scholarly journals Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2

2020 ◽  
Author(s):  
Yvonne CF Su ◽  
Danielle E Anderson ◽  
Barnaby E Young ◽  
Feng Zhu ◽  
Martin Linster ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Human Population ◽  
Host Adaptation ◽  
Open Reading Frame ◽  
N Gene ◽  
Regulatory Sequence ◽  
Reading Frame ◽  
Replicative Fitness ◽  
Similar Variation ◽  
Entire Open Reading Frame

To date, the SARS-CoV-2 genome has been considered genetically more stable than SARS-CoV or MERS-CoV. Here we report a 382-nt deletion covering almost the entire open reading frame 8 (ORF8) of SARS-CoV-2 obtained from eight hospitalized patients in Singapore. The deletion also removes the ORF8 transcription-regulatory sequence (TRS), which in turn enhances the downstream transcription of the N gene. We also found that viruses with the deletion have been circulating for at least four weeks. During the SARS-CoV outbreak in 2003, a number of genetic variants were observed in the human population [1], and similar variation has since been observed across SARS-related CoVs in humans and bats. Overwhelmingly these viruses had mutations or deletions in ORF8, that have been associated with reduced replicative fitness of the virus [2]. This is also consistent with the observation that towards the end of the outbreak sequences obtained from human SARS cases possessed an ORF8 deletion that may be associated with host adaptation [1]. We therefore hypothesise that the major deletion revealed in this study may lead to an attenuated phenotype of SARS-CoV-2.

scholarly journals SatR Is a Repressor of Fluoroquinolone Efflux Pump SatAB

2013 ◽  
Vol 57 (7) ◽  
pp. 3430-3433 ◽  
Author(s):  
Jose Antonio Escudero ◽  
Alvaro San Millan ◽  
Natalia Montero ◽  
Belen Gutierrez ◽  
Cristina Martinez Ovejero ◽  
...  
Keyword(s):  
Abc Transporter ◽  
High Mortality ◽  
Human Population ◽  
Efflux Pump ◽  
Streptococcus Suis ◽  
Open Reading Frame ◽  
Fluoroquinolone Resistance ◽  
Content Type ◽  
Reading Frame

ABSTRACTStreptococcus suisis an emerging zoonotic agent responsible for high-mortality outbreaks among the human population in China. In this species, the ABC transporter SatAB mediates fluoroquinolone resistance when overexpressed. Here, we describe and characterizesatR, an open reading frame (ORF) encoding a MarR superfamily regulator that acts as a repressor ofsatAB. satRis cotranscribed withsatAB, and its interruption entails the overexpression of the pump, leading to a clinically relevant increase in resistance to fluoroquinolones.

scholarly journals Regulation of an Osmoticum-Responsive Gene in Anabaena sp. Strain PCC 7120

1998 ◽  
Vol 180 (23) ◽  
pp. 6332-6337 ◽  
Author(s):  
Steven H. Schwartz ◽  
Todd A. Black ◽  
Karin Jäger ◽  
Jean-Michel Panoff ◽  
C. Peter Wolk
Keyword(s):  
Genomic Sequence ◽  
Response Regulator ◽  
Sequence Similarity ◽  
Open Reading Frame ◽  
Response Regulators ◽  
Reading Frame ◽  
Regulatory Systems ◽  
Entire Open Reading Frame ◽  
Anabaena Sp ◽  
Pcc 7120

ABSTRACT Salt-induced genes in the cyanobacterium Anabaena sp. strain PCC 7120 were identified by use of a Tn5-based transposon bearing luxAB as a reporter. The genomic sequence adjacent to one site of insertion of the transposon was identical in part to the sequence of thelti2 gene, which was previously identified in a differential screen for cold-induced transcripts in Anabaena variabilis. The lti2-like gene was induced by sucrose and other osmotica and by low temperature, in addition to salt. Regulatory components necessary for the induction of this gene by osmotica were sought by a further round of transposon mutagenesis. One mutant that displayed reduced transcriptional activity of thelti2-like gene in response to exposure to osmotica had an insertion in an open reading frame, which was denoted orrA, whose predicted product showed sequence similarity to response regulators from two-component regulatory systems. The corresponding mutation was reconstructed and was shown, like the second-site transposon mutation, to result in reduced response to osmotic stress. Induction of the lux reporter gene by osmotica was restored by complementation with a genomic fragment containing the entire open reading frame for the presumptive response regulator, whereas a fragment containing a truncated copy of the open reading frame for the response regulator did not complement the mutation.

scholarly journals Recombinant GRA4 or ROP2 Protein Combined with Alum or the gra4 Gene Provides Partial Protection in Chronic Murine Models of Toxoplasmosis

2004 ◽  
Vol 11 (4) ◽  
pp. 704-710 ◽  
Author(s):  
Valentina Martin ◽  
Alicia Supanitsky ◽  
Pablo C. Echeverria ◽  
Silvana Litwin ◽  
Tamara Tanos ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Open Reading Frame ◽  
Interleukin 4 ◽  
Murine Models ◽  
Protective Level ◽  
Partial Protection ◽  
Reading Frame ◽  
C3h Mice ◽  
Entire Open Reading Frame ◽  
Brain Cysts

ABSTRACT The efficacy of vaccination with Toxoplasma gondii recombinant GRA4 (rGRA4) and ROP2 (rRPO2) proteins and a mix of both combined with alum were evaluated in C57BL/6 and C3H mice. In C57BL/6 mice, rGRA4 and rGRA4-rROP2 immunizations generated similar levels of immunoglobulin G1 (IgG1) and IgG2a isotypes against GRA4, whereas immunizations with rROP2 and the mix induced a predominant IgG1 production against ROP2. All groups of C3H vaccinated mice exhibited higher levels of IgG1 than IgG2a. rGRA4-stimulated splenocytes from vaccinated mice produced primarily gamma interferon while those stimulated with rROP2 produced interleukin-4. Challenge of rGRA4- or rGRA4-rROP2-vaccinated mice from both strains with ME49 cysts resulted in fewer brain cysts than the controls, whereas vaccination with rROP2 alone only conferred protection to C3H mice. Immunization with a plasmid carrying the entire open reading frame of GRA4 showed a protective level similar to that of rGRA4 combined with alum. These results suggest that GRA4 can be a good candidate for a multiantigen anti-T. gondii vaccine based on the use of alum as an adjuvant.

scholarly journals Molecular Cloning, Sequencing, Expression, and Characterization of an Immunogenic 43-Kilodalton Lipoprotein of Bartonella bacilliformis That Has Homology to NlpD/LppB

2000 ◽  
Vol 68 (9) ◽  
pp. 4972-4979 ◽  
Author(s):  
Indira Padmalayam ◽  
Timothy Kelly ◽  
Barbara Baumstark ◽  
Robert Massung
Keyword(s):  
Bartonella Henselae ◽  
High Titer ◽  
Polyclonal Antiserum ◽  
Open Reading Frame ◽  
Bartonella Bacilliformis ◽  
Reading Frame ◽  
Dna Library ◽  
Bacillary Angiomatosis ◽  
Genomic Dna Library ◽  
Entire Open Reading Frame

ABSTRACT A recombinant clone expressing an immunoreactive antigen ofBartonella bacilliformis was isolated by screening a genomic DNA library with serum from a patient with the chronic verruga phase of bartonellosis. The clone, pBIPIM-17, contained a partial open reading frame that expressed an immunoreactive fusion protein. Subsequent rescreening of the library by plaque hybridization resulted in the isolation of recombinant clones that contain the entire open reading frame. The open reading frame (ORF-401) is capable of encoding a protein of 401 amino acids with a predicted molecular mass of 43 kDa. The deduced amino acid sequence of the encoded protein was found to be highly homologous to a recently identified bacterial lipoprotein (LppB/NlpD) which has been associated with virulence. Evidence has been provided to show that the 43-kDa antigen of B. bacilliformis is a lipoprotein and that it is likely to use the same biosynthetic pathway as other bacterial lipoproteins. This is the first report to date that characterizes a lipoprotein of B. bacilliformis. The immunogenicity of the B. bacilliformis LppB homologue was demonstrated by Western blot analysis using sera from patients with clinical bartonellosis. Sera from patients who had a high titer forBartonella henselae, the causative agent of bacillary angiomatosis and cat scratch disease, also recognized the recombinant 43-kDa antigen, suggesting that a homologue of this antigen is present in B. henselae. Using a cocktail of synthetic peptides corresponding to predicted major antigenic sites, polyclonal antiserum specific for the LppB homologue of B. bacilliformis was generated. This antiserum did not recognize the NlpD homologue of Escherichia coli or the 43-kDa antigen ofB. henselae.

Single nucleotide polymorphisms in the open reading frame of the stearoyl-CoA desaturase gene and resulting genetic variants in Canadian Holstein and Jersey cows

DNA Sequence ◽  
2007 ◽  
Vol 18 (5) ◽  
pp. 357-362 ◽  
Author(s):  
Patrick M. Kgwatalala ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
Patrick M. Kgwatalala ◽  
Eveline M. Ibeagha-Awemu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Variants ◽  
Open Reading Frame ◽  
Nucleotide Polymorphisms ◽  
Desaturase Gene ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Stearoyl Coa Desaturase ◽  
Jersey Cows

scholarly journals Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Yvonne C. F. Su ◽  
Danielle E. Anderson ◽  
Barnaby E. Young ◽  
Martin Linster ◽  
Feng Zhu ◽  
...  
Keyword(s):  
Hot Spot ◽  
Regulatory Sequence ◽  
Genetic Changes ◽  
Reading Frame ◽  
Replicative Fitness ◽  
Deletion Variant ◽  
Robust Immune Response ◽  
Genomic Characterization ◽  
Successful Control

ABSTRACT To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans. IMPORTANCE During the SARS epidemic in 2003/2004, a number of deletions were observed in ORF8 of SARS-CoV, and eventually deletion variants became predominant, leading to the hypothesis that ORF8 was an evolutionary hot spot for adaptation of SARS-CoV to humans. However, due to the successful control of the SARS epidemic, the importance of these deletions for the epidemiological fitness of SARS-CoV in humans could not be established. The emergence of multiple SARS-CoV-2 strains with ORF8 deletions, combined with evidence of a robust immune response to ORF8, suggests that the lack of ORF8 may assist with host immune evasion. In addition to providing a key insight into the evolutionary behavior of SARS-CoV-2 as the virus adapts to its new human hosts, the emergence of ORF8 deletion variants may also impact vaccination strategies.

scholarly journals Evidence for an Ancestral Association of Human Coronavirus 229E with Bats

2015 ◽  
Vol 89 (23) ◽  
pp. 11858-11870 ◽  
Author(s):  
Victor Max Corman ◽  
Heather J. Baldwin ◽  
Adriana Fumie Tateno ◽  
Rodrigo Melim Zerbinati ◽  
Augustina Annan ◽  
...  
Keyword(s):  
Small Sample ◽  
Open Reading Frame ◽  
Evolutionary Origin ◽  
Regulatory Sequence ◽  
Intermediate Hosts ◽  
Human Coronavirus ◽  
Reading Frame ◽  
Human Viruses ◽  
African Bats ◽  
Human Coronavirus 229E

ABSTRACTWe previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in theRNA-dependent RNA polymerase(RdRp) andspikegenes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3′ end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E.IMPORTANCEThe ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a large sample of African bats and characterizing several bat viruses on a full-genome level. Our evolutionary analyses show that animal and human viruses are genetically closely related, can exchange genetic material, and form a single viral species. We show that the putative host switches leading to the formation of HCoV-229E were accompanied by major genomic changes, including deletions in the viral spike glycoprotein gene and loss of an open reading frame. We reanalyze a previously described genetically related alpaca virus and discuss the role of camelids as potential intermediate hosts between bat and human viruses. The evolutionary history of HCoV-229E likely shares important characteristics with that of the recently emerged highly pathogenic Middle East respiratory syndrome (MERS) coronavirus.

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