keyword
https://read.qxmd.com/read/38510921/vipera-viral-intra-patient-evolution-reporting-and-analysis
#21
JOURNAL ARTICLE
Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas, Mireia Coscollá
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection...
2024: Virus Evolution
https://read.qxmd.com/read/38510920/high-hiv-diversity-recombination-and-superinfection-revealed-in-a-large-outbreak-among-persons-who-inject-drugs-in-kentucky-and-ohio-usa
#22
JOURNAL ARTICLE
William M Switzer, Anupama Shankar, Hongwei Jia, Sergey Knyazev, Frank Ambrosio, Reagan Kelly, HaoQiang Zheng, Ellsworth M Campbell, Roxana Cintron, Yi Pan, Neeraja Saduvala, Nivedha Panneer, Rhiannon Richman, Manny B Singh, Douglas A Thoroughman, Erin F Blau, George M Khalil, Sheryl Lyss, Walid Heneine
We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase ( pol ) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21...
2024: Virus Evolution
https://read.qxmd.com/read/38508364/co-infecting-viruses-of-species-bovine-rhinitis-b-virus-picornaviridae-and-bovine-nidovirus-1-tobaniviridae-identified-for-the-first-time-from-a-post-mortem-respiratory-sample-of-a-sheep-ovis-aries-in-hungary
#23
JOURNAL ARTICLE
Fruzsina Tóth, Gábor Gáspár, Péter Pankovics, Péter Urbán, Róbert Herczeg, Mihály Albert, Gábor Reuter, Ákos Boros
In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time...
March 18, 2024: Infection, Genetics and Evolution
https://read.qxmd.com/read/38508151/changing-and-evolution-of-influenza-virus-is-it-a-trivial-flu
#24
REVIEW
Grazia Pavia, Fabio Scarpa, Alessandra Ciccozzi, Chiara Romano, Francesco Branda, Angela Quirino, Nadia Marascio, Giovanni Matera, Daria Sanna, Massimo Ciccozzi
BACKGROUND: Influenza viruses are etiological agents which cause contagious respiratory, seasonal epidemics and, for Influenza A subtypes, pandemics. The clinical picture of Influenza has undergone continuous change over the years, due to intrinsic viral evolution as well as "reassortment" of its genomic segments. The history of Influenza highlights its ability to adapt and to rapidly evolve, without specific circumstances. This reflects the complexity of this pathology and poses the fundamental question about its assumption as a "common illness" and its impact on public health...
March 20, 2024: Chemotherapy
https://read.qxmd.com/read/38508136/sars-cov-2-ba-1-and-ba-2-breakthrough-infections-boost-antibody-responses-to-early-omicron-subvariants-but-not-bq-1-1-or-xbb-1-5
#25
JOURNAL ARTICLE
Anass Abbad, Temima Yellin, Gagandeep Singh, Miriam Fried, Ariel Raskin, Johnstone Tcheou, Brian Monahan, Charles Gleason, Viviana Simon, Juan Manuel Carreño, Florian Krammer
Subvariants of the Omicron lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) efficiently escape neutralizing antibody responses induced by both vaccination and infection with antigenically distinct variants. Here, we describe the potency and breadth of neutralizing and binding antibody responses against a large panel of variants following an Omicron BA.1 or BA.2 breakthrough infection in a heterogeneous cohort of individuals with diverse exposure histories. Both BA.1 and BA.2 breakthrough infections significantly boost antibody levels and broaden antibody reactivity...
March 19, 2024: Cell reports medicine
https://read.qxmd.com/read/38507665/correlated-allele-frequency-changes-reveal-clonal-structure-and-selection-in-temporal-genetic-data
#26
JOURNAL ARTICLE
Yunxiao Li, John P Barton
In evolving populations where the rate of beneficial mutations is large, subpopulations of individuals with competing beneficial mutations can be maintained over long times. Evolution with this kind of clonal structure is commonly observed in a wide range of microbial and viral populations. However, it can be difficult to completely resolve clonal dynamics in data. This is due to limited read lengths in high-throughput sequencing methods, which are often insufficient to directly measure linkage disequilibrium or determine clonal structure...
March 20, 2024: Molecular Biology and Evolution
https://read.qxmd.com/read/38505291/genome-and-evolution-of-tibet-orbivirus-tibov-genus-orbivirus-family-reoviridae
#27
JOURNAL ARTICLE
Tingting Gao, Minghua Li, Hong Liu, Shihong Fu, Huanyu Wang, Guodong Liang
Tibet orbivirus (TIBOV) was first isolated from Anopheles maculatus mosquitoes in Xizang, China, in 2009. In recent years, more TIBOV strains have been isolated in several provinces across China, Japan, East Asia, and Nepal, South Asia. Furthermore, TIBOVs have also been isolated from Culex mosquitoes, and several midge species. Additionally, TIBOV neutralizing antibodies have been detected in serum specimens from several mammals, including cattle, sheep, and pigs. All of the evidence suggests that the geographical distribution of TIBOVs has significantly expanded in recent years, with an increased number of vector species involved in its transmission...
2024: Frontiers in Cellular and Infection Microbiology
https://read.qxmd.com/read/38501860/lncrnas-expression-profile-in-a-family-household-cluster-of-covid-19-patients
#28
JOURNAL ARTICLE
Iulia Virginia Iancu, Carmen Cristina Diaconu, Adriana Plesa, Alina Fudulu, Adrian Albulescu, Ana Iulia Neagu, Ioana Madalina Pitica, Laura Denisa Dragu, Coralia Bleotu, Mihaela Chivu-Economescu, Lilia Matei, Cristina Mambet, Saviana Nedeianu, Corneliu Petru Popescu, Camelia Sultana, Simona Maria Ruta, Anca Botezatu
More than 3 years after the start of SARS-CoV-2 pandemic, the molecular mechanisms behind the viral pathogenesis are still not completely understood. Long non-coding RNAs (lncRNAs), well-known players in viral infections, can represent prime candidates for patients' risk stratification. The purpose of the current study was to investigate the lncRNA profile in a family cluster of COVID-19 cases with different disease progression, during the initial wave of the pandemic and to evaluate their potential as biomarkers for COVID-19 evolution...
April 2024: Journal of Cellular and Molecular Medicine
https://read.qxmd.com/read/38501663/functional-dissection-of-the-spike-glycoprotein-s1-subunit-and-identification-of-cellular-cofactors-for-regulation-of-swine-acute-diarrhea-syndrome-coronavirus-entry
#29
JOURNAL ARTICLE
Yong-Le Yang, Bin Wang, Wentao Li, Hou-Li Cai, Qian-Yu Qian, Yu Qin, Fang-Shu Shi, Berend-Jan Bosch, Yao-Wei Huang
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine enteric coronavirus, and the broad interspecies infection of SADS-CoV poses a potential threat to human health. This study provides experimental evidence to dissect the roles of distinct domains within the SADS-CoV spike S1 subunit in cellular entry. Specifically, we expressed the S1 and its subdomains, S1A and S1B . Cell binding and invasion inhibition assays revealed a preference for the S1B subdomain in binding to the receptors on the cell surface, and this unknown receptor is not utilized by the porcine epidemic diarrhea virus...
March 19, 2024: Journal of Virology
https://read.qxmd.com/read/38497066/astrovirology-and-terrestrial-life-survival
#30
EDITORIAL
Paul Shapshak, Milad Zandi, Charurut Somboonwit, John T Sinnott
Microbial organisms have been implicated in several mass extinction events throughout Earth's planetary history. Concurrently, it can be reasoned from recent viral pandemics that viruses likely exacerbated the decline of life during these periods of mass extinction. The fields of exovirology and exobiology have evolved significantly since the 20th century, with early investigations into the varied atmospheric compositions of exoplanets revealing complex interactions between metallic and non-metallic elements...
2024: Bioinformation
https://read.qxmd.com/read/38496628/ongoing-evolution-of-sars-cov-2-drives-escape-from-mrna-vaccine-induced-humoral-immunity
#31
Alex L Roederer, Yi Cao, Kerri St Denis, Maegan L Sheehan, Chia Jung Li, Evan C Lam, David J Gregory, Mark C Poznansky, A John Iafrate, David H Canaday, Stefan Gravenstein, Wilfredo F Garcia-Beltran, Alejandro B Balazs
Since the COVID-19 pandemic began in 2020, viral sequencing has documented 131 individual mutations in the viral spike protein across 48 named variants. To determine the ability of vaccine-mediated humoral immunity to keep pace with continued SARS-CoV-2 evolution, we assessed the neutralization potency of sera from 76 vaccine recipients collected after 2 to 6 immunizations against a comprehensive panel of mutations observed during the pandemic. Remarkably, while many individual mutations that emerged between 2020 and 2022 exhibit escape from sera following primary vaccination, few escape boosted sera...
March 7, 2024: medRxiv
https://read.qxmd.com/read/38495668/compositional-features-analysis-by-machine-learning-in-genome-represents-linear-adaptation-of-monkeypox-virus
#32
JOURNAL ARTICLE
Sen Zhang, Ya-Dan Li, Yu-Rong Cai, Xiao-Ping Kang, Ye Feng, Yu-Chang Li, Yue-Hong Chen, Jing Li, Li-Li Bao, Tao Jiang
Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495558/drug-resistance-revealed-by-in-silico-deep-mutational-scanning-and-mutation-tracker
#33
Dong Chen, Gengzhuo Liu, Hongyan Du, Junjie Wee, Rui Wang, Jiahui Chen, Jana Shen, Guo-Wei Wei
As COVID-19 enters its fifth year, it continues to pose a significant global health threat, with the constantly mutating SARS-CoV-2 virus challenging drug effectiveness. A comprehensive understanding of virus-drug interactions is essential for predicting and improving drug effectiveness, especially in combating drug resistance during the pandemic. In response, the Path Laplacian Transformer-based Prospective Analysis Framework (PLFormer-PAF) has been proposed, integrating historical data analysis and predictive modeling strategies...
March 5, 2024: ArXiv
https://read.qxmd.com/read/38495283/changes-in-the-etiology-of-liver-cirrhosis-and-the-corresponding-management-strategies
#34
EDITORIAL
Jin-Jin Dai, Yue-Ying Liu, Zhen-Hua Zhang
We read with interest the article by Xing Wang, which was published in the recent issue of the World Journal of Hepatology 2023; 15: 1294-1306. This article focuses particularly on the prevalence and trends in the etiology of liver cirrhosis (LC), prognosis for patients suffering from cirrhosis-related complications and hepatocellular carcinoma (HCC), and management strategies. The etiology of cirrhosis varies according to geographical, economic, and population factors. Viral hepatitis is the dominant cause in China...
February 27, 2024: World Journal of Hepatology
https://read.qxmd.com/read/38494248/bioinformatics-approach-for-prediction-and-analysis-of-the-non-structural-protein-4b-nsp4b-of-the-zika-virus
#35
JOURNAL ARTICLE
Mohamed E Hasan, Aya Samir, Magdy M Khalil, Medhat W Shafaa
BACKGROUND: The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS: The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B...
March 2024: Journal, Genetic Engineering & Biotechnology
https://read.qxmd.com/read/38494148/molecular-insights-into-the-binding-interactions-and-energetics-of-the-omicron-spike-variant-with-hace2-and-a-neutralizing-antibody
#36
JOURNAL ARTICLE
Vipul Kumar, Seyad Shefrin, Durai Sundar
The global spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) since 2019 has led to a continuous evolution of viral variants, with the latest concern being the Omicron (B.1.1.529) variant. In this study, classical molecular dynamics simulations were conducted to elucidate the biophysical aspects of the Omicron spike protein's receptor-binding domain (RBD) in its interaction with human angiotensin-converting enzyme 2 (hACE2) and a neutralizing antibody, comparing it to the wildtype (WT). To model the Omicron variant, 15 in silico mutations were introduced in the RBD region of WT (retrieved from PDB)...
March 15, 2024: Journal of Structural Biology
https://read.qxmd.com/read/38490198/immunological-imprinting-shapes-the-specificity-of-human-antibody-responses-against-sars-cov-2-variants
#37
JOURNAL ARTICLE
Timothy S Johnston, Shuk Hang Li, Mark M Painter, Reilly K Atkinson, Naomi R Douek, David B Reeg, Daniel C Douek, E John Wherry, Scott E Hensley
The spike glycoprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to accumulate substitutions, leading to breakthrough infections of vaccinated individuals. It remains unclear if exposures to antigenically distant SARS-CoV-2 variants can overcome memory B cell biases established by initial SARS-CoV-2 encounters. We determined the specificity and functionality of antibody and B cell responses following exposure to BA.5 and XBB variants in individuals who received ancestral SARS-CoV-2 mRNA vaccines...
March 8, 2024: Immunity
https://read.qxmd.com/read/38486802/genetic-consequences-of-effective-and-suboptimal-dosing-with-mutagenic-drugs-in-a-hamster-model-of-sars-cov-2-infection
#38
JOURNAL ARTICLE
Christopher J R Illingworth, Jose A Guerra-Assuncao, Samuel Gregg, Oscar Charles, Juanita Pang, Sunando Roy, Rana Abdelnabi, Johan Neyts, Judith Breuer
Mutagenic antiviral drugs have shown promise against multiple viruses, but concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Recently, genetic signatures associated with molnupiravir use have been identified in the global SARS-COV-2 population. Here, we examine the consequences of using favipiravir and molnupiravir to treat SARS-CoV-2 infection in a hamster model, comparing viral genome sequence data collected from (1) untreated hamsters, and (2) from hamsters receiving effective and suboptimal doses of treatment...
2024: Virus Evolution
https://read.qxmd.com/read/38486143/spatio-temporal-spread-and-evolution-of-lassa-virus-in-west-africa
#39
JOURNAL ARTICLE
Xia Wang, Xianwei Ye, Ruihua Li, Xiaodong Zai, Mingda Hu, Shaoyan Wang, Hongguang Ren, Yuan Jin, Junjie Xu, Junjie Yue
BACKGROUND: Lassa fever is a hemorrhagic disease caused by Lassa virus (LASV), which has been classified by the World Health Organization as one of the top infectious diseases requiring prioritized research. Previous studies have provided insights into the classification and geographic characteristics of LASV lineages. However, the factor of the distribution and evolution characteristics and phylodynamics of the virus was still limited. METHODS: To enhance comprehensive understanding of LASV, we employed phylogenetic analysis, reassortment and recombination detection, and variation evaluation utilizing publicly available viral genome sequences...
March 14, 2024: BMC Infectious Diseases
https://read.qxmd.com/read/38485563/temporary-increase-in-circulating-replication-competent-latent-hiv-infected-resting-cd4-t-cells-after-switch-to-an-integrase-inhibitor-based-antiretroviral-regimen
#40
JOURNAL ARTICLE
Roux-Cil Ferreira, Steven J Reynolds, Adam A Capoferri, Owen R Baker, Erin E Brown, Ethan Klock, Jernelle Miller, Jun Lai, Sharada Saraf, Charles Kirby, Briana Lynch, Jada Hackman, Sarah N Gowanlock, Stephen Tomusange, Samiri Jamiru, Aggrey Anok, Taddeo Kityamuweesi, Paul Buule, Daniel Bruno, Craig Martens, Rebecca Rose, Susanna L Lamers, Ronald M Galiwango, Art F Y Poon, Thomas C Quinn, Jessica L Prodger, Andrew D Redd
BACKGROUND: The principal barrier to an HIV cure is the presence of the latent viral reservoir (LVR), which has been understudied in African populations. From 2018 to 2019, Uganda instituted a nationwide rollout of ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen of one NNRTI and the same two NRTI. METHODS: Changes in the inducible replication-competent LVR (RC-LVR) of ART-suppressed Ugandans with HIV (n = 88) from 2015 to 2020 were examined using the quantitative viral outgrowth assay...
March 4, 2024: EBioMedicine
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