally characterise the effect of the nirsevimab binding-site substitutions identified between 2015 and 2021. METHOD(S): We assessed the geotemporal prevalence of RSV A and B and nirsevimab binding-site conservation between 2015 and 2021 from three prospective RSV molecular surveillance studies (the US-based OUTSMART-RSV, the global INFORM-RSV, and a pilot study in South Africa). Nirsevimab binding-site substitutions were assessed in an RSV microneutralisation susceptibility assay. We contextualised our findings by assessing fusion-protein sequence diversity from 1956 to 2021 relative to other respiratory-virus envelope glycoproteins using RSV fusion protein sequences published in NCBI GenBank. FINDINGS: We identified 5675 RSV A and RSV B fusion protein sequences (2875 RSV A and 2800 RSV B) from the three surveillance studies (2015-2021). Nearly all (25 [100%] of 25 positions of RSV A fusion proteins and 22 [88%] of 25 positions of RSV B fusion proteins) amino acids within the nirsevimab binding site remained highly conserved between 2015 and 2021. A highly prevalent (ie, >40.0% of all sequences) nirsevimab binding-site Ile206Met:Gln209Arg RSV B polymorphism arose between 2016 and 2021. Nirsevimab neutralised a diverse set of recombinant RSV viruses, including new variants containing binding-site substitutions. RSV B variants with reduced susceptibility to nirsevimab neutralisation were detected at low frequencies (ie, prevalence <1.0%) between 2015 and 2021. We used 3626 RSV fusion-protein sequences published in NCBI GenBank between 1956 and 2021 (2024 RSV and 1602 RSV B) to show that the RSV fusion protein had lower genetic diversity than influenza haemagglutinin and SARS-CoV-2 spike proteins. INTERPRETATION: The nirsevimab binding site was highly conserved between 1956 and 2021. Nirsevimab escape variants were rare and have not increased over time. FUNDING: AstraZeneca and Sanofi.Copyright © 2023 Elsevier Ltd. All rights reserved.
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Throughout its nearly two hundred year existence, the National Library of Medicine (NLM) (https://www.nlm.nih.gov/) has advanced biomedicine and public health by acquiring, organizing, preserving, and disseminating knowledge essential to health and medicine. NLM has devised many innovations including standard terminologies and messaging formats such as the Journal Article Tag Suite (https://dtd.nlm.nih.gov/) to organize and manage biomedical literature. While scientific communication largely relied on books and journals over the last two hundred years, digital data are quickly forming the substrate of scientific communications. Data come in forms with much less structure than that afforded by publications, and these can vary from observations made during carefully controlled clinical trials to streams of genomic sequences to the counts of footfalls captured by personal devices. Coincidently, an increasingly diverse set of users - from clinicians to laypeople to public health to big pharma to scientists - bring unique perspectives as they draw meaning from new sets of scientific output. How does a modern library meet its mission to acquire, organize, preserve, and disseminate the many outputs of contemporary science? What role do standards play? How does NLM help this diverse set of stakeholders derive meaning from its resources? © 2022 - The authors. Published by IOS Press.
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Background. SARS-CoV-2 E gene PCRs have been widely used as the first-line assay with a higher sensitivity than those targeting N or RdRp gene. Given the currently available primers and probes were designed at the onset of the pandemic, it is unknown whether the SARS-CoV-2 VOCs have accumulated significant mutations that may affect E gene PCRs. In this study we aim to perform a comprehensive genetic analysis of SARS-CoV-2 E gene sequences to evaluate the impact of the emerging VOCs on E gene PCR performance. Methods. 600 whole-genome sequences of 7 species of human coronaviruses (HCoVs) were retrieved from GenBank and GISAID, including Sarbecoviruses (SARS-CoV-2 variants B1.1.7, B1.351, P.1, B.1.617.2 and B.1.1.529, and SARS-CoV), Embecovirus (OC43, HKU1), Merbecovirus (MERS) and Alphacoronaviruses (229E, NL63). The E gene sequences were retrieved from fulllength genomes of corresponding viruses and aligned by ClustalW multiple alignment. Phylogenetic, conservation and mutation analyses analysis of the enrolled sequences was performed. Results. E gene-based phylogenetic analysis yielded HCoVs typing results consistent with whole genome typing, suggesting E gene is a reliable locus for phylogenetic analysis and typing of HCoVs. Four pan-Sarbecovirus conserved E gene regions were identified with 100% conserved nucleotide similarity among SARS-CoV-2 and its VOCs, as well as SARS-CoV. These regions have appropriate G/C content which may be suitable for primer/probe design for E gene-based pan-Sarbecovirus screening assay. No significant E mutations were found in 137 retrieved SARS-CoV-2 and its VOCs. Interestingly, two novel variations, C26299U and T26354A, were identified in two of our SARS-CoV-2 strains. The latter variation occurred at the 3' end of the target region of the widely used Charite/Berlin (WHO) probe. This variant may lead to a potential failure of the first-line E gene PCR. Conclusion. Our data shed light on the genetic diversity and conservation of E gene of SARS-CoV-2 and may be beneficial for future primer/probe design for novel first-line assay or SARS-CoV-2-specific E gene PCR. SARS-CoV-2 VOCs have not accumulated significant mutations in E gene so far. The impact of novel E gene variations C26299U and T26354A on molecular diagnostic testing warrants further investigation.
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Nebovirus (NeV) is an emerge diarrhea-causing virus in calves, the aim of this study is to establish an insulated isothermal RT-PCR(iiRT-PCR) for detecting NeV on field. Based on the RdRp sequences of NeV in GenBank database, a pair of primers and a fluorescent TaqMan probe were designed and synthesized. After optimizing the react system and condition, the iiRT-PCR method for detection of NeV was established. The iiRT-PCR assay could amplify specific fragment of NeV, without amplification of irrelevant pathogens, including bovine coronavirus, bovine norovirus, bovine rotavirus, bovine viral diarrhea virus, bovine torovirus, bovine Cryptosporidium parvum, bovine Eimeria. The intra- and inter-coefficients of variation were 3.07%-3.12% and 2.45%-3.01%, respectively, and the detection limit of viral nucleic acid of the assay was 5.38 copies•μL-1. One hundred and one calf diarrhea samples, collected from Hongyuan County, Ruoergai Prefecture, Xichang City, Liangshan Yi Autonomous Prefecture and Langzhong City in Sichuan Province during 2020-2021, were used to detect NeV, and 64.36% samples were detected as NeV positive. The study established an iiRT-PCR method for NeV detection with good specificity and reproducible as well as high sensitivity. Moreover, combined with the premixed detection reagent and PetNAD nucleic acid extraction kit, this assay could be used to NeV detect on-site, and only 1 hour from nucleic acid extraction to result report, which contribute to the fast detection for NeV.
ABSTRACT
According to the Argentinian Wildlife Foundation census on the coast of Buenos Aires province, 80% of the wastes were petrochemicals plastics and microplastics. Since last year, due to the influence of the COVID-19 pandemic, the use of plastics has increased, especially in containers for prepared food and single-use plastics. For this reason, the world market for bioplastics is growing steadily. The aim of this work was to evaluate the biodegradation of injected molded bioplastics in vermicompost using a bacterium isolated with extracellular enzymatic activity for the depolymerization of polyhydroxyalkanoates (PHAs). Vermicompost (Californian red worm) was sieved through 5 mm opening size. Phylogenetic analysis: the sequence of the 16S rDNA from the isolated Actinomycetes was compared with the EMBL and GenBank databases. The phylogenetic tree was constructed. The morphological characteristics were performed in ISP media and the biochemical tests were carried out according to the Bergeýs manual. Biodegradation analysis: injected molded PHAs samples consisted in rectangular (1.00 ± 0.05 cm width and 3.00 ± 0.05 cm length, thickness: 200 μm) and circular samples (diameter 2 cm, thickness 0.2 cm). Biodegradation by extracellular depolymerase activity was measured at 650 nm by turbidity decrease and by halo formation around colonies (ISP media, 12 days, 30 °C). PHAs surfaces were observed using a microscope. 28 Actinomycetes were isolated with PHAs biodegradation capacity, with different types of growth, colony morphology and extracellular enzyme production. Based on the biodegradation halo area, isolates were classified into three groups: low, medium and high enzymatic activity. From the last group, the one with the highest degradative activity under different environmental conditions was selected. The bacterium was identified as Streptomyces omiyaensis by phylogenetic studies, 16S rDNA sequencing, morphological characterization and biochemical tests and it was determined as GRAS. The strain was deposited in the AGRAL FAUBA culture collection as S. omiyaensis SSM5670. The PHAs samples in vermicompost inoculated with S. omiyaensis SSM5670 showed the deterioration of their surfaces, with the presence of surface irregularities and roughness, until the total biodegradation of the samples. The inoculation of vermicompost with an Actinomycetes isolate with extracellular PHAs degradation activity, would improve the bioplastics degradation, which would be critical given that the global production capacity of bioplastics has been estimated to increase to approximately 2.44 million tonnes in 2022.
ABSTRACT
Covid-19 viral (SARS-CoV-2) infection evolved very rapidly to spreading geographically to become a global pandemic as declared by World Health Organization (WHO) within the first months of 2020. Viral respiratory infection such as severe acute coronavirus-2 disease (SARS-CoV-2), bacterial co-infections commonly are identified and are a major cause of morbidity and mortality requiring prompt and antibacterial diagnosis. Specimens were collected from 100 patients were included 68 male and 32 female with age ranged between 16 -85 years for the period from the beginning of October 2020 to the end of March 2021. Naso-oropharyngeal swabs were collected from each person with symptoms according to the WHO guideline for SARS Cov2. The results of the viral mutations showed the open reading frame 8 (ORF8) of SARS-CoV-2. The sequences were obtained from seven patients infected with SARS-CoV-2 by PCR using ORF8 specific primer. The amplified fragment of ORF8 was 366 bp. The nucleotide sequences of the seven open reading frames of ORF8 of SARS-CoV-2 were submitted in the GenBank under the accession numbers: MZ025969- MZ025975. The results of phylogenetic tree appeared that categorize of the seven ORF8 nucleotide sequences into three clades. SARS-CoV-2 ORF8 represents a major component in determining the viral pathogenicity and the outcome of the respiratory disease, and coding sequence analysis of this segment might help in track variants evolution in any location. General understanding of how SARS-CoV-2 mutations contribute to make disease progression is extremely critical not only for understanding of SARS-CoV-2 pathogenesis but also for SARS-CoV-2 vaccine development.
ABSTRACT
Coronavirus Disease 2019 (COVID-19) is a sudden viral contagion that appeared at the end of last year in Wuhan city, the Chinese province of Hubei, China. The fast spread of COVID-19 has led to a dangerous threat to worldwide health. Also in the last two decades, several viral epidemics have been listed like the severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002/2003, the influenza H1N1 in 2009 and recently the Middle East respiratory syndrome coronavirus (MERS-CoV) which appeared in Saudi Arabia in 2012. In this research, an automated system is created to differentiate between the COVID-19, SARS-CoV and MERS-CoV epidemics by using their genomic sequences recorded in the NCBI GenBank in order to facilitate the diagnosis process and increase the accuracy of disease detection in less time. The selected database contains 76 genes for each epidemic. Then, some features are extracted like a discrete Fourier transform (DFT), discrete cosine transform (DCT) and the seven moment invariants to two different classifiers. These classifiers are the k-nearest neighbor (KNN) algorithm and the trainable cascade-forward back propagation neural network where they give satisfying results to compare. To evaluate the performance of classifiers, there are some effective parameters calculated. They are accuracy (ACC), F1 score, error rate and Matthews correlation coefficient (MCC) that are 100%, 100%, 0 and 1, respectively, for the KNN algorithm and 98.89%, 98.34%, 0.0111 and 0.9754, respectively, for the cascade-forward network.