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The complete genomic sequence of an HTLV-II isolate from a Guahibo Indian from Venezuela.

A polyclonal CD3(+), CD8(+) T-cell line, G2, was derived from the peripheral blood of a seropositive, PCR-positive, HTLV-IIB infected Guahibo Indian from Venezuela. The cell line is productively infected with HTLV-IIB. The entire HTLV-II G2 proviral DNA was sequenced via PCR using overlapping HTLV-II primer pairs. Phylogenetic analyses indicate that HTLV-II G2 is the most divergent HTLV-IIB strain identified to date. Characterization of its deduced proteins and its relationship to other members of the PTLV/BLV genus of retroviruses are discussed.

Amino Acid Sequence↗

The complete genome sequence of PM2, the first lipid-containing bacterial virus To Be isolated.

Bacteriophage PM2 was isolated from the Pacific Ocean off the coast of Chile in the late 1960s. It was a new virus type, later classified as Corticoviridae, and also the first bacterial virus for which it was demonstrated that lipids are part of the virion structure. Here we report the determination and analysis of the 10, 079-bp circular dsDNA genome sequence. Noteworthy discoveries are the replication initiation system, which is related to the rolling circle mechanism described for phages such as φX174 and P2, and a 1.2-kb sequence that is similar to the maintenance region of a plasmid found in a marine Pseudoalteromonas sp. strain A28.

Amino Acid Sequence↗

The complete genomic sequence of a BLV strain from a Holstein cow from Argentina.

DNA was extracted from the peripheral blood of a seropositive, PCR-positive, BLV-infected Holstein cow (No. 38) from Argentina. The DNA was amplified via PCR with a series of overlapping primers encompassing the entire BLV proviral DNA. The amplified BLV ARG 38 DNA was cloned, sequenced, and compared phylogenetically to three other full-length BLV sequences. Characterization of its deduced proteins and its relationship to other members of the PTLV/BLV genus of retroviruses are discussed.

Amino Acid Sequence↗

Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T.

Lactococcus lactis phage BK5-T and Streptococcus thermophilus phage Sfi21, two cos-site temperate Siphoviridae with 40-kb genomes, share an identical genome organization, sequence similarity at the amino acid level over about half of their genomes, and nucleotide sequence identity of 60% over the DNA packaging and head morphogenesis modules. Siphoviridae with similarly organized genomes and substantial protein sequence similarity were identified in several genera of low-GC-content Gram-positive bacteria. These phages demonstrated a gradient of relatedness ranging from nucleotide sequence similarity to protein sequence similarity to gene map similarity over the DNA packaging and head morphogenesis modules. Interestingly, the degree of relatedness was correlated with the evolutionary distance separating their bacterial hosts. These observations suggest elements of vertical evolution in phages. The structural genes from BK5-T shared no sequence relationships with corresponding genes/proteins from lactococcal phages belonging to distinct lactococcal phage species, including phage sk1 (phage species 936) that showed a closely related gene map. Despite a clearly distinct genome organization, lactococcal phages sk1 and c2 showed nine sequence-related proteins. Over the early gene cluster phage BK5-T shared nine regions of high nucleotide sequence similarity, covering at most two adjacent genes, with lactococcal phage r1t (phage species P335). Over the structural genes, the closest relatives of phage r1t were not lactococcal phages belonging to other phage species, but Siphoviridae from Mycobacteria (high-GC-content Gram-positive bacteria). Evidence for recent horizontal gene transfer between distinct phage species was obtained for dairy phages, but these transfers were limited to phages infecting the same bacterial host species.

Computational Biology↗

Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector.

We recently developed a model for flavivirus infection in mice and hamsters using the Modoc virus (MODV), a flavivirus with no known vector (P. Leyssen, A. Van Lommel, C. Drosten, H. Schmitz, E. De Clercq, and J. Neyts, 2001, Virology 279, 27-37). We now present the coding and noncoding sequence of MODV. The Modoc virus genome was determined to be 10,600 nucleotides in length with a single open reading frame extending from nucleotides 110 to 10,234, encoding 3374 amino acids. The deduced gene order of the single open reading frame is C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5, which is exactly the same as that of the mosquito- and tick-borne flaviviruses. It is flanked by a 5'- and 3'-untranslated region (UTR) of 109 and 366 nucleotides, respectively. Alignment of the MODV amino acid sequence with that of 20 other flaviviruses revealed several regions with high sequence similarity corresponding to functionally important domains (e.g., the serine protease/helicase/NTPase of NS3 and the methyltransferase/RNA-dependent RNA polymerase of NS5) and conserved sites for proteolytic cleavage by viral and cellular proteases. Phylogenetic analysis of the entire coding region confirmed the classification of MODV within the flaviviruses with no known vector, which is in agreement with previous findings based on partial NS5 sequences. A detailed comparative analysis of the putative folding patterns of the 5'- and 3'-UTR of MODV and of the tick- and mosquito-borne viruses was carried out. Structural elements in the 5'- and 3' UTR of MODV that are preserved among vector-borne flaviviruses were noted and so were structural elements distinguishing the MODV UTRs from mosquito-borne and tick-borne flaviviruses. Also the putative secondary structure of circularized MODV RNA is presented.

3' Untranslated Regions↗

The complete genome sequence, organization and affinities of carrot red leaf virus.

A sequence of 5723 nucleotides (GenBank accession number: AY695933) is reported for the RNA genome of an isolate of Carrot red leaf virus (CtRLV). The sequence is predicted to contain six large open reading frames and non coding sequences of 28 nucleotides at the 5' end, 110 nucleotides at the 3' end, and 215 nucleotides between the two main blocks of coding sequences. The 5' coding region encodes two polypeptides with calculated molecular masses (Mr) of 28.6 kDa (P0) and 68.2 kDa (P1) that overlap in different reading frames. Circumstantially, the third ORF in the 5' block is putatively translated by frameshift read-through to yield a polypeptide (P1 + P2) with a calculated Mr of 116.9 kDa. Frameshifting is predicted at a "shifty" sequence (GGGAAAC; nt 1523-1529) also found in most members of the genus Polerovirus. The C-terminal region of the 116.9 kDa polypeptide includes the consensus sequence for the viral RNA-directed RNA polymerase. The 3' block of coding sequence defines three putative polypeptides of: 23.0 kDa (P3), 21.3 kDa (P4, in a different reading frame) and 77.2 kDa (P3 + P5, by read-through of P3) respectively. From the genome structure of CtRLV, it is suggested that this virus belongs to the genus Polerovirus, rather than either the genus Luteovirus or the genus Enamovirus.

5' Flanking Region↗

Complete Genome Sequence of Atractylodes virus A, a Novel Carlavirus Infecting Atractylodes lancea.

Atractylodes lancea is an important medicinal crop, but viral diseases have become increasingly severe in recent years. Viruses in the genus Carlavirus are common plant pathogens that are primarily transmitted by aphids and can cause stunted growth and reduced yields in their host plants. In this study, a novel carlavirus, tentatively named Atractylodes virus A (AVA), was identified from A. lancea plants exhibiting virus-like symptoms. The full-length genome of AVA is 8,817 nt in length and contains six open reading frames, displaying the typical genomic organization of the genus Carlavirus. The replicase and CP exhibit 53.43% and 56.72% amino acid identity, respectively, with those of previously characterized carlaviruses, indicating that AVA represents a novel species in the genus Carlavirus. This study expands our understanding of viral diversity in A. lancea and provides a scientific foundation for the prevention and control of viral diseases as well as for resistance breeding.

Genome, Viral↗

Insights in metabolism and toxin production from the complete genome sequence of Clostridium tetani.

The decryption of prokaryotic genome sequences progresses rapidly and provides the scientific community with an enormous amount of information. Clostridial genome sequencing projects have been finished only recently, starting with the genome of the solvent-producing Clostridium acetobutylicum in 2001. A lot of attention has been devoted to the genomes of pathogenic clostridia. In 2002, the genome sequence of C. perfringens, the causative agent of gas gangrene, has been released. Currently in the finishing stage and prior to publication are the genomes of the foodborne botulism-causing C. botulinum and of C. difficile, the causative agent of a wide spectrum of clinical manifestations such as antibiotic-associated diarrhea. Our team sequenced the genome of neuropathogenic C. tetani, a Gram-positive spore-forming bacterium predominantly found in the soil. In deep wound infections it occasionally causes spastic paralysis in humans and vertebrate animals, known as tetanus disease, by the secretion of potent neurotoxin, designated tetanus toxin. The toxin blocks the release of neurotransmitters from presynaptic membranes of interneurons of the spinal cord and the brainstem, thus preventing muscle relaxation. Fortunately, this disease is successfully controlled through immunization with tetanus toxoid, a formaldehyde-treated tetanus toxin, but nevertheless, an estimated 400,000 cases still occur each year, mainly of neonatal tetanus. The World Health Organization has stated that neonatal tetanus is the second leading cause of death from vaccine preventable diseases among children worldwide. This minireview focuses on an analysis of the genome sequence of C. tetani E88, a vaccine production strain, which is a toxigenic non-sporulating variant of strain Massachusetts. The genome consists of a 2,799,250 bp chromosome encoding 2618 open reading frames. The tetanus toxin is encoded on a 74,082 kb plasmid, containing 61 genes. Additional virulence-related factors as well as an insight into the metabolic strategy of C. tetani with regard to its pathogenic phenotype will be presented. The information from other clostridial genomes by means of comparative analysis will also be explored.

Journal Article↗

Complete genome sequence of an antibiotic-resistant and virulent Escherichia marmotae isolate recovered from a urinary tract infection.

OBJECTIVES: We aimed at analyzing the whole genome of the antibiotic-resistant Escherichia marmotae isolate 23-MO01035-0, which was obtained from a urinary tract infection of a male patient in Germany. The study focused on the characterization of mobile genetic elements and genetic factors that contribute to antibiotic resistance and pathogenicity. METHODS: Phenotypic antimicrobial susceptibility testing was performed and genomic DNA was sequenced using Illumina NextSeq (2 × 151 bp) and a MinION Mk1C device followed by de novo hybrid assembly using Unicycler v0.4.8. Resistance genes, virulence factors, plasmids, and mobile elements were identified with the bakcharak pipeline and PathogenFinder. RESULTS: The isolate belonged to sequence type ST133 and the 5,041,084 bp whole genome, consisting of one chromosome and five plasmids with an average GC content of 50.4%, revealed resistance genes for various antibiotic classes on an IncFII plasmid that had not yet been described. The isolate was predicted to be a potential human pathogen due to the presence of multiple virulence genes. CONCLUSION: Here, we report one of the first detailed genomic characterization of an antibiotic-resistant and virulent E. marmotae isolate from Germany. Considering that this bacterium was isolated from the urinary tract and possibly belonged to the faecal microbiota of the patient at that time, E. marmotae might contribute to the spread of antibiotic resistance in humans. This underscores the importance of genomic surveillance of E. marmotae, which causes human infections, but may be misidentified as E. coli.

Escherichia marmotae↗

Complete genome sequence of bacteriophage T5.

The 121,752-bp genome sequence of bacteriophage T5 was determined; the linear, double-stranded DNA is nicked in one of the strands and has large direct terminal repeats of 10,139 bp (8.3%) at both ends. The genome structure is consistently arranged according to its lytic life cycle. Of the 168 potential open reading frames (ORFs), 61 were annotated; these annotated ORFs are mainly enzymes involved in phage DNA replication, repair, and nucleotide metabolism. At least five endonucleases that believed to help inducing nicks in T5 genomic DNA, and a DNA ligase gene was found to be split into two separate ORFs. Analysis of T5 early promoters suggests a probable motif AAA{3, 4 T}nTTGCTT{17, 18 n}TATAATA{12, 13 W}{10 R} for strong promoters that may strengthen the step modification of host RNA polymerase, and thus control transcription of phage DNA. The distinct protein domain profile and a mosaic genome structure suggest an origin from the common genetic pool.

Bacteriophages↗

Complete genome sequences of the two viral variants of the Graffi MuLV: phylogenetic relationship with other murine leukemia retroviruses.

A detailed phylogenetic analysis of two variants of the Graffi murine retrovirus, GV-1.2 and GV-1.4, showed that they are closely related to SRS 19-6 and Moloney MuLVs. Two stretches of sequence testify to the divergence between Graffi and SRS 19-6 MuLVs, one corresponding to a recombination event of Graffi MuLV with a xenotropic virus. Moloney MuLV was found more distant, particularly in the GAG region. Our study encompasses every class of MuLVs (ecotropic, amphotropic, xenotropic, polytropic) with some focus on exogenous ecotropic viruses and further adds to previous phylogenetic studies. Graffi, SRS 19-6, Moloney, Friend and Rauscher MuLVs form a cluster that appears to share a common ancestor with the Casitas-amphotropic and -ecotropic MuLVs but are more distant to the Akv-type and xenotropic MuLVs. The analysis also revealed that the ENV region of HEMV, the prototype of the MuLV ancestor, was closely related to the corresponding region of Cas-Br-E.

Base Sequence↗

Complete genome sequencing of dengue virus type 1 isolated in Buenos Aires, Argentina.

Dengue (DEN) constitutes a major viral arthropod-borne human illness. South America was last considered free of dengue two decades ago when a dramatic increase in the number of dengue fever and hemorrhagic dengue cases had been reported. Five viruses were isolated in Buenos Aires City from the 1999-2000 Paraguay outbreak. RT-PCRs obtained directly from plasma were cloned into pGemT vectors and sequences of the structural genes and NS1 were analyzed. Three viruses were full-length sequenced from RT-PCR obtained from cell-culture isolates. Excess of synonymous over non-synonymous mutations suggested that the structural proteins were under strong functional constraints while a weak purifying selection was operating in the whole polyprotein. Sequence diversity and selective pressures varied among patients but results were significantly above the procedure threshold. One sample showed small-plaque phenotype and impaired growth coupled to 3'untranslated region mutations. Phylogenetic analysis of full-length sequences split Buenos Aires isolates into two clusters within American DEN-1 genotype V: Clade I was phylogenetically linked to Brazilian samples and Clade II with samples from Paraguay and Northeastern Argentina. In Buenos Aires City, only dengue virus serotype 1 imported from Paraguay has been detected, though without evidence of local transmission.

3' Untranslated Regions↗

Complete genome sequence of an Ebola virus (Sudan species) responsible for a 2000 outbreak of human disease in Uganda.

The entire genomic RNA of the Gulu (Uganda 2000) strain of Ebola virus was sequenced and compared to the genomes of other filoviruses. This data represents the first comprehensive genetic analysis for a representative isolate of the Sudan species of Ebola virus. The genome organization of the Sudan species is nearly identical to that of the Zaire species, but the presence of a gene overlap (between GP and VP30 genes) and a longer trailer sequence distinguish it from that of the Reston species. As has been observed with other filoviruses, stemloop structures were predicted to form at the 5' end of Ebola Sudan mRNA molecules, and the genomic RNA termini showed a high degree of sequence complimentarity. Comparisons of the amino acid sequences of encoded gene products shows that there is a comparable level of identity or similarity between Ebola virus species, with Sudan and Zaire actually showing a slightly closer relationship to the Reston species than to one another. These comparisons also indicated that the VP24 is the most conserved Ebola virus protein (followed closely by the VP40 and L proteins), while the GP is the least conserved gene product. The most divergent regions were seen in the C-terminus of GP1 (mucin-like region) and within the C-terminal third of the nucleoprotein sequence.

5' Untranslated Regions↗