Viral Landscape Research Articles

Genomic characteristics, disease outcome and heterologous vaccine effectiveness among cases with SARS CoV-2 infection

BackgroundIn the pursuit of global health security, continuous monitoring of vaccine effectiveness across various viral strains emerges as a crucial imperative. The emergence of SARS-CoV-2 major variants of concern (VOCs), including Alpha, Beta, Delta, and Omicron, has added complexity to the COVID-19 vaccination landscape.ObjectivesTo assess illness severity, evaluate vaccine efficacy across varying doses and types, and determine effectiveness against major VOCs within the population.MethodsThis retrospective cohort study, conducted in Abu Dhabi, United Arab Emirates, focuses on a cohort of 44,073 SARS-CoV-2 positive cases from February 2021 to May 2022, dominated by the Delta and Omicron variants. The study employed a nested case-control design, analyzing hospital admissions for confirmed SARS-CoV-2 infection.ResultsVaccine effectiveness was higher among heterologus-boosted individuals at 87% (95% CI:79%-93%) compared to homologus-boosted individuals at 59% (95% CI: 48%-68%) and fully vaccinated, non-boosted adults at 53% (95% CI: 46%-59%). These findings highlight the importance of heterologous boosting, particularly against rapidly evolving viral variants, offering valuable insights for refining pandemic response strategies.ConclusionThe study underscores the critical need for ongoing assessment and adaptation of vaccination strategies to the evolving viral landscape.

Genetic and phenotypic changes to Venezuelan equine encephalitis virus following treatment with β-D-N4-hydroxycytidine, an RNA mutagen

The high mutation rate of RNA viruses provides viral populations with the ability to adapt to new environments but also makes them vulnerable to extinction due to the deleterious effects of mutations, which is the conceptual basis for the antiviral activity of RNA mutagens. However, there are still gaps in the quantitative understanding of the dynamics between the mutations induced by an RNA mutagen and its effects on viral fitness. To address this, we used Venezuelan Equine Encephalitis Virus (VEEV) and the potent RNA mutagen β-d-N4-hydroxycytidine (NHC) as a model to analyze virus replication competency and mutation frequency following treatment in the total and replication-competent viral populations separately. We found that NHC induced transition mutations in a concentration dependent manner in the total population, while the replication-competent population maintained itself within an increased, yet narrow, mutation spectrum. The incorporation of NHC mainly happened during the positive sense RNA synthesis of VEEV. A growth kinetic analysis of VEEV population treated with NHC pointed to a lower but more diverse distribution in mutational fitness, demonstrating that NHC-induced mutations negatively and broadly affect the fitness of the virus. Together, our study provides mechanistic insight into how RNA mutagens affect viral population landscape and the potential of RNA mutagens as an antiviral strategy for alphaviruses.

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape

The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region. Our comprehensive exploration of DNA viral diversity in the Southern Ocean reveals a unique and largely uncharted viral landscape, of which 75% was previously unidentified in other oceanic areas. We uncover novel viral taxa at high taxonomic ranks, expanding our understanding of crassphage, polinton-like virus, and virophage diversity. Nucleocytoviricota viruses represent an abundant and diverse group of Antarctic viruses, highlighting their potential as important regulators of phytoplankton population dynamics. Our temporal analysis reveals complex seasonal patterns in marine viral communities (bacteriophages, eukaryotic viruses) which underscores the apparent interactions with their microbial hosts, whilst deepening our understanding of their roles in the world’s most sensitive and rapidly changing ecosystem.

HIV-1 reservoir landscape of post-treatment control.

This review explores the viral reservoir landscape in individuals who control viral replication after treatment interruption (TI), designated as post-treatment controllers (PTCs). Identifying their virologic features is crucial to inform drug-free HIV remission strategies. Traditionally characterized as small, likely due to early treatment, the viral reservoir of PTCs, after TI, exhibits limited transcriptional activity, residual viral replication and subsequent proviral diversity. Intact proviruses are found to be restricted. In nonhuman primate PTCs, this depletion of intact proviruses is already observed in lymph nodes before TI, suggesting that control mechanisms begin during antiretroviral therapy. Furthermore, recent studies suggest immune-driven proviral deep latency associated with repressive epigenetic features and integration sites in PTCs. While molecular mapping of virological features of PTCs is increasingly precise and coupled with in-depth immunologic assays, robust predictive biomarkers of PTCs are still lacking. Despite limited sample sizes and heterogeneous definitions, common virologic features of PTCs include restricted reservoir size and transcriptional activity, fewer intact proviruses and deep proviral latency. Ongoing research using innovative technologies will further elucidate the mechanisms underlying post-treatment control, paving the way for successful HIV cure interventions.

Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.

Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.

Navigating the Dynamic Landscape of SARS-CoV-2: The Dual Role of Neutralizing Antibodies, Variability in Responses, and Strategies for Adaptive Pandemic Control

The global pandemic sparked by the emergence of SARS-CoV-2 and its variants has imposed a substantial burden of morbidity and mortality. Central to the battle against these viral threats is the immune response, with a spotlight on the pivotal role played by neutralizing antibodies. This comprehensive review delves into current research, unravelling the dual functionality of neutralizing antibodies acting as formidable barriers to viral replication and crucial facilitators of adaptive immune memory. Beyond this dual purpose, the review illuminates the nuanced variability characterizing neutralizing antibody responses to SARS-CoV-2. Emphasizing the dynamic nature of these responses, the review advocates for the plausible challenges in targeted therapeutic interventions. This review also attempts to compare various vaccination approaches and their impact on SARS-CoV-2, as well as offer insights into various Omicron variations. Recognizing the ever-evolving viral landscape, this exploration underscores the necessity of flexible approaches to address the diverse challenges posed by SARS-CoV-2 and its variants, contributing valuable insights to the ongoing global efforts in pandemic mitigation and public health safeguarding.

Evolving pathogen trends and spatial–temporal dynamics of hand, foot, and mouth disease in Fengxian District, Shanghai (2009–2022)

Hand, foot, and mouth disease (HFMD) is a prevalent acute infectious disease caused by enteroviruses, presenting substantial public health challenges in Shanghai, especially among children. The dynamic nature of HFMD’s etiology necessitates an ongoing evaluation of its epidemiological and virological trends to inform effective control strategies. This study aims to investigate the epidemiological patterns and viral evolution of HFMD in Fengxian District, Shanghai, China, with a focus on shifts in predominant viral strains over a 14-year period. We conducted a retrospective analysis of HFMD cases reported to the National Notifiable Disease Reporting System in Fengxian District from January 1, 2009 to December 31, 2022. Epidemiological trends, strain prevalence, and demographic impacts were assessed. A total of 27,272 HFMD cases were documented during the study period, with incidence showing pronounced seasonal fluctuations—peaking in spring and summer and a lesser peak in autumn. The disease incidence demonstrated significant positive correlations with several meteorological variables: daily average temperature (r = 0.30, P < 0.05), relative humidity (r = 0.20, P < 0.05), wind speed (r = 0.17, P < 0.05), and precipitation (r = 0.17, P < 0.05). Geographically, Nanqiao Town, Fengcheng Town, and Xidu Subdistrict reported the highest incidence rates. The demographic analysis revealed a male-to-female ratio of 1.60:1, predominantly affecting children aged 1–3 years. Prior to 2017, Enterovirus 71 (EV71) and Coxsackievirus A16 (CoxA16) were the primary detected strains; post-2017, Coxsackievirus A6 (CoxA6) emerged as the dominant strain. Statistical analysis confirmed significant year-to-year variations in virus detection rates, with decreasing trends for EV71 and other enteroviruses and an increasing trend for CoxA6. The findings indicate a distinct seasonal incidence of HFMD in Fengxian District. This study underscores the need for targeted public health education, enhanced surveillance, and proactive measures in childcare facilities to mitigate disease spread during peak seasons. Moreover, the evolving viral landscape warrants accelerated efforts in vaccine development against new strains to reduce HFMD incidence.

#Nature is trending: Social media, viral landscapes, and digital environmental activism in Oman

Influenced by social media and COVID-19, human relations with ‘nature’ are increasingly shaped by media infrastructures and logics, leading to a global surge of interest in nature tourism and outdoor activities. This article examines the mediatization of relations with nature—or, the more-than-human world—in the Arabian Gulf country of Oman, where nature tourism has developed in the past decade. Through a mixed-methods approach involving fieldwork and interviews between 2022–2024, relations with nature in Oman are shown to be informed by global social media logics, as with the trend of ‘viral landscapes’ in which a nature destination is popularized due to its high value in social media attention economies. However, local practices are also platformed, as Instagram users in Oman exploit three affordances to address the environmental problem of litter. Mediatization may thus entail a circulation of global discourses and practices as well as the emergence of syncretic sociocultural formations.

Viral ecologies: Refiguring ‘psychic immunology’, in the art of Helen Chadwick

This article examines the artist Helen Chadwick’s 1989 digital montage series Viral Landscapes as an intervention in discourses of immunity circulating around the HIV/AIDS epidemic in the UK. The Viral Landscapes are unusual for art of this period in working closely with medical concepts and technologies, if only to problematise the ways in which these were mobilised. Strategically appropriating ideas of ‘psychic immunology’ emergent at the time, the work, I argue, formulates an affective ground for the extension of immunological responsibility beyond the confines of human bodies and societies. Through a close examination of the artist’s methods and the work’s aesthetics, I identify therein an alternative model of the subject from the closed bodily system and fixed identity presupposed by contemporary biomedicine. Influenced in particular by Deleuzo-Guattarian theories of machinic desire, as well as queer-theoretical constructions of the sexual subject as polymorphous, Chadwick’s model of the psychically immune subject seems to be grounded in a vital sexual energy, constructed through interpenetration by multiple, diffuse entities in ecological relation.

Varroa destructor shapes the unique viral landscapes of the honey bee populations of the Azores archipelago.

The worldwide dispersal of the ectoparasitic mite Varroa destructor from its Asian origins has fundamentally transformed the relationship of the honey bee (Apis mellifera) with several of its viruses, via changes in transmission and/or host immunosuppression. The extent to which honey bee-virus relationships change after Varroa invasion is poorly understood for most viruses, in part because there are few places in the world with several geographically close but completely isolated honey bee populations that either have, or have not, been exposed long-term to Varroa, allowing for separate ecological, epidemiological, and adaptive relationships to develop between honey bees and their viruses, in relation to the mite's presence or absence. The Azores is one such place, as it contains islands with and without the mite. Here, we combined qPCR with meta-amplicon deep sequencing to uncover the relationship between Varroa presence, and the prevalence, load, diversity, and phylogeographic structure of eight honey bee viruses screened across the archipelago. Four viruses were not detected on any island (ABPV-Acute bee paralysis virus, KBV-Kashmir bee virus, IAPV-Israeli acute bee paralysis virus, BeeMLV-Bee macula-like virus); one (SBV-Sacbrood virus) was detected only on mite-infested islands; one (CBPV-Chronic bee paralysis virus) occurred on some islands, and two (BQCV-Black queen cell virus, LSV-Lake Sinai virus,) were present on every single island. This multi-virus screening builds upon a parallel survey of Deformed wing virus (DWV) strains that uncovered a remarkably heterogeneous viral landscape featuring Varroa-infested islands dominated by DWV-A and -B, Varroa-free islands naïve to DWV, and a refuge of the rare DWV-C dominating the easternmost Varroa-free islands. While all four detected viruses investigated here were affected by Varroa for one or two parameters (usually prevalence and/or the Richness component of ASV diversity), the strongest effect was observed for the multi-strain LSV. Varroa unambiguously led to elevated prevalence, load, and diversity (Richness and Shannon Index) of LSV, with these results largely shaped by LSV-2, a major LSV strain. Unprecedented insights into the mite-virus relationship were further gained from implementing a phylogeographic approach. In addition to enabling the identification of a novel LSV strain that dominated the unique viral landscape of the easternmost islands, this approach, in combination with the recovered diversity patterns, strongly suggests that Varroa is driving the evolutionary change of LSV in the Azores. This study greatly advances the current understanding of the effect of Varroa on the epidemiology and adaptive evolution of these less-studied viruses, whose relationship with Varroa has thus far been poorly defined.

An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.

Targeting ribosomal frameshifting has emerged as a potential therapeutic intervention strategy against Covid-19. During ribosomal translation, a fraction of elongating ribosomes slips by one base in the 5' direction and enters a new reading frame for viral protein synthesis. Any interference with this process profoundly affects viral replication and propagation. For Covid-19, two RNA sites associated with ribosomal frameshifting for SARS-CoV-2 are positioned on the 5' and 3' of the frameshifting residues. Although much attention has been on the 3' frameshift element (FSE), the 5' stem-loop (attenuator hairpin, AH) can play a role. The formation of AH has been suggested to occur as refolding of the 3' RNA structure is triggered by ribosomal unwinding. However, the attenuation activity and the relationship between the two regions are unknown. To gain more insight into these two related viral RNAs and to further enrich our understanding of ribosomal frameshifting for SARS-CoV-2, we explore the RNA folding of both 5' and 3' regions associated with frameshifting. Using our graph-theory-based modeling tools to represent RNA secondary structures, "RAG" (RNA- As-Graphs), and conformational landscapes to analyze length-dependent conformational distributions, we show that AH coexists with the 3-stem pseudoknot of the 3' FSE (graph 3_6 in our dual graph notation) and alternative pseudoknot (graph 3_3) but less likely with other 3' FSE alternative folds (such as 3-way junction 3_5). This is because an alternative length-dependent Stem 1 (AS1) can disrupt the FSE pseudoknots and trigger other folds. In addition, we design four mutants for long lengths that stabilize or disrupt AH, AS1 or FSE pseudoknot to illustrate the deduced AH/AS1 roles and favor the 3_5, 3_6 or stem-loop. These mutants further show how a strengthened pseudoknot can result from a weakened AS1, while a dominant stem-loop occurs with a strengthened AS1. These structural and mutational insights into both ends of the FSE in SARS-CoV-2 advance our understanding of the SARS-CoV-2 frameshifting mechanism by suggesting a sequence of length-dependent folds, which in turn define potential therapeutic intervention techniques involving both elements. Our work also highlights the complexity of viral landscapes with length-dependent folds, and challenges in analyzing these multiple conformations.

Exploring the viral landscape of saffron through metatranscriptomic analysis

Saffron (Crocus sativus L.), a historically significant crop valued for its nutraceutical properties, has been poorly explored from a phytosanitary perspective. This study conducted a thorough examination of viruses affecting saffron samples from Spanish cultivars, using high-throughput sequencing alongside a systematic survey of transcriptomic datasets from Crocus sativus at the Sequence Read Archive. Our analysis unveiled a broad diversity and abundance, identifying 17 viruses across the 52 analyzed libraries, some of which were highly prevalent. This includes known saffron-infecting viruses and previously unreported ones. In addition, we discovered 7 novel viruses from the Alphaflexiviridae, Betaflexiviridae, Potyviridae, Solemoviridae, and Geminiviridae families, with some present in libraries from various locations. These findings indicate that the saffron-associated virome is more complex than previously reported, emphasizing the potential of phytosanitary analysis to enhance saffron productivity.

Simultaneous Detection of Grapevine Viruses via Multiplex Reverse Transcription Polymerase Chain Reaction: An Academic Approach

Grapevine viruses pose a significant threat to the viticulture industry, resulting in reduced grape yield, poor fruit quality, and economic loss. Accurate and timely detection of multiple viruses are essential for effective disease management and the implementation of appropriate control measures. The aim of this study was to assess the presence of grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine leafroll-associated virus‑1 (GLRaV-1), arabis mosaic virus (ArMV), and grapevine virus A (GVA) in 320 plant samples collected from the Aegean region of Turkey using the powerful technique of multiplex reverse transcription-polymerase chain reaction (RT-PCR). Through comprehensive analysis, 119 of the 320 infected samples were identified using PCR. The distribution of the detected viruses revealed the presence of 28 GFLV, 31 GLRaV‑1, 12 GFkV, 21 GVA, and 27 ArMV. By comprehensively analyzing the samples, the researchers were able to simultaneously detect and identify the target viruses using a single, cost-effective assay. These results reveal the prevalence and distribution of these viruses in the Aegean region, providing valuable insights into the viral landscape of grapevines in this important viticultural area. The high detection rates of these viruses highlight the urgent need for improved disease management strategies to safeguard vine health and productivity.

Transcription termination and readthrough in African swine fever virus.

African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that encodes its own host-like RNA polymerase (RNAP) and factors required to produce mature mRNA. The formation of accurate mRNA 3' ends by ASFV RNAP depends on transcription termination, likely enabled by a combination of sequence motifs and transcription factors, although these are poorly understood. The termination of any RNAP is rarely 100% efficient, and the transcriptional "readthrough" at terminators can generate long mRNAs which may interfere with the expression of downstream genes. ASFV transcriptome analyses reveal a landscape of heterogeneous mRNA 3' termini, likely a combination of bona fide termination sites and the result of mRNA degradation and processing. While short-read sequencing (SRS) like 3' RNA-seq indicates an accumulation of mRNA 3' ends at specific sites, it cannot inform about which promoters and transcription start sites (TSSs) directed their synthesis, i.e., information about the complete and unprocessed mRNAs at nucleotide resolution. Here, we report a rigorous analysis of full-length ASFV transcripts using long-read sequencing (LRS). We systematically compared transcription termination sites predicted from SRS 3' RNA-seq with 3' ends mapped by LRS during early and late infection. Using in-vitro transcription assays, we show that recombinant ASFV RNAP terminates transcription at polyT stretches in the non-template strand, similar to the archaeal RNAP or eukaryotic RNAPIII, unaided by secondary RNA structures or predicted viral termination factors. Our results cement this T-rich motif (U-rich in the RNA) as a universal transcription termination signal in ASFV. Many genes share the usage of the same terminators, while genes can also use a range of terminators to generate transcript isoforms varying enormously in length. A key factor in the latter phenomenon is the highly abundant terminator readthrough we observed, which is more prevalent during late compared with early infection. This indicates that ASFV mRNAs under the control of late gene promoters utilize different termination mechanisms and factors to early promoters and/or that cellular factors influence the viral transcriptome landscape differently during the late stages of infection.

Temporal Dynamics and Genomic Landscape of SARS-CoV-2 After Four Years of Evolution.

Introduction Since its emergence, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive genomic evolution, impacting public health policies, diagnosis, medication, and vaccine development. This study leverages advanced bioinformatics to assess the virus's temporal and regional genomic evolution from December 2019 to October 2023. Methods Our analysis incorporates 16,575 complete SARS-CoV-2 sequences collected from 214 countries. These samples were comparatively analyzed, with a detailed characterization of nucleic mutations, lineages, distribution, and evolutionary patterns during each year, using the Wuhan-Hu-1 strain as the reference. Results Our analysis has identified a total of 21,580 mutations that we classified into transient mutations, which diminished over time, and persistent mutations with steadily increasing frequencies. This mutation landscape led to a notable surge in the evolutionary rate, rising from 13 mutations per sample in 2020 to 96 by 2023, with minor geographic variations. The phylogenetic analysis unveiled three distinct evolutionary branches, each representing unique viral evolution pathways. These lineages exhibited a tendency for a reduced duration of dominance with a shortening prevalence period over time, as dominant strains were consistently replaced by more fit variants. Notably, the emergence of the Alpha and Delta variants in 2021 was followed by the subsequent dominance of Omicron clade variants that have branched into several recombinant variants in 2022, marking a significant shift in the viral landscape. Conclusion This study sheds light on the dynamic nature of SARS-CoV-2 evolution, emphasizing the importance of continuous and vigilant genomic surveillance. The dominance of recombinant lineages, coupled with the disappearance of local variants, underscores the virus's adaptability.

Unravelling Insights into the Evolution and Management of SARS-CoV-2

Worldwide, the COVID-19 pandemic, caused by the brand-new coronavirus SARS-CoV-2, has claimed a sizable number of lives. The virus’ rapid spread and impact on every facet of human existence necessitate a continuous and dynamic examination of its biology and management. Despite this urgency, COVID-19 does not currently have any particular antiviral treatments. As a result, scientists are concentrating on repurposing existing antiviral medications or creating brand-new ones. This comprehensive review seeks to provide an in-depth exploration of our current understanding of SARS-CoV-2, starting with an analysis of its prevalence, pathology, and evolutionary trends. In doing so, the review aims to clarify the complex network of factors that have contributed to the varying case fatality rates observed in different geographic areas. In this work, we explore the complex world of SARS-CoV-2 mutations and their implications for vaccine efficacy and therapeutic interventions. The dynamic viral landscape of the pandemic poses a significant challenge, leading scientists to investigate the genetic foundations of the virus and the mechanisms underlying these genetic alterations. Numerous hypotheses have been proposed as the pandemic has developed, covering various subjects like the selection pressures driving mutation, the possibility of vaccine escape, and the consequences for clinical therapy. Furthermore, this review will shed light on current clinical trials investigating novel medicines and vaccine development, including the promising field of drug repurposing, providing a window into the changing field of treatment approaches. This study provides a comprehensive understanding of the virus by compiling the huge and evolving body of knowledge on SARS-CoV-2, highlighting its complexities and implications for public health, and igniting additional investigation into the control of this unprecedented global health disaster.

In vivo functional phenotypes from a computational epistatic model of evolution

Computational models of evolution are valuable for understanding the dynamics of sequence variation, to infer phylogenetic relationships or potential evolutionary pathways and for biomedical and industrial applications. Despite these benefits, few have validated their propensities to generate outputs with in vivo functionality, which would enhance their value as accurate and interpretable evolutionary algorithms. We demonstrate the power of epistasis inferred from natural protein families to evolve sequence variants in an algorithm we developed called sequence evolution with epistatic contributions (SEEC). Utilizing the Hamiltonian of the joint probability of sequences in the family as fitness metric, we sampled and experimentally tested for in vivo [Formula: see text]-lactamase activity in Escherichia coli TEM-1 variants. These evolved proteins can have dozens of mutations dispersed across the structure while preserving sites essential for both catalysis and interactions. Remarkably, these variants retain family-like functionality while being more active than their wild-type predecessor. We found that depending on the inference method used to generate the epistatic constraints, different parameters simulate diverse selection strengths. Under weaker selection, local Hamiltonian fluctuations reliably predict relative changes to variant fitness, recapitulating neutral evolution. SEEC has the potential to explore the dynamics of neofunctionalization, characterize viral fitness landscapes, and facilitate vaccine development.

Mining genomic repositories to further our knowledge of the extent of SARS-CoV-2 co-infections.

Recombination events between Delta and Omicron SARS-CoV-2 lineages highlight the need for co-infection research. Existing studies focus on late-phase co-infections, with few examining earlier pandemic stages. This new study aims to globally identify and characterize co-infections using a bioinformatic pipeline to analyse genomic data from diverse locations and pandemic phases. Among 26988 high-quality SARS-CoV-2 isolates from 11 diverse project databases, we identified 141 potential co-infection cases (0.52%), surpassing previous prevalence estimates. These co-infections were observed throughout the pandemic timeline, with an increase noted after the emergence of the Omicron variant. Co-infections involving the Omicron variant were the most prevalent, potentially influenced by the high level of diversity within this lineage and its impact on the viral landscape. Additionally, we found co-infections involving the pre-Alpha/Alpha lineages, which have been rarely described, raising possibilities of contributing to new lineage emergence through recombination events. The analysis revealed co-infection cases involving both different and the same lineages/sublineages. Our study showcases the potential of our pipeline to leverage valuable information stored in global sequence repositories, advancing our understanding of SARS-CoV-2 co-infections. The prevalence of co-infections highlights the importance of monitoring viral diversity and its potential implications on disease dynamics. Integrating clinical data with genomic findings can further shed light on the clinical implications and outcomes of co-infections.

EVEscape: Revealing potential escape sites based on the viral variation landscape.

EVEscape: Revealing potential escape sites based on the viral variation landscape.

A Narrative Review on the Specific Pattern of HBV Genotype in Bangladesh: Clinical Implications for Management.

Bangladesh's unique epidemiological landscape presents an intriguing puzzle. This South Asian nation, with its complex sociodemographic and environmental factors, is home to a diverse array of hepatitis-B virus (HBV) genotypes, identified as Genotype C, with Genotypes D and A also making a significant contribution to the viral landscape. Reviewing such insights is necessary not only to underscore the country's regional diversity in HBV strains but also to bring into focus the clinical implications these genetic variations may have on disease progression and management. A thorough database search covered various sources using relevant keywords like "Hepatitis B virus genotypes", "HBV genotypes in Bangladesh", and "HBV clinical implications". The review synthesized findings and analyzed HBV genotype prevalence and clinical implications in Bangladesh. Genotypes C and D collectively represent 82% of chronic hepatitis-B infection (CHB) cases in Bangladesh, underscoring their regional prevalence. The geographic context is pivotal in understanding HBV infection dynamics and disease progression in this area. Notably, genotype C and the presence of A1762T/G1764A mutations appear to have a distinct impact on disease development, potentially affecting the immune response in CHB patients. This highlights the need for tailored management approaches in this specific region. Further research is vital to confirm and elaborate on these findings, particularly in relation to how these mutations influence the host's immune response. In summary, studies on HBV genotypes in Bangladesh stress the need for genotype-specific clinical considerations and more research to improve diagnostics and therapies. Raihan R, Akbar SMF. A Narrative Review on the Specific Pattern of HBV Genotype in Bangladesh: Clinical Implications for Management. Euroasian J Hepato-Gastroenterol 2023;13(2):152-158.