ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Heparan sulfate proteoglycans remodel SARS-CoV-2 spike conformation to allow integrin interaction and infection of endothelial cells

SARS-CoV-2 infects ACE2-negative primary HL-mECs through the interaction of an RGD motif, included in all spike proteins, up to the Omicron BA.1 subvariant, with αvβ3 integrin. Following its entry, SARS-CoV-2 remodels ECs phenotype and promotes angiogenesis in the absence of productive viral replication. Moreover, lack of spike/αvβ3 interaction, occurring in Omicron BA.5 which contains the D405N mutation in the RGD motif, inhibits HL-mECs infection and dysfunction. It is worth noting that anti-spike antibodies do not impact SARS-CoV-2 entry into HL-mECs. This data highlights the fact that i) the RGD motif is not exposed in the entire spike protein and ii) the need of a cofactor favoring spike/αvβ3 interaction. HSPGs are used by different viruses as receptors and coreceptors for their entry into host cells. Here, we use different approaches to scrutinize the role exerted by HSPGs in favoring SARS-CoV-2 infection of ECs. We highlight HSPGs as key molecules responsible for RGD exposure allowing its binding to the αvβ3 integrin as the first step toward viral entry by endocytosis. Indeed, SPR analysis showed lack of spike/αvβ3 interaction in the absence of heparin. This data was further corroborated by immunofluorescence and infectivity assays. Interestingly, the use of Heparinase III or sodium chlorate counteracts the release of proangiogenic molecules and inhibits signaling pathways induced by SARS-CoV-2 infection. Thus, HSPGs may represent a target for preventing SARS-CoV-2 infection of ECs and EC dysfunction-related COVID-19 severity.

Phylodynamics and phylogeography of watermelon mosaic virus: Multiple local invasion routes in southern France and recombination-driven limits to global analysis

Watermelon mosaic virus (WMV) is a major plant pathogen, infecting over 170 plant species, including cucurbits and legumes. Though mostly propagated locally by aphids in a non-persistent manner, long-range dispersal can occur through human-induced plant or vector movements. Understanding patterns of local and global spread of WMV is crucial to help formulate adequate control strategies. We used phylodynamic methods based on partial and whole-genome sequences collected in France between 2000 and 2017 to reconstruct the introduction of new lineages in the past 30 years and their subsequent diffusion in the country. We identified at least 11 different introduction events, hailing from different parts of the global diversity of WMV, highlighting the critical role international exchanges play in the spread of plant pathogens. For three of these lineages, we estimated the time and location of their introduction in the mid-1990s in the south of France and the speed at which they spread in this specific landscape. We also showed that the highly recombinogenic nature of WMV, as with most potyviruses, makes the use of whole genomes necessary to classify these viruses on a global scale and must be taken into consideration to reconstruct viral evolutionary history. Our results demonstrate how genomic sequencing of plant viruses can help reconstruct specific viral outbreaks and understand global circulation patterns of plant pathogens.

Integrated Seroprevalence and Genome-Based Study of SARS-CoV-2 Viral Strains in N'Djamena: Insights Into Chad's COVID-19 Epicenter

The COVID-19 epidemic has shown regional variations in transmission and outcomes. As a primary hotspot in Chad, N'Djamena is crucial for comprehensive epidemiological investigation. Our study employed two methodologies: seroprevalence data collection and whole-genome sequencing of SARS-CoV-2 strains. This dual approach assessed population exposure and virus genetic diversity. Seroprevalence data indicated broader exposure than confirmed cases suggested, and genome sequencing identified multiple strains, including globally recognized variants of concern. Integrating these data provided insights into transmission dynamics, potential herd immunity thresholds, and the impact of specific variants on disease progression. Our findings underscore the importance of integrated, multidisciplinary research in infectious disease epidemiology and inform targeted public health strategies, including social measures and vaccination, to combat infectious diseases in N'Djamena.

Biological warfare between two bacterial viruses in a defense archipelago sheds light on the spread of CRISPR-Cas systems

CRISPR-Cas systems are adaptive immunity systems of bacteria and archaea that prevent infection by viruses and other external mobile genetic elements. It is currently known that these defense systems can be co-opted by the same viruses. We have found one of these viruses in the opportunistic pathogen Acinetobacter baumannii, and the same system has been also found in an integration hotspot of the bacterial genome that harbors other multiple defense systems. The CRISPR-Cas system appears to especially target another virus that could compete with the system itself for the same integration site. This virus is prevalent in strains of the species belonging to the so-called Global Clone 2, which causes the most frequent outbreaks worldwide. Knowledge of this viral warfare involving antiviral systems could be useful in the fight against infections caused by bacteria, and it would also shed light on how CRISPR-Cas systems expand in bacteria.

From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida

The continual evolution of SARS-CoV-2 has significantly influenced the global response to the COVID-19 pandemic, with the emergence of highly transmissible and immune-evasive variants posing persistent challenges. The Omicron variant, first identified in November 2021, rapidly replaced the Delta variant, becoming the predominant strain worldwide. In Florida, Omicron was first detected in December 2021, leading to an unprecedented surge in cases that surpassed all prior waves, despite extensive vaccination efforts. This study investigates the molecular evolution and transmission dynamics of the Omicron lineages during Florida's Omicron waves, supported by a robust dataset of over 1000 sequenced genomes. Through phylogenetic and phylodynamic analyses, we capture the rapid diversification of the Omicron lineages, identifying significant importation events, predominantly from California, Texas, and New York, and exportation to North America, Europe, and South America. Variants such as BA.1, BA.2, BA.4, and BA.5 exhibited distinct transmission patterns, with BA.2 showing the ability to reinfect individuals previously infected with BA.1. Despite the high transmissibility and immune evasion of the Omicron sub-lineages, the plateauing of cases by late 2022 suggests increasing population immunity from prior infection and vaccination. Our findings underscore the importance of continuous genomic surveillance in identifying variant introductions, mapping transmission pathways, and guiding public health interventions to mitigate current and future pandemic risks.

Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023

BACKGROUND

Italy was significantly affected by the COVID-19 pandemic, experiencing multiple waves of infection following the sequential emergence of new variants. Understanding the transmission patterns and evolution of SARS-CoV-2 is vital for future preparedness.

METHODS

We conducted an analysis of viral genome sequences, integrating epidemiological and phylodynamic approaches, to characterize how SARS-CoV-2 variants have spread within the country.

RESULTS

Our findings indicate bidirectional international transmission, with Italy transitioning between importing and exporting the virus. Italy experienced four distinct epidemic waves, each associated with a significant reduction in fatalities from 2021 to 2023. These waves were primarily driven by the emergence of VOCs such as Alpha, Delta, and Omicron, which were reflected in observed transmission dynamics and effectiveness of public health measures.

CONCLUSIONS

The changing patterns of viral spread and variant prevalence throughout Italy's pandemic response underscore the continued importance of flexible public health strategies and genomic surveillance, both of which are crucial for tracking the evolution of variants and adapting control measures effectively to ensure preparedness for future outbreaks.

DiMA: sequence diversity dynamics analyser for viruses

Sequence diversity is one of the major challenges in the design of diagnostic, prophylactic, and therapeutic interventions against viruses. DiMA is a novel tool that is big data-ready and designed to facilitate the dissection of sequence diversity dynamics for viruses. DiMA stands out from other diversity analysis tools by offering various unique features. DiMA provides a quantitative overview of sequence (DNA/RNA/protein) diversity by use of Shannon's entropy corrected for size bias, applied via a user-defined k-mer sliding window to an input alignment file, and each k-mer position is dissected to various diversity motifs. The motifs are defined based on the probability of distinct sequences at a given k-mer alignment position, whereby an index is the predominant sequence, while all the others are (total) variants to the index. The total variants are sub-classified into the major (most common) variant, minor variants (occurring more than once and of incidence lower than the major), and the unique (singleton) variants. DiMA allows user-defined, sequence metadata enrichment for analyses of the motifs. The application of DiMA was demonstrated for the alignment data of the relatively conserved Spike protein (2,106,985 sequences) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the relatively highly diverse pol gene (2637) of the human immunodeficiency virus-1 (HIV-1). The tool is publicly available as a web server (https://dima.bezmialem.edu.tr), as a Python library (via PyPi) and as a command line client (via GitHub).

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1

Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization.

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant

In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.

Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022

This study examines the epidemiological and genomic characteristics, along with the transmission dynamics, of SARS-CoV-2 within prison units I and II in Campo Grande, Mato Grosso do Sul, Brazil. Conducted between May and October 2022, it reveals how the virus spreads in the confined settings of prisons, emphasizing the roles of overcrowded cells, frequent transfers, and limited healthcare access. The research involved 1927 participants (83.93% of the total prison population) and utilized nasopharyngeal swabs and RT-qPCR testing for detection. Contact tracing monitored exposure within cells. Out of 2108 samples, 66 positive cases were identified (3.13%), mostly asymptomatic (77.27%), with the majority aged 21-29 and varying vaccination statuses. Next-generation sequencing generated 28 whole genome sequences, identifying the Omicron variant (subtypes BA.2 and BA.5) with 99% average coverage. Additionally, the study seeks to determine the relationship between immunization levels and the incidence of SARS-CoV-2 cases within this enclosed population. The findings underscore the necessity of comprehensive control strategies in prisons, including rigorous screening, isolation protocols, vaccination, epidemiological monitoring, and genomic surveillance to mitigate disease transmission and protect both the incarcerated population and the broader community.

Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil

Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols.

Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent

Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of new viral genomes. To tackle these problems, we propose an approach that uses short-read mappers to create whole-genome maps, and gradient descent to isolate the homologous fraction and calculate the final distance value. We implement this approach as Mottle. With the use of simulated and biological sequences, Mottle was able to remain stable to 0.66-0.96 substitutions per base pair and identify viral outgroup genomes with 95% accuracy at the family-order level. Our results indicate that Mottle performs as well as existing programs in identifying taxonomic relationships, with more accurate numerical estimation of genomic distance over greater divergences. By contrast, one limitation is a reduced numerical accuracy at low divergences, and on genomes where insertions and deletions are uncommon, when compared to alternative approaches. We propose that Mottle may therefore be of particular interest in the study of viruses, viral relationships, and notably for viral discovery platforms, helping in benchmarking of homology search tools and defining the limits of taxonomic classification methods. The code for Mottle is available at https://github.com/tphoward/Mottle_Repo.

Classification of a Massive Number of Viral Genomes and Estimation of Time of Most Recent Common Ancestor (tMRCA) of SARS-CoV-2 Using Phylodynamic Analysis

Estimating the time of most recent common ancestor (tMRCA) is important to trace the origin of pathogenic viruses. This analysis is based on the genetic diversity accumulated in a certain time period. There have been thousands of mutant sites occurring in the genomes of SARS-CoV-2 since the COVID-19 pandemic started; six highly linked mutation sites occurred early before the start of the pandemic and can be used to classify the genomes into three main haplotypes. Tracing the origin of those three haplotypes may help to understand the origin of SARS-CoV-2. In this article, we present a complete protocol for the classification of SARS-CoV-2 genomes and calculating tMRCA using Bayesian phylodynamic method. This protocol may also be used in the analysis of other viral genomes. Key features • Filtering and alignment of a massive number of viral genomes using custom scripts and ViralMSA. • Classification of genomes based on highly linked sites using custom scripts. • Phylodynamic analysis of viral genomes using Bayesian evolutionary analysis sampling trees (BEAST). • Visualization of posterior distribution of tMRCA using Tracer.v1.7.2. • Optimized for the SARS-CoV-2.

Scalable neighbour search and alignment with uvaia

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions

A feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of the ORF7a: H47Y mutation, in which the 47th residue of ORF7a has been mutated from a histidine (H) to a tyrosine (Y). Here, we evaluated the effect of this mutation on the three main functions ascribed to the SARS-CoV-2 ORF7a protein. Our findings show that H47Y mutation impairs the ability of SARS-CoV-2 ORF7a to antagonize the type I interferon (IFN-I) response and to downregulate major histocompatibility complex I (MHC-I) cell surface levels, but had no effect in its anti-SERINC5 function. Overall, our results suggest that the H47Y mutation of ORF7a affects important functions of this protein, resulting in changes in virus pathogenesis.

Virological characteristics of the SARS-CoV-2 Omicron XBB.1.5 variant

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the S486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determine the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. We provide the intrinsic pathogenicity of XBB.1 and XBB.1.5 in hamsters. Importantly, we find that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC suppression. In vivo experiments using recombinant viruses reveal that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, our study identifies the two viral functions defined the difference between XBB.1 and XBB.1.5.

Updated Insights into the Phylogenetics, Phylodynamics, and Genetic Diversity of Nipah Virus (NiV)

Nipah virus (NiV), a biosafety level 4 agent, was first identified in human clinical cases during an outbreak in 1998 in Malaysia and Singapore. While flying foxes are the primary host and viral vector, the infection is associated with a severe clinical presentation in humans, resulting in a high mortality rate. Therefore, NiV is considered a virus with an elevated epidemic potential which is further underscored by its recent emergence (September 2023) as an outbreak in India. Given the situation, it is paramount to understand the molecular dynamics of the virus to shed more light on its evolution and prevent potential future outbreaks. In this study, we conducted Bayesian phylogenetic analysis on all available NiV complete genomes, including partial N-gene NiV sequences (≥1000 bp) in public databases since the first human case, registered in 1998. We observed the distribution of genomes into three main clades corresponding to the genotypes Malaysia, Bangladesh and India, with the Malaysian clade being the oldest in evolutionary terms. The Bayesian skyline plot showed a recent increase in the viral population size since 2019. Protein analysis showed the presence of specific protein families (Hendra_C) in bats that might keep the infection in an asymptomatic state in bats, which also serve as viral vectors. Our results further indicate a shortage of complete NiV genomes, which would be instrumental in gaining a better understanding of NiV's molecular evolution and preventing future outbreaks. Our investigation also underscores the critical need to strengthen genomic surveillance based on complete NiV genomes that will aid thorough genetic characterization of the circulating NiV strains and the phylogenetic relationships between the henipaviruses. This approach will better prepare us to tackle the challenges posed by the NiV virus and other emerging viruses.

ViralWasm: a client-side user-friendly web application suite for viral genomics

MOTIVATION

The genomic surveillance of viral pathogens such as SARS-CoV-2 and HIV-1 has been critical to modern epidemiology and public health, but the use of sequence analysis pipelines requires computational expertise, and web-based platforms require sending potentially sensitive raw sequence data to remote servers.

RESULTS

We introduce ViralWasm, a user-friendly graphical web application suite for viral genomics. All ViralWasm tools utilize WebAssembly to execute the original command line tools client-side directly in the web browser without any user setup, with a cost of just 2-3x slowdown with respect to their command line counterparts.

AVAILABILITY AND IMPLEMENTATION

The ViralWasm tool suite can be accessed at: https://niema-lab.github.io/ViralWasm.

Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding

MOTIVATION

Multiple sequence alignment (MSA) is one of the hotspots of current research and is commonly used in sequence analysis scenarios. However, there is no lasting solution for MSA because it is a Nondeterministic Polynomially complete problem, and the existing methods still have room to improve the accuracy.

RESULTS

We propose Deep reinforcement learning with Positional encoding and self-Attention for MSA, based on deep reinforcement learning, to enhance the accuracy of the alignment Specifically, inspired by the translation technique in natural language processing, we introduce self-attention and positional encoding to improve accuracy and reliability. Firstly, positional encoding encodes the position of the sequence to prevent the loss of nucleotide position information. Secondly, the self-attention model is used to extract the key features of the sequence. Then input the features into a multi-layer perceptron, which can calculate the insertion position of the gap according to the features. In addition, a novel reinforcement learning environment is designed to convert the classic progressive alignment into progressive column alignment, gradually generating each column's sub-alignment. Finally, merge the sub-alignment into the complete alignment. Extensive experiments based on several datasets validate our method's effectiveness for MSA, outperforming some state-of-the-art methods in terms of the Sum-of-pairs and Column scores.

AVAILABILITY AND IMPLEMENTATION

The process is implemented in Python and available as open-source software from https://github.com/ZhangLab312/DPAMSA.

The panzootic potential of SARS-CoV-2

Each year, SARS-CoV-2 is infecting an increasingly unprecedented number of species. In the present article, we combine mammalian phylogeny with the genetic characteristics of isolates found in mammals to elaborate on the host-range potential of SARS-CoV-2. Infections in nonhuman mammals mirror those of contemporary viral strains circulating in humans, although, in certain species, extensive viral circulation has led to unique genetic signatures. As in other recent studies, we found that the conservation of the ACE2 receptor cannot be considered the sole major determinant of susceptibility. However, we are able to identify major clades and families as candidates for increased surveillance. On the basis of our findings, we argue that the use of the term panzootic could be a more appropriate term than pandemic to describe the ongoing scenario. This term better captures the magnitude of the SARS-CoV-2 host range and would hopefully inspire inclusive policy actions, including systematic screenings, that could better support the management of this worldwide event.

Genome analysis of SARS-CoV-2 haplotypes: separation and parallel evolution of the major haplotypes occurred considerably earlier than their emergence in China

More than 3 years have passed since the outbreak of COVID-19 and yet, the origin of the causal virus SARS-CoV-2 remains unknown. We examined the evolutionary trajectory of SARS-CoV-2 by analyzing non-redundant genome sets classified based on six closely linked mutations. The results indicated that SARS-CoV-2 emerged in February 2019 or earlier and evolved into three main haplotypes (GL, DS, and DL) before May 2019, which then continued to evolve in parallel. The dominant haplotype GL had spread worldwide in the summer (May to July) of 2019 and then evolved into virulent strains in December 2019 that triggered the global pandemic, whereas haplotypes DL and DS arrived in China in October 2019 and caused the epidemic in China in December 2019. Therefore, haplotype GL neither originated in China nor from the viral strains that caused the epidemic in China. Accordingly, considering data solely from China would be inadequate to reveal the mysterious origin of SARS-CoV-2, emphasizing the necessity of global cooperation.

Genomic Epidemiology and Lineage Dynamics of SARS-CoV-2 in Bulgaria: Insights from a Three-Year Pandemic Analysis

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS-CoV-2 in Bulgaria over a three-year period. Through extensive genomic sequencing and data analysis, we investigated the evolution of the virus, the emergence of variants of concern (VOCs), and their impact on the country's pandemic trajectory. We also assessed the relationship between viral diversity and COVID-19 morbidity and mortality in Bulgaria. Our findings shed light on the temporal and spatial distribution of SARS-CoV-2 lineages and provide crucial insights into the dynamics of the pandemic in the country. The interplay between international travel and viral transmission plays a significant role in the emergence and dissemination of different SARS-CoV-2 variants. The observed proportions of exportation to various continents provide insights into the potential pathways through which these lineages spread globally. Understanding the genomic epidemiology of SARS-CoV-2 in Bulgaria is essential for formulating targeted public health strategies, enhancing vaccination efforts, and effectively managing future outbreaks.

Early Detection of the Recombinant SARS-CoV-2 XAN Variant in Bulgaria: Initial Genomic Insights into Yet Another Piece of the Growing Puzzle of Recombinant Clades

The first recombinant SARS-CoV-2 variants were identified in 2022, causing public health concerns. The importance of recombinant variants has increased especially since the WHO designated the recombinant variant XBB and its lineages as subvariants that require monitoring on 20 November 2022. In this study, we provide the first insights into the new SARS-CoV-2 variant named XAN, a recombinant composed of Omicron sub-lineages BA.2 and BA.5. To our knowledge, this is the first report on the recombinant SARS-CoV-2 XAN variant identified in Bulgaria.

A collaborative approach to improving representation in viral genomic surveillance

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building 'next generation' genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness.

Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru

At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.

Traceability of SARS-CoV-2 transmission through quasispecies analysis

During COVID-19 pandemic, consensus genomic sequences were used for rapidly monitor the spread of the virus worldwide. However, less attention was paid to intrahost genetic diversity. In fact, in the infected host, SARS-CoV-2 consists in an ensemble of replicating and closely related viral variants so-called quasispecies. Here we show that intrahost single nucleotide variants (iSNVs) represent a target for contact tracing analysis. Our data indicate that in the acute phase of infection, in highly likely transmission links, the number of viral particles transmitted from one host to another (bottleneck size) is large enough to propagate iSNVs among individuals. Furthermore, we demonstrate that, during SARS-CoV-2 outbreaks when the consensus sequences are identical, it is possible to reconstruct the transmission chains by genomic investigations of iSNVs. Specifically, we found that it is possible to identify transmission chains by limiting the analysis of iSNVs to only three well-conserved genes, namely nsp2, ORF3, and ORF7.

SARS-CoV CH.1.1 Variant: Genomic and Structural Insight

In early February 2023, the Omicron subvariant XBB.1.5, also known as "Kraken", accounted for more than 44% of new COVID-19 cases worldwide, whereas a relatively new Omicron subvariant named CH.1.1, deemed "Orthrus", accounted for less than 6% of new COVID-19 cases during the subsequent weeks. This emerging variant carries a mutation, L452R, previously observed in the highly pathogenic Delta and the highly transmissible BA.4 and BA.5 variants, necessitating a shift to active surveillance to assure adequate preparedness for likely future epidemic peaks. We provide a preliminary understanding of the global distribution of this emerging SARS-CoV-2 variant by combining genomic data with structural molecular modeling. In addition, we shield light on the number of specific point mutations in this lineage that may have functional significance, thereby increasing the risk of disease severity, vaccine resistance, and increased transmission. This variant shared about 73% of the mutations with Omicron-like strains. Our homology modeling analysis revealed that CH.1.1 may have a weakened interaction with ACE2 and that its electrostatic potential surface appears to be more positive than that of the reference ancestral virus. Finally, our phylogenetic analysis revealed that this likely-emerging variant was already cryptically circulating in European countries prior to its first detection, highlighting the importance of having access to whole genome sequences for detecting and controlling emerging viral strains.

Modeling mRNA-based vaccine YFV.E1988 against yellow fever virus E-protein using immuno-informatics and reverse vaccinology approach

To surmount constraints of live-attenuated vaccines we have in silico designed mRNA vaccine using envelope protein as a target antigen. From the alignment of 216 envelope proteins, a consensus sequence was obtained which was used for codon optimization. The secondary structure was predicted using Mfold and RNAfold tool. IEDB server was used to predict T-cell and B-cell epitopes, epitope conservancy, immunogenicity, and population coverage. Antigenicity, allergenicity, and toxicity were predicted using Vaxijen, AllerTOP, and ToxinPred tools, respectively. Interactions between MHC and identified epitopes were confirmed by docking and molecular dynamics simulation. In silico immune simulation was done using the C-ImmSim server. Vaccine peptide 3D structure was predicted and validated based on the Ramachandran plot. Finally, we designed the vaccine construct for simulating restriction cloning using the SnapGene tool. Our optimization of consensus E protein is highly immunogenic, conserved, has immune-dominance characteristics, and suggests high translational efficiency in the host cell. We validated the presence of T and B cell epitopes and interestingly we found one CD4+ and four CD8+ T-cell epitopes that satisfied all the criteria of an effective vaccine candidate. We found high-affinity interactions between epitope and HLA alleles that can stimulate the T-cell response. The immune simulation verified the immune cell response to eliminate the antigen. To ensure effective expression of the vaccine, a circular plasmid has been designed using in silico cloning approach for the in vitro transcription process. Obtained results suggest that the vaccine YFV.E1988 will elicit specific immune responses against YFV and it is a potential model ready for laboratory testing. HighlightsThe envelope (E) protein was found to be highly conserved and it has the potential to protect individuals against YFV infection.YFV.E1988 vaccine has been capable to stimulate both the CD8+ and CD4+ T cell, solving the major limitations of the current live-attenuated vaccines against YFV.Presence of T- and B-cell epitopes across the antigen have been validated using several computational tools.Molecular docking ensured the epitope-allele binding and protein-TLR/MR interaction. The vaccine was found to be immune-stimulatory, safe, and stable.The codons were optimized for efficient translation and increased stability into the human host. The UTR regions and poly (A) tail used for the development of YFV.E1988 showed immune stimulatory potential in several experiments.Communicated by Ramaswamy H. Sarma.

Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project

Background

Schools are high-risk settings for SARS-CoV-2 transmission, but necessary for children's educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown.

Methods

The objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 - March 2021.

Findings

In 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88% - 98%); 67% were associated with a positive wastewater sample (95% CI: 57% - 77%), and 40% were associated with a positive surface sample (95% CI: 29% - 52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples.

Interpretation

Passive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy.

Funding

County of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control.

The D405N Mutation in the Spike Protein of SARS-CoV-2 Omicron BA.5 Inhibits Spike/Integrins Interaction and Viral Infection of Human Lung Microvascular Endothelial Cells

Severe COVID-19 is characterized by angiogenic features, such as intussusceptive angiogenesis, endothelialitis, and activation of procoagulant pathways. This pathological state can be ascribed to a direct SARS-CoV-2 infection of human lung ECs. Recently, we showed the capability of SARS-CoV-2 to infect ACE2-negative primary human lung microvascular endothelial cells (HL-mECs). This occurred through the interaction of an Arg-Gly-Asp (RGD) motif, endowed on the Spike protein at position 403-405, with αvβ3 integrin expressed on HL-mECs. HL-mEC infection promoted the remodeling of cells toward a pro-inflammatory and pro-angiogenic phenotype. The RGD motif is distinctive of SARS-CoV-2 Spike proteins up to the Omicron BA.1 subvariant. Suddenly, a dominant D405N mutation was expressed on the Spike of the most recently emerged Omicron BA.2, BA.4, and BA.5 subvariants. Here we demonstrate that the D405N mutation inhibits Omicron BA.5 infection of HL-mECs and their dysfunction because of the lack of Spike/integrins interaction. The key role of ECs in SARS-CoV-2 pathogenesis has been definitively proven. Evidence of mutations retrieving the capability of SARS-CoV-2 to infect HL-mECs highlights a new scenario for patients infected with the newly emerged SARS-CoV-2 Omicron subvariants, suggesting that they may display less severe disease manifestations than those observed with previous variants.

Genomic monitoring unveils a high prevalence of severe acute respiratory syndrome coronavirus 2 Omicron variant in vaccine breakthrough cases in Bahia, Brazil

OBJECTIVE

Genome sequencing has been proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by severe acute respiratory syndrome coronavirus 2, i.e., coronavirus disease 2019. Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern. To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different variants of concern in these cases.

METHODS

Nasopharyngeal swabs from infected (symptomatic and asymptomatic), vaccinated or unvaccinated individuals (n=29), and quantitative reverse transcription polymerase chain reaction cycle threshold value (Ct values) of ≤30 were subjected to viral sequencing using nanopore technology.

RESULTS

Our analysis revealed that the Omicron variant was found in 99% of cases and the Delta variant was found in only one case. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of variants of concern not neutralized by the currently available vaccines.

CONCLUSION

It is important to acknowledge the limitations of these vaccines and to develop new vaccines to emergent variants of concern, as is the case of influenza vaccine; going through new doses of the same coronavirus vaccines is "more of the same."

Initial introduction and spread of the SARS-CoV-2 AY.4.2.1 Delta variant in Bulgaria, a genomic insight

The evolution of the emerging SARS-CoV-2 variants carrying mutations in the spike protein raises concerns about the possibility of accelerated transmission in the ever-evolving COVID-19 pandemic worldwide. AY.4.2, a sublineage of the Delta variant, was considered a variant under investigation (VUI) and also gained the nickname "Delta Plus," due to its extra mutations, Y145H and A222V. In this study, using genomic epidemiology, we provide the first insights into the introduction of AY.4.2 in Bulgaria and the AY.4.2.1 sublineage that found larger dissemination only in Bulgaria and the United Kingdom.

A collaborative approach to improve representation in viral genomic surveillance

The lack of routine viral genomic surveillance delayed the initial detection of SARS-CoV-2, allowing the virus to spread unfettered at the outset of the U.S. epidemic. Over subsequent months, poor surveillance enabled variants to emerge unnoticed. Against this backdrop, long-standing social and racial inequities have contributed to a greater burden of cases and deaths among minority groups. To begin to address these problems, we developed a new variant surveillance model geared toward building microbial genome sequencing capacity at universities in or near rural areas and engaging the participation of their local communities. The resulting genomic surveillance network has generated more than 1,000 SARS-CoV-2 genomes to date, including the first confirmed case in northeast Louisiana of Omicron, and the first and sixth confirmed cases in Georgia of the emergent BA.2.75 and BQ.1.1 variants, respectively. In agreement with other studies, significantly higher viral gene copy numbers were observed in Delta variant samples compared to those from Omicron BA.1 variant infections, and lower copy numbers were seen in asymptomatic infections relative to symptomatic ones. Collectively, the results and outcomes from our collaborative work demonstrate that establishing genomic surveillance capacity at smaller academic institutions in rural areas and fostering relationships between academic teams and local health clinics represent a robust pathway to improve pandemic readiness.

Author summary

Genomic surveillance involves decoding a pathogen’s genetic code to track its spread and evolution. During the pandemic, genomic surveillance programs around the world provided valuable data to scientists, doctors, and public health officials. Knowing the complete SARS-CoV-2 genome has helped detect the emergence of new variants, including ones that are more transmissible or cause more severe disease, and has supported the development of diagnostics, vaccines, and therapeutics. The impact of genomic surveillance on public health depends on representative sampling that accurately reflects the diversity and distribution of populations, as well as rapid turnaround time from sampling to data sharing. After a slow start, SARS-CoV-2 genomic surveillance in the United States grew exponentially. Despite this, many rural regions and ethnic minorities remain poorly represented, leaving significant gaps in the data that informs public health responses. To address this problem, we formed a network of universities and clinics in Louisiana, Georgia, and Mississippi with the goal of increasing SARS-CoV-2 sequencing volume, representation, and equity. Our results demonstrate the advantages of rapidly sequencing pathogens in the same communities where the cases occur and present a model that leverages existing academic and clinical infrastructure for a powerful decentralized genomic surveillance system.

Genomic Epidemiology Unveil the Omicron Transmission Dynamics in Rome, Italy

Since 2020, the COVID-19 pandemic represented an important worldwide burden. Well-structured surveillance by reliable and timely genomic data collection is crucial. In this study, a genomic monitoring analysis of all SARS-CoV-2 positive samples retrieved at the Fondazione Policlinico Universitario Campus Bio-Medico, in Rome, Italy, between December 2021 and June 2022, was performed. Two hundred and seventy-four SARS-CoV-2-positive samples were submitted to viral genomic sequencing by Illumina MiSeqII. Consensus sequences were generated by de novo assembling using the iVar tool and deposited on the GISAID database. Lineage assignment was performed using the Pangolin lineage classification. Sequences were aligned using ViralMSA and maximum-likelihood phylogenetic analysis was performed by IQ-TREE2. TreeTime tool was used to obtain dated trees. Our genomic monitoring revealed that starting from December 2021, all Omicron sub-lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) were circulating, although BA.1 was still the one with the highest prevalence thought time in this early period. Phylogeny revealed that Omicron isolates were scattered throughout the trees, suggesting multiple independent viral introductions following national and international human mobility. This data represents a sort of thermometer of what happened from July 2021 to June 2022 in Italy. Genomic monitoring of the circulating variants should be encouraged considering that SARS-CoV-2 variants or sub-variants emerged stochastically and unexpectedly.

Persistence of Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant in Children and Utility of Rapid Antigen Testing as an Indicator of Culturable Virus

We screened 65 longitudinally collected nasal swab samples from 31 children aged 0-16 years who were positive for severe acute respiratory syndrome coronavirus 2 Omicron BA.1. By day 7 after onset of symptoms, 48% of children remained positive by rapid antigen test. In a sample subset, we found 100% correlation between antigen test results and virus culture.

gofasta: command-line utilities for genomic epidemiology research

SUMMARY

gofasta comprises a set of command-line utilities for handling alignments of short assembled genomes in a genomic epidemiology context. It was developed for processing large numbers of closely related SARS-CoV-2 viral genomes and should be useful with other densely sampled pathogen genomic datasets. It provides functions to convert sam-format pairwise alignments between assembled genomes to fasta format; to annotate mutations in multiple sequence alignments, and to extract sets of sequences by genetic distance measures for use in outbreak investigations.

AVAILABILITY AND IMPLEMENTATION

gofasta is an open-source project distributed under the MIT license. Binaries are available at https://github.com/virus-evolution/gofasta, from Bioconda, and through the Go programming language's package management system. Source code and further documentation, including walkthroughs for common use cases, are available on the GitHub repository.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. Maximum likelihood phylogenetic trees were used to infer viruses' geographic origins, enabling identification of 2263 (95% confidence interval: 2159-2366) introductions, including 680 (658-703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501-1663) singletons, introductions with no sampled descendants. Of the sublineages seeded during the first wave, 49% (46-52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4-66.5) sublineages per week to 10.3-fold (8.3-15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). By the end of February 2021, there had been an estimated 30 (19-41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave.Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.

Co-Circulation of Different Hepatitis E Virus Genotype 3 Subtypes in Pigs and Wild Boar in North-East Germany, 2019

Hepatitis E is a major cause of acute liver disease in humans worldwide. The infection is caused by hepatitis E virus (HEV) which is transmitted in Europe to humans primarily through zoonotic foodborne transmission from domestic pigs, wild boar, rabbits, and deer. HEV belongs to the family Hepeviridae, and possesses a positive-sense, single stranded RNA genome. This agent usually causes an acute self-limited infection in humans, but in people with low immunity, e.g., immunosuppressive therapy or underlying liver diseases, the infection can evolve to chronicity and is able to induce a variety of extrahepatic manifestations. Pig and wild boar have been identified as the primary animal reservoir in Europe, and consumption of raw and undercooked pork is known to pose a potential risk of foodborne HEV infection. In this study, we analysed pig and wild boar liver, faeces, and muscle samples collected in 2019 in Mecklenburg-Western Pomerania, north-east Germany. A total of 393 animals of both species were investigated using quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), conventional nested RT-PCR and sequence analysis of amplification products. In 33 animals, HEV RNA was detected in liver and/or faeces. In one individual, viral RNA was detected in muscle tissue. Sequence analysis of a partial open reading frame 1 region demonstrated a broad variety of genotype 3 (HEV-3) subtypes. In conclusion, the study demonstrates a high, but varying prevalence of HEV RNA in swine populations in Mecklenburg-Western Pomerania. The associated risk of foodborne HEV infection needs the establishment of sustainable surveillance and treatment strategies at the interface between humans, animals, and the environment within a One Health framework.

Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design

BACKGROUND

As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive.

OBJECTIVE

To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently.

METHODS

A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5'-/3'-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignments identified conserved sequences and specific primer sets were designed against these regions using a conventional tool. Primer sets chosen among the candidates were evaluated by in silico PCR and RT-qPCR.

RESULTS

Out of 17 conserved sequences (totaling 4.3 kb), two primer sets targeting the nsp2 and ORF3a genes were picked that exhibited > 99.9% in silico amplification coverage against the original dataset (230,163 genomes) when a 5% mismatch between the primers and target was allowed. In addition, the primer sets successfully detected nine SARS-CoV-2 variant RNA samples (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Iota, and Kappa) in experimental RT-qPCR validations.

CONCLUSION

In addition to the RdRp, E, N, and S genes that are targeted commonly, our approach can be used to identify novel primer targets in SARS-CoV-2 and should be a priority strategy in the event of novel SARS-CoV-2 variants or other pandemic outbreaks.

Developments in Algorithms for Sequence Alignment: A Review

The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately. A number of algorithms and tools for sequence alignment have been designed to meet the various needs of biologists. Here, the ideas that prevail in the research of sequence alignment and some quality estimation methods for multiple sequence alignment tools are summarized.

Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019. The highly contagious B.1.617.2 (Delta) variant of concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the US. Understanding the local transmission dynamics of early SARS-CoV-2 introductions may inform actionable mitigation efforts during subsequent pandemic waves. Yet, despite considerable genomic analysis of SARS-CoV-2 in the US, several gaps remain. Here, we explore the early emergence of the Delta variant in Florida, US using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions led to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses.

A survey on the algorithm and development of multiple sequence alignment

Multiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as phylogenetic analysis, protein analysis and genomic analysis. However, MSA faces new challenges with the gradual increase in sequence scale and the increasing demand for alignment accuracy. Therefore, developing an efficient and accurate strategy for MSA has become one of the research hotspots in bioinformatics. In this work, we mainly summarize the algorithms for MSA and its applications in bioinformatics. To provide a structured and clear perspective, we systematically introduce MSA's knowledge, including background, database, metric and benchmark. Besides, we list the most common applications of MSA in the field of bioinformatics, including database searching, phylogenetic analysis, genomic analysis, metagenomic analysis and protein analysis. Furthermore, we categorize and analyze classical and state-of-the-art algorithms, divided into progressive alignment, iterative algorithm, heuristics, machine learning and divide-and-conquer. Moreover, we also discuss the challenges and opportunities of MSA in bioinformatics. Our work provides a comprehensive survey of MSA applications and their relevant algorithms. It could bring valuable insights for researchers to contribute their knowledge to MSA and relevant studies.

CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants

The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.

SARS-CoV-2 Reverse Zoonoses to Pumas and Lions, South Africa

Reverse-zoonotic infections of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) from humans to wildlife species internationally raise concern over the emergence of new variants in animals. A better understanding of the transmission dynamics and pathogenesis in susceptible species will mitigate the risk to humans and wildlife occurring in Africa. Here we report infection of an exotic puma (July 2020) and three African lions (July 2021) in the same private zoo in Johannesburg, South Africa. One Health genomic surveillance identified transmission of a Delta variant from a zookeeper to the three lions, similar to those circulating in humans in South Africa. One lion developed pneumonia while the other cases had mild infection. Both the puma and lions remained positive for SARS-CoV-2 RNA for up to 7 weeks.

SARS-CoV-2 AY.4.2 variant circulating in Italy: Genomic preliminary insight

The appearance of emerging variants of SARS‐CoV‐2 carrying mutations into the spike protein has recently raised concern with respect to tracking their transmission and mitigating the impact in the evolving pandemic across countries. AY.4.2, a recently detected Delta variant sublineage, is considered a new variant under investigation (VUI) as it carries specific genetic signatures present in the spike protein, called Y145H and A222V. Here, using genomic epidemiology, we provide the first preliminary insight regarding the circulation of this emerging VUI in Italy.

Genomic epidemiology suggests that multiple independent introductions have occurred trough time likely‐mediated by European countries.

Virus migration generally followed patterns of national and international human mobility, illustrating how the easing of restriction measures might facilitate the spread of those emerging variants worldwide.

Our data reveal how crucial appear to be the implementation of a widespread genomic monitoring to detect variants previously not yet identified across the country.

Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the virus' genome are crucial to our understanding of the adaptation of SARS-CoV-2. Moreover, how the temporal dynamics of these mutations is influenced by control measures and non-pharmaceutical interventions (NPIs) is poorly understood. Using 1,058,020 SARS-CoV-2 from sequenced COVID-19 cases from 98 countries (totaling 714 country-month combinations), we perform a normalization by COVID-19 cases to calculate the relative frequency of SARS-CoV-2 mutations and explore their dynamics over time. We found 115 mutations estimated to be present in more than 3% of global COVID-19 cases and determined three types of mutation dynamics: high-frequency, medium-frequency, and low-frequency. Classification of mutations based on temporal dynamics enable us to examine viral adaptation and evaluate the effects of implemented control measures in virus evolution during the pandemic. We showed that medium-frequency mutations are characterized by high prevalence in specific regions and/or in constant competition with other mutations in several regions. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency.

A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity

An unprecedented amount of SARS-CoV-2 sequencing has been performed, however, novel bioinformatic tools to cope with and process these large datasets is needed. Here, we have devised a bioinformatic pipeline that inputs SARS-CoV-2 genome sequencing in FASTA/FASTQ format and outputs a single Variant Calling Format file that can be processed to obtain variant annotations and perform downstream population genetic testing. As proof of concept, we have analyzed over 229,000 SARS-CoV-2 viral sequences up until November 30, 2020. We have identified over 39,000 variants worldwide with increased polymorphisms, spanning the ORF3a gene as well as the 3' untranslated (UTR) regions, specifically in the conserved stem loop region of SARS-CoV-2 which is accumulating greater observed viral diversity relative to chance variation. Our analysis pipeline has also discovered the existence of SARS-CoV-2 hypermutation with low frequency (less than in 2% of genomes) likely arising through host immune responses and not due to sequencing errors. Among annotated non-sense variants with a population frequency over 1%, recurrent inactivation of the ORF8 gene was found. This was found to be present in the newly identified B.1.1.7 SARS-CoV-2 lineage that originated in the United Kingdom. Almost all VOC-containing genomes possess one stop codon in ORF8 gene (Q27∗), however, 13% of these genomes also contains another stop codon (K68∗), suggesting that ORF8 loss does not interfere with SARS-CoV-2 spread and may play a role in its increased virulence. We have developed this computational pipeline to assist researchers in the rapid analysis and characterization of SARS-CoV-2 variation.

Novel Mutation of SARS-CoV-2, Vietnam, July 2020

A cluster of severe acute respiratory syndrome coronavirus 2 infections in Danang, Vietnam, began July 25, 2020, and resulted in 551 confirmed cases and 35 deaths as of February 2021. We analyzed 26 sequences from this cluster and identified a novel shared mutation in nonstructural protein 9, suggesting a single introduction into Vietnam.

Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic

Since the identification of SARS-CoV-2, a large number of genomes have been sequenced with unprecedented speed around the world. This marks a unique opportunity to analyze virus spreading and evolution in a worldwide context. Currently, there is not a useful haplotype description to help to track important and globally scattered mutations. Also, differences in the number of sequenced genomes between countries and/or months make it difficult to identify the emergence of haplotypes in regions where few genomes are sequenced but a large number of cases are reported. We propose an approach based on the normalization by COVID-19 cases of relative frequencies of mutations using all the available data to identify major haplotypes. Furthermore, we can use a similar normalization approach to tracking the temporal and geographic distribution of haplotypes in the world. Using 171,461 genomes, we identify five major haplotypes or operational taxonomic units (OTUs) based on nine high-frequency mutations. OTU_3 characterized by mutations R203K and G204R is currently the most frequent haplotype circulating in four of the six continents analyzed (South America, North America, Europe, Asia, Africa, and Oceania). On the other hand, during almost all months analyzed, OTU_5 characterized by the mutation T85I in nsp2 is the most frequent in North America. Recently (since September), OTU_2 has been established as the most frequent in Europe. OTU_1, the ancestor haplotype, is near to extinction showed by its low number of isolations since May. Also, we analyzed whether age, gender, or patient status is more related to a specific OTU. We did not find OTU's preference for any age group, gender, or patient status. Finally, we discuss structural and functional hypotheses in the most frequently identified mutations, none of those mutations show a clear effect on the transmissibility or pathogenicity.