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1.
J Med Virol ; 95(6): e28848, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-20239679

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Quasispecies , Pandemics , Genome, Viral
2.
Front Cell Infect Microbiol ; 13: 1155938, 2023.
Article in English | MEDLINE | ID: covidwho-20234677

ABSTRACT

Background: The SARS-CoV-2 virus has caused unprecedented mortality since its emergence in late 2019. The continuous evolution of the viral genome through the concerted action of mutational forces has produced distinct variants that became dominant, challenging human immunity and vaccine development. Aim and methods: In this work, through an integrative genomic approach, we describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City. Results: Our results revealed differential levels of the evolutionary forces across the genome and specific mutational processes that have shaped the first two epidemiological waves of the pandemic in Mexico. Through phylogenetic analyses, we observed a genomic transition in the circulating SARS-CoV-2 genomes from several lineages prevalent in the first wave to a dominance of the B.1.1.519 variant (defined by T478K, P681H, and T732A mutations in the spike protein) in the second wave. Conclusion: This work contributes to a better understanding of the evolutionary dynamics and selective pressures that act at the genomic level, the prediction of more accurate variants of clinical significance, and a better comprehension of the molecular mechanisms driving the evolution of SARS-CoV-2 to improve vaccine and drug development.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , Pandemics , Mexico/epidemiology , Phylogeny , Genome, Viral , Mutation
3.
Viruses ; 15(5)2023 04 26.
Article in English | MEDLINE | ID: covidwho-20233711

ABSTRACT

The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Humans , SARS-CoV-2/genetics , Phylogeny , Pandemics , Genome, Viral , Spike Glycoprotein, Coronavirus/genetics
4.
Int J Mol Sci ; 24(10)2023 May 22.
Article in English | MEDLINE | ID: covidwho-20242323

ABSTRACT

Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/genetics , Mutation , Nucleotides , Genome, Viral
6.
Epidemiol Infect ; 149: e110, 2021 04 30.
Article in English | MEDLINE | ID: covidwho-2316878

ABSTRACT

The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.


Subject(s)
COVID-19/virology , Genome, Viral/physiology , Mutation , SARS-CoV-2/genetics , Animals , Coronavirus Nucleocapsid Proteins/genetics , Genome, Viral/genetics , Humans , Multigene Family , Phosphoproteins/genetics , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/genetics , Viral Regulatory and Accessory Proteins/genetics , Virulence/genetics
7.
Nucleic Acids Res ; 50(D1): D27-D38, 2022 01 07.
Article in English | MEDLINE | ID: covidwho-2312875

ABSTRACT

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.


Subject(s)
Databases, Factual , Animals , China , Computational Biology , Databases, Genetic , Databases, Pharmaceutical , Dogs , Epigenome , Genome, Human , Genome, Viral , Genomics , Humans , Methylation , Neoplasms/genetics , Neoplasms/pathology , Regeneration , SARS-CoV-2/genetics , Single-Cell Analysis , Software , Synthetic Biology
8.
Gigascience ; 122022 12 28.
Article in English | MEDLINE | ID: covidwho-2313424

ABSTRACT

BACKGROUND: Since the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus; most notably, the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade. RESULTS: In this article, we leverage the frequency chaos game representation (FCGR) and convolutional neural networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieved an $96.29\%$ overall accuracy, while a similar tool, Covidex, obtained a $77,12\%$ overall accuracy. As far as we know, our method is the first using deep learning and FCGR for intraspecies classification. Furthermore, by using some feature importance methods, CouGaR-g allows to identify k-mers that match SARS-CoV-2 marker variants. CONCLUSIONS: By combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on random forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants. AVAILABILITY: The trained models can be tested online providing a FASTA file (with 1 or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.


Subject(s)
COVID-19 , Deep Learning , Puma , Animals , SARS-CoV-2/genetics , Puma/genetics , Genome, Viral
9.
Mol Biol Evol ; 40(4)2023 04 04.
Article in English | MEDLINE | ID: covidwho-2292366

ABSTRACT

SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.


Subject(s)
COVID-19 , Severe acute respiratory syndrome-related coronavirus , Animals , Humans , SARS-CoV-2 , Mutation , Mutation Rate , Genome, Viral
10.
J Gen Virol ; 104(4)2023 04.
Article in English | MEDLINE | ID: covidwho-2305800

ABSTRACT

The family Coronaviridae includes viruses with positive-sense RNA genomes of 22-36 kb that are expressed through a nested set of 3' co-terminal subgenomic mRNAs. Members of the subfamily Orthocoronavirinae are characterized by 80-160 nm diameter, enveloped virions with spike projections. The orthocoronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome-related coronavirus are extremely pathogenic for humans and in the last two decades have been responsible for the SARS and MERS epidemics. Another orthocoronavirus, severe acute respiratory syndrome coronavirus 2, was responsible for the recent global COVID-19 pandemic. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Coronaviridae which is available at www.ictv.global/report/coronaviridae.


Subject(s)
COVID-19 , Coronaviridae , Viruses , Humans , Coronaviridae/genetics , Pandemics , Viruses/genetics , Virion/genetics , Genome, Viral , Virus Replication
11.
Nat Commun ; 14(1): 2308, 2023 04 21.
Article in English | MEDLINE | ID: covidwho-2304491

ABSTRACT

Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (~30 kb). Here, we present a plasmid-based viral genome assembly and rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.


Subject(s)
COVID-19 , Coronavirus Nucleocapsid Proteins , SARS-CoV-2 , Animals , Coronavirus Nucleocapsid Proteins/genetics , Genome, Viral/genetics , RNA, Viral/genetics , SARS-CoV-2/genetics
12.
Methods Mol Biol ; 2621: 279-292, 2023.
Article in English | MEDLINE | ID: covidwho-2296486

ABSTRACT

In this chapter, next-generation sequencing of the entire viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is described. Successful sequencing of the SARS-CoV-2 virus is dependent upon quality of the specimen, adequate coverage of the entire genome, and up-to-date annotation. Some of the advantages of performing SARS-CoV-2 surveillance using next-generation sequencing are scalability, high-throughput, cost, and full genome analysis. Some of the disadvantages can be expensive instrumentation, large upfront reagent and supply costs, increased time-to-result, computational needs, and complicated bioinformatics. This chapter will provide an overview of a modified FDA Emergency Use Authorization procedure for the genomic sequencing of SARS-CoV-2. The procedure is also referred to as the research use only (RUO) version.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/genetics , Genome, Viral , High-Throughput Nucleotide Sequencing/methods , SARS-CoV-2/genetics
13.
mBio ; 14(3): e0025023, 2023 06 27.
Article in English | MEDLINE | ID: covidwho-2306588

ABSTRACT

Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.


Subject(s)
COVID-19 , RNA Viruses , Humans , RNA, Viral/genetics , Cohort Studies , COVID-19/genetics , SARS-CoV-2/genetics , Genome, Viral , RNA Viruses/genetics , Antiviral Agents
14.
Sci Rep ; 13(1): 6461, 2023 04 20.
Article in English | MEDLINE | ID: covidwho-2298135

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) pandemic has led to extensive virological monitoring by whole genome sequencing (WGS). Investigating the advantages and limitations of different protocols is key when conducting population-level WGS. SARS-CoV-2 positive samples with Ct values of 14-30 were run using three different protocols: the Twist Bioscience SARS­CoV­2 protocol with bait hybridization enrichment sequenced with Illumina, and two tiled amplicon enrichment protocols, ARTIC V3 and Midnight, sequenced with Illumina and Oxford Nanopore Technologies, respectively. Twist resulted in better coverage uniformity and coverage of the entire genome, but has several drawbacks: high human contamination, laborious workflow, high cost, and variation between batches. The ARTIC and Midnight protocol produced an even coverage across samples, and almost all reads were mapped to the SARS-CoV-2 reference. ARTIC and Midnight represent robust, cost-effective, and highly scalable methods that are appropriate in a clinical environment. Lineage designations were uniform across methods, representing the dominant lineages in Sweden during the period of collection. This study provides insights into methodological differences in SARS­CoV­2 sequencing and guidance in selecting suitable methods for various purposes.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Whole Genome Sequencing/methods , Sequence Analysis , Nucleic Acid Hybridization , Genome, Viral/genetics
15.
Braz J Biol ; 83: e247237, 2021.
Article in English | MEDLINE | ID: covidwho-2266085

ABSTRACT

Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.


Subject(s)
COVID-19 , Chiroptera , Animals , Computer Simulation , Genome, Viral/genetics , Humans , Phylogeny , SARS-CoV-2
16.
Nucleic Acids Res ; 49(22): 13019-13030, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-2285864

ABSTRACT

SARS-CoV-2 is a positive-sense RNA virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, which continues to cause significant morbidity, mortality and economic strain. SARS-CoV-2 can cause severe respiratory disease and death in humans, highlighting the need for effective antiviral therapies. The RNA synthesis machinery of SARS-CoV-2 is an ideal drug target and consists of non-structural protein 12 (nsp12), which is directly responsible for RNA synthesis, and numerous co-factors involved in RNA proofreading and 5' capping of viral RNAs. The formation of the 5' 7-methylguanosine (m7G) cap structure is known to require a guanylyltransferase (GTase) as well as a 5' triphosphatase and methyltransferases; however, the mechanism of SARS-CoV-2 RNA capping remains poorly understood. Here we find that SARS-CoV-2 nsp12 is involved in viral RNA capping as a GTase, carrying out the addition of a GTP nucleotide to the 5' end of viral RNA via a 5' to 5' triphosphate linkage. We further show that the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase) domain performs this reaction, and can be inhibited by remdesivir triphosphate, the active form of the antiviral drug remdesivir. These findings improve understanding of coronavirus RNA synthesis and highlight a new target for novel or repurposed antiviral drugs against SARS-CoV-2.


Subject(s)
Adenosine Triphosphate/analogs & derivatives , Antiviral Agents/pharmacology , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Nucleotidyltransferases/antagonists & inhibitors , RNA, Viral/biosynthesis , SARS-CoV-2/enzymology , Adenosine Triphosphate/pharmacology , Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors , Genome, Viral/genetics , Guanosine/analogs & derivatives , Guanosine/metabolism , Humans , Nucleotidyltransferases/metabolism , RNA Caps/genetics , SARS-CoV-2/genetics , Vaccinia virus/enzymology , Vaccinia virus/metabolism , COVID-19 Drug Treatment
17.
Front Cell Infect Microbiol ; 12: 966870, 2022.
Article in English | MEDLINE | ID: covidwho-2276215

ABSTRACT

The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 has resulted in enormous deaths around the world. Clues from genomic sequences of parent and their mutants can be obtained to understand the evolving pathogenesis of this virus. Apart from the viral proteins, virus-encoded microRNAs (miRNAs) have been shown to play a vital role in regulating viral pathogenesis. Thus we sought to investigate the miRNAs encoded by SARS-CoV-2, its mutants, and the host. Here, we present the results obtained using a dual approach i.e (i) identifying host-encoded miRNAs that might regulate viral pathogenesis and (ii) identifying viral-encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing the first approach resulted in the identification of ten host-encoded miRNAs that could target the SARS, SARS-CoV-2, and its mutants. Interestingly our analysis revealed that there is a significantly higher number of host miRNAs that could target the SARS-CoV-2 genome as compared to the SARS reference genome. Results from the second approach resulted in the identification of a set of virus-encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar "GA" rich motif in the SARS-CoV-2 and its mutant genomes that was shown to play a vital role in lung pathogenesis during severe SARS infections. In summary, we have identified human and virus-encoded miRNAs that might regulate the pathogenesis of SARS coronaviruses and describe similar non-coding RNA sequences in SARS-CoV-2 that were shown to regulate SARS-induced lung pathology in mice.


Subject(s)
Genome, Viral , MicroRNAs , SARS-CoV-2 , Animals , Humans , Mice , COVID-19 , MicroRNAs/genetics , Pandemics , SARS-CoV-2/genetics , Viral Proteins/genetics
18.
Virol J ; 20(1): 36, 2023 02 25.
Article in English | MEDLINE | ID: covidwho-2275795

ABSTRACT

BACKGROUND: Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS: Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS: We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION: The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.


Subject(s)
Alphacoronavirus , COVID-19 , Humans , SARS-CoV-2/genetics , COVID-19/genetics , Alphacoronavirus/genetics , 5' Untranslated Regions , Base Sequence , Genome, Viral
19.
Genes (Basel) ; 14(3)2023 03 09.
Article in English | MEDLINE | ID: covidwho-2275547

ABSTRACT

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/genetics , Whole Genome Sequencing/methods , Gene Library , Genome, Viral
20.
BMC Bioinformatics ; 24(1): 92, 2023 Mar 11.
Article in English | MEDLINE | ID: covidwho-2256663

ABSTRACT

BACKGROUND: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. RESULTS: In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. CONCLUSIONS: The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.


Subject(s)
COVID-19 , Deep Learning , Humans , COVID-19/genetics , Genome, Viral , Genomics , SARS-CoV-2/genetics
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