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1.
Nature ; 609(7929): 994-997, 2022 09.
Article in English | MEDLINE | ID: covidwho-1991628

ABSTRACT

Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses1-4. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral evolution5. Here, we use a new phylogenomic method to search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. In a 1.6 million sample tree from May 2021, we identify 589 recombination events, which indicate that around 2.7% of sequenced SARS-CoV-2 genomes have detectable recombinant ancestry. Recombination breakpoints are inferred to occur disproportionately in the 3' portion of the genome that contains the spike protein. Our results highlight the need for timely analyses of recombination for pinpointing the emergence of recombinant lineages with the potential to increase transmissibility or virulence of the virus. We anticipate that this approach will empower comprehensive real-time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.


Subject(s)
COVID-19 , Genome, Viral , Pandemics , Phylogeny , Recombination, Genetic , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , Genome, Viral/genetics , Humans , Mutation , Recombination, Genetic/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Selection, Genetic/genetics , Spike Glycoprotein, Coronavirus/genetics , Virulence/genetics
2.
Signal Transduct Target Ther ; 7(1): 138, 2022 04 26.
Article in English | MEDLINE | ID: covidwho-1815515

ABSTRACT

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, 18 core mutations of BA.1 (frequency >99%) and 27 core mutations of BA.2 (nine more than BA.1) were identified, of which 15 are specific to Omicron. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations in BA.1 than BA.2, and BA.1 is phylogenetically closer to Alpha than other variants. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1. Most notably, multiple characteristic amino acid mutations in the Delta spike protein have been also identified in the "Deltacron"-like Omicron Variants isolated since November 11, 2021 in South Africa, which implies the recombination events occurring between the Omicron and Delta variants. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.


Subject(s)
COVID-19 , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Amino Acids , COVID-19/virology , Genome, Viral/genetics , Humans , Mutation/genetics , Recombination, Genetic/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
4.
PLoS Genet ; 16(12): e1009272, 2020 12.
Article in English | MEDLINE | ID: covidwho-1388879

ABSTRACT

The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Recombination, Genetic/genetics , Spike Glycoprotein, Coronavirus/genetics , Crossing Over, Genetic/genetics , Genes, Viral/genetics , Genome, Viral/genetics , Host Specificity/genetics , Models, Genetic , Polymorphism, Genetic , SARS-CoV-2/classification , SARS-CoV-2/genetics , Viral Tropism/genetics
5.
Mol Ther ; 29(11): 3293-3304, 2021 11 03.
Article in English | MEDLINE | ID: covidwho-1253754

ABSTRACT

Nucleoside-modified messenger RNA (mRNA)-lipid nanoparticles (LNPs) are the basis for the first two EUA (Emergency Use Authorization) COVID-19 vaccines. The use of nucleoside-modified mRNA as a pharmacological agent opens immense opportunities for therapeutic, prophylactic and diagnostic molecular interventions. In particular, mRNA-based drugs may specifically modulate immune cells, such as T lymphocytes, for immunotherapy of oncologic, infectious and other conditions. The key challenge, however, is that T cells are notoriously resistant to transfection by exogenous mRNA. Here, we report that conjugating CD4 antibody to LNPs enables specific targeting and mRNA interventions to CD4+ cells, including T cells. After systemic injection in mice, CD4-targeted radiolabeled mRNA-LNPs accumulated in spleen, providing ∼30-fold higher signal of reporter mRNA in T cells isolated from spleen as compared with non-targeted mRNA-LNPs. Intravenous injection of CD4-targeted LNPs loaded with Cre recombinase-encoding mRNA provided specific dose-dependent loxP-mediated genetic recombination, resulting in reporter gene expression in about 60% and 40% of CD4+ T cells in spleen and lymph nodes, respectively. T cell phenotyping showed uniform transfection of T cell subpopulations, with no variability in uptake of CD4-targeted mRNA-LNPs in naive, central memory, and effector cells. The specific and efficient targeting and transfection of mRNA to T cells established in this study provides a platform technology for immunotherapy of devastating conditions and HIV cure.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , Lipids/genetics , Lipids/immunology , Nanoparticles/administration & dosage , RNA, Messenger/genetics , RNA, Messenger/immunology , Recombination, Genetic/genetics , Animals , COVID-19/immunology , COVID-19 Vaccines/immunology , Humans , Immunotherapy/methods , Lymph Nodes/immunology , Mice , Mice, Inbred C57BL , Recombination, Genetic/immunology , SARS-CoV-2/immunology , Spleen/immunology , Transfection/methods
6.
Cladistics ; 37(5): 461-488, 2021 10.
Article in English | MEDLINE | ID: covidwho-1201590

ABSTRACT

The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.


Subject(s)
Chiroptera/virology , Host-Pathogen Interactions/physiology , Middle East Respiratory Syndrome Coronavirus/physiology , Phylogeny , SARS Virus/physiology , SARS-CoV-2/physiology , Animals , Genome, Viral , Humans , Likelihood Functions , Pangolins/virology , Recombination, Genetic/genetics , Spike Glycoprotein, Coronavirus/metabolism
7.
J Med Virol ; 93(3): 1786-1791, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196491

ABSTRACT

Pangolin metagenomic data obtained from public databases were used to assemble partial or complete viral genomes showing genetic relationship to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sendai virus, flavivirus, picornavirus, parvovirus, and genomovirus, respectively. Most of these virus genomes showed genomic recombination signals. Phylogeny based on the SARS-CoV-2-related virus sequences assembled in this study and those recently published indicated that pangolin SARS-CoV-2-related viruses were clustered into two sub-lineages according to geographic sampling sites. These findings suggest the need for further pangolin samples, from different countries, to be collected and analyzed for coronavirus to elucidate whether pangolins are intermittent hosts for SARS-CoV-2.


Subject(s)
COVID-19/virology , Genome, Viral/genetics , Metagenome/genetics , Pangolins/virology , SARS-CoV-2/genetics , Animals , Host Specificity/genetics , Metagenomics/methods , Phylogeny , Recombination, Genetic/genetics
8.
Nat Commun ; 12(1): 780, 2021 02 16.
Article in English | MEDLINE | ID: covidwho-1087442

ABSTRACT

Novel pathogenic coronaviruses - such as SARS-CoV and probably SARS-CoV-2 - arise by homologous recombination between co-infecting viruses in a single cell. Identifying possible sources of novel coronaviruses therefore requires identifying hosts of multiple coronaviruses; however, most coronavirus-host interactions remain unknown. Here, by deploying a meta-ensemble of similarity learners from three complementary perspectives (viral, mammalian and network), we predict which mammals are hosts of multiple coronaviruses. We predict that there are 11.5-fold more coronavirus-host associations, over 30-fold more potential SARS-CoV-2 recombination hosts, and over 40-fold more host species with four or more different subgenera of coronaviruses than have been observed to date at >0.5 mean probability cut-off (2.4-, 4.25- and 9-fold, respectively, at >0.9821). Our results demonstrate the large underappreciation of the potential scale of novel coronavirus generation in wild and domesticated animals. We identify high-risk species for coronavirus surveillance.


Subject(s)
Coronavirus/physiology , Host-Pathogen Interactions , Mammals/virology , Animals , Coronavirus Infections/virology , Humans , Models, Biological , Phylogeny , Recombination, Genetic/genetics , Reproducibility of Results
9.
PLoS Biol ; 18(9): e3000827, 2020 09.
Article in English | MEDLINE | ID: covidwho-807960

ABSTRACT

Matrix proteins are encoded by many enveloped viruses, including influenza viruses, herpes viruses, and coronaviruses. Underneath the viral envelope of influenza virus, matrix protein 1 (M1) forms an oligomeric layer critical for particle stability and pH-dependent RNA genome release. However, high-resolution structures of full-length monomeric M1 and the matrix layer have not been available, impeding antiviral targeting and understanding of the pH-dependent transitions involved in cell entry. Here, purification and extensive mutagenesis revealed protein-protein interfaces required for the formation of multilayered helical M1 oligomers similar to those observed in virions exposed to the low pH of cell entry. However, single-layered helical oligomers with biochemical and ultrastructural similarity to those found in infectious virions before cell entry were observed upon mutation of a single amino acid. The highly ordered structure of the single-layered oligomers and their likeness to the matrix layer of intact virions prompted structural analysis by cryo-electron microscopy (cryo-EM). The resulting 3.4-Å-resolution structure revealed the molecular details of M1 folding and its organization within the single-shelled matrix. The solution of the full-length M1 structure, the identification of critical assembly interfaces, and the development of M1 assembly assays with purified proteins are crucial advances for antiviral targeting of influenza viruses.


Subject(s)
Imaging, Three-Dimensional , Viral Matrix Proteins/chemistry , Amino Acid Sequence , Cross-Linking Reagents/chemistry , Hydrogen-Ion Concentration , Models, Molecular , Mutation/genetics , Protein Multimerization , Protein Structure, Secondary , Protein Subunits/chemistry , Recombination, Genetic/genetics , Viral Matrix Proteins/genetics , Virion/ultrastructure
10.
Viruses ; 12(5)2020 05 14.
Article in English | MEDLINE | ID: covidwho-260386

ABSTRACT

Rousettus bat coronavirus GCCDC1 (RoBat-CoV GCCDC1) is a cross-family recombinant coronavirus that has previously only been reported in wild-caught bats in Yúnnan, China. We report the persistence of a related strain in a captive colony of lesser dawn bats captured in Singapore. Genomic evidence of the virus was detected using targeted enrichment sequencing, and further investigated using deeper, unbiased high throughput sequencing. RoBat-CoV GCCDC1 Singapore shared 96.52% similarity with RoBat-CoV GCCDC1 356 (NC_030886) at the nucleotide level, and had a high prevalence in the captive bat colony. It was detected at five out of six sampling time points across the course of 18 months. A partial segment 1 from an ancestral Pteropine orthoreovirus, p10, makes up the recombinant portion of the virus, which shares high similarity with previously reported RoBat-CoV GCCDC1 strains that were detected in Yúnnan, China. RoBat-CoV GCCDC1 is an intriguing, cross-family recombinant virus, with a geographical range that expands farther than was previously known. The discovery of RoBat-CoV GCCDC1 in Singapore indicates that this recombinant coronavirus exists in a broad geographical range, and can persist in bat colonies long-term.


Subject(s)
Betacoronavirus/isolation & purification , Chiroptera/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Animals , Betacoronavirus/genetics , Disease Reservoirs/virology , Genome, Viral/genetics , Geography , High-Throughput Nucleotide Sequencing , Phylogeny , Recombination, Genetic/genetics , Singapore/epidemiology
11.
Nature ; 579(7798): 265-269, 2020 03.
Article in English | MEDLINE | ID: covidwho-258

ABSTRACT

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1-3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here 'WH-Human 1' coronavirus (and has also been referred to as '2019-nCoV'). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.


Subject(s)
Betacoronavirus/classification , Communicable Diseases, Emerging/complications , Communicable Diseases, Emerging/virology , Coronavirus Infections/complications , Coronavirus Infections/virology , Pneumonia, Viral/complications , Pneumonia, Viral/virology , Severe Acute Respiratory Syndrome/etiology , Severe Acute Respiratory Syndrome/virology , Adult , Betacoronavirus/genetics , COVID-19 , China , Communicable Diseases, Emerging/diagnostic imaging , Communicable Diseases, Emerging/pathology , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/pathology , Genome, Viral/genetics , Humans , Lung/diagnostic imaging , Male , Phylogeny , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/pathology , RNA, Viral/genetics , Recombination, Genetic/genetics , SARS-CoV-2 , Severe Acute Respiratory Syndrome/diagnostic imaging , Severe Acute Respiratory Syndrome/pathology , Tomography, X-Ray Computed , Whole Genome Sequencing
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