Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.We determined complete genome sequences of lineage 2 West Nile virus West Nile virus, microorganism and the infection resulting from it, which typically produces no symptoms or a flulike condition. The virus is a flavivirus and is related to a number of viruses that cause encephalitis. (WNV WNV West Nile Virus
WNV World Net Visions ) strains isolated from patients in South Africa South Africa, Afrikaans Suid-Afrika, officially Republic of South Africa, republic (2005 est. pop. 44,344,000), 471,442 sq mi (1,221,037 sq km), S Africa. who had mild or severe WNV infections. These strains had previously been shown to produce either highly or less neuroinvasive infection and induced genes similar to corresponding highly or less neuroinvasive lineage 1 strains in mice. Phylogenetic phy·lo·ge·net·ic
1. Of or relating to phylogeny or phylogenetics.
2. Relating to or based on evolutionary development or history. and amino acid amino acid (əmē`nō), any one of a class of simple organic compounds containing carbon, hydrogen, oxygen, nitrogen, and in certain cases sulfur. These compounds are the building blocks of proteins. comparison of highly and less neuroinvasive lineage 2 strains demonstrated that the nonstructural genes, especially the nonstructural protein 5 gene, were most variable. All South African lineage 2 strains possessed the envelope-protein glycosylation site previously postulated to be associated with virulence. Major deletions existed in the 3' noncoding region of 2 lineage 2 strains previously shown to be either less or not neuroinvasive relative to the highly neuroinvasive strains sequenced in this study.
West Nile virus (WNV) is endemic to Africa, Asia, Europe, and Australia and was introduced into the Western Hemisphere Western Hemisphere
Part of Earth comprising North and South America and the surrounding waters. Longitudes 20° W and 160° E are often considered its boundaries. in 1999. In the Northern Hemisphere, an apparent increase in human case fatality rates case fatality rate
The proportion of individuals contracting a disease who die of that disease. , neurologic infections, and horse and bird deaths due to WNV has raised the question whether WNV strains with increased pathogenicity have emerged in the Northern Hemisphere, or whether the virulence of the virus and the severity of the disease are underestimated in South Africa.
Two major phylogenetic lineages of WNV have been demonstrated: lineage 1 includes viruses from North Africa, Europe, Asia, the Americas, and Australia (Kunjin virus Kunjin virus
a strain of West Nile virus, generally considered apathogenic but has been isolated from horses with encephalomyelitis. See also encephalitis. ); lineage 2 consists exclusively of viruses from southern Africa
Any of the more powerful accipiters (hawks in the genus Accipiter), primarily short-winged, forest-dwelling bird catchers. Best known is the northern goshawk, which reaches about 2 ft (60 cm) in length with a 4.3-ft (1. fledgling that died of encephalitis encephalitis (ĕnsĕf'əlī`təs), general term used to describe a diffuse inflammation of the brain and spinal cord, usually of viral origin, often transmitted by mosquitoes, in contrast to a bacterial infection of the meninges in Hungary, which suggests that lineage 2 strains may also be spread by migratory birds outside of Africa (5).
Lineage 1 viruses that have phenotypes of reduced virulence in mice and inefficient growth in culture have been identified in Mexico. Mutations leading to loss of envelope (E) protein glycosylation together with mutations in the nonstructural (NS) protein genes may be associated with attenuation Loss of signal power in a transmission.
The reduction in level of a transmitted quantity as a function of a parameter, usually distance. It is applied mainly to acoustic or electromagnetic waves and is expressed as the ratio of power densities. of these viruses (6). Comparisons between the prototype Uganda strain (B956) and a variant of this strain, which was obtained by molecular mutation (B956D117B3), showed changes in the E and NS genes, which resulted in reduced virulence in mice (7). These attenuations could not, however, be correlated with clinical disease in humans because these strain were either isolated from birds or modified in culture.
The NS4B protein may play an important role in virulence phenotype determination (6,8-10), predicted to be involved in viral replication Viral replication is the term used by virologists to describe the propagation of biological viruses during the infection process in the target host cells. When used in the strictest sense, the term refers specifically to the amplification of the viral genome and evasion of host innate immune defenses (8). Substitution of cysteine cysteine (sĭs`tēn), organic compound, one of the 20 amino acids commonly found in animal proteins. Only the l-stereoisomer participates in the biosynthesis of mammalian protein. at position 102 with serine serine (sĕr`ēn), organic compound, one of the 20 amino acids commonly found in animal proteins. Only the l-stereoisomer appears in mammalian protein. (Cys 102Ser) led to the formation of a temperature-sensitive phenotype at 41[degrees]C as well as attenuation of the neuroinvasive and neurovirulent phenotypes in mice (8). An adaptive mutation In mainstream biological thought it is held that while mutagenesis is non-random in many ways, the utility of a genetic mutation to the organism in which it occurs does not affect the rate at which it occurs. (E249G) in the NS4B gene resulted in reduced RNA RNA: see nucleic acid.
in full ribonucleic acid
One of the two main types of nucleic acid (the other being DNA), which functions in cellular protein synthesis in all living cells and replaces DNA as the carrier of genetic synthesis in host cells (9). An in vitro in vitro /in vi·tro/ (in ve´tro) [L.] within a glass; observable in a test tube; in an artificial environment.
In an artificial environment outside a living organism. study compared infectious clones of the NY99 strain, which is highly virulent in American crows, with a Kenya strain (KEN-3829), which is less virulent for American crows. After 72 days at 44[degrees]C, reduction in viral RNA production by the KEN-3829 strain was 6,500-fold, compared with the NY99 strain reduction of 17-fold. This finding suggested that efficient replication at high temperatures, as occurs in American crows, could be an important virulence factor Virulence factors are molecules produced by a pathogen that specifically influence their host's function to allow the pathogen to thrive. Factors that are used in general life processes, such as metabolism or bacterial cell structural components, may be vital to the pathogen's that determines the pathogenic phenotype of the NY99 strain (10).
To further investigate the molecular determinants of virulence of lineage 2 WNV strains, we sequenced the genomes of highly and less neuroinvasive lineage 2 strains that were isolated from patients in South Africa and that had previously been characterized with respect to gene expression and pathogenicity (4). These complete genome sequences of highly neuroinvasive lineage 2 WNV strains enable comprehensive comparison with highly and less neuroinvasive lineage 1 strains.
Materials and Methods
South African WNV isolates SPU SPU Seattle Pacific University
SPU Seattle Public Utilities
SPU Strategy and Policy Unit
SPU Sripatum University (Thailand)
SPU Split, Croatia (Airport Code)
SPU Synergistic Processor Unit 116/89, SA93/01, SA381/00, and H442 were obtained from the Special Pathogens Unit, National Institute for Communicable Diseases communicable diseases, illnesses caused by microorganisms and transmitted from an infected person or animal to another person or animal. Some diseases are passed on by direct or indirect contact with infected persons or with their excretions. , South Africa, as freeze-dried mouse brain passages 2-4. They were replicated by 1 passage in Vero cells for this study.
Viral RNA was extracted from cell culture supernatant supernatant /su·per·na·tant/ (-na´tant) the liquid lying above a layer of precipitated insoluble material.
the liquid lying above a layer of precipitated insoluble material. with the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany) according to according to
1. As stated or indicated by; on the authority of: according to historians.
2. In keeping with: according to instructions.
3. the manufacturer's instructions. For cDNA synthesis, 10 [micro]L of RNA and 0.4 [micro]g of random hexanucleotides (Roche Diagnostics Roche Diagnostics Division is a subsidiary of Hoffmann-La Roche which manufactures equipment and reagents for research and medical diagnostic applications. Internally, it is organized into six major business areas: Roche Applied Science, Roche Centralized Diagnostics, Roche , Mannheim, Germany) were incubated at 65[degrees]C for 10 min before cooling on ice. Then 1 x Expand Reverse Transcriptase Reverse transcriptase
Any of the deoxyribonucleic acid (DNA) polymerases present in particles of retroviruses which are able to carry out DNA synthesis using an RNA template. buffer, 100 mmol/L dithiothreitol, 200 [micro]mol of each deoxynucleotide triphosphate triphosphate /tri·phos·phate/ (tri-fos´fat) a salt containing three phosphate radicals.
A salt or ester containing three phosphate groups. , 20 U RNase Inhibitor and 50 U Expand Reverse Transcriptase (Roche Diagnostics) were added and incubated at 30[degrees]C for 10 min, followed by 1 h at 43[degrees]C. For PCR PCR polymerase chain reaction.
polymerase chain reaction
Polymerase chain reaction (PCR) amplification, 10 [micro]L of the cDNA reaction was added to the PCR master mix consisting of 3.75 U of Expand High Fidelity high fidelity
The electronic reproduction of sound, especially from broadcast or recorded sources, with minimal distortion.
high Polymerase and 30 pmol of each specific primer (primer sequences available on request) and cycled as follows: 94[degrees]C for 2 min (94[degrees]C for 15 s, followed by primer-specific annealing annealing (ənēl`ĭng), process in which glass, metals, and other materials are treated to render them less brittle and more workable. temperature for 30 s, 72[degrees]C for 2 min) x 35 and 72[degrees]C for 7 min. Expand Long Template PCR Polymerase (Roche Diagnostics) was used for products >2 kb with 300 [micro]mol of each dNTP, 1 x buffer, and 30 pmol of each specific primer and cycled at 94[degrees]C for 2 min (94[degrees]C for 10 s, 50[degrees]C for 30 s, 68[degrees]C for 3 min) x 10; followed by 30 cycles of 94[degrees]C for 15 s, 50[degrees]C for 30 s, 68[degrees]C for 5 min plus 5 s per cycle, and 72[degrees]C for 7 min.
DNA Sequencing DNA sequencing
The determination of the sequence of nucleotides in a sample of DNA.
PCR products were purified with Wizard SV gel and PCR clean-up system (Promega, Southampton, UK). DNA DNA: see nucleic acid.
or deoxyribonucleic acid
One of two types of nucleic acid (the other is RNA); a complex organic compound found in all living cells and many viruses. It is the chemical substance of genes. cycle sequencing was performed with the BigDye Terminator V3.1 kit and analyzed on an ABI Abi (ā`bī) [short for Abijah], in the Bible, King Hezekiah's mother.
(Application Binary Interface) A specification for a specific hardware platform combined with the operating system. PRISM 3100/3130 genetic analyzer (both from Applied Biosystems Applied Biosystems, Inc. (formerly NASDAQ: ABIO) is the original name of a pioneer biotechnology company founded in 1981 in Foster City, California, among the Silicon Valley cities of the southern San Francisco Bay Area. , Foster City, CA, USA).
Genome editing and assembling were performed by using Vector NTI NTI NewTech Infosystems (software company, Irvine, California)
NTI Nuclear Threat Initiative
NTI National Transit Institute (New Brunswick, New Jersey)
NTI Nunavut Tunngavik Incorporated 9.1.0 (Invitrogen, Carlsbad, CA, USA); multiple sequence alignments, with ClustalW (11); and amino acid analysis, with GeneDoc for Windows (12). Amino acid changes considered to have a potential effect on the secondary structure of the proteins included substitution of hydrophilic hydrophilic /hy·dro·phil·ic/ (-fil´ik) readily absorbing moisture; hygroscopic; having strongly polar groups that readily interact with water.
adj. for hydrophobic hydrophobic /hy·dro·pho·bic/ (-fo´bik)
1. pertaining to hydrophobia (rabies).
2. not readily absorbing water, or being adversely affected by water.
3. amino acids or vice versa VICE VERSA. On the contrary; on opposite sides. and substitutions of cysteine, glycine glycine (glī`sēn), organic compound, one of the 20 amino acids commonly found in animal proteins. Glycine is the only one of these amino acids that is not optically active, i.e. , and proline proline (prō`lēn), organic compound, one of the 20 amino acids commonly found in animal proteins. Only the l-stereoisomer appears in mammalian protein. residues (12).
Comparisons are relative to the top sequence (SA381/00); numbering refers to the sequence position of isolate SA381/00. Neighbor-joining trees were drawn with MEGA version 3.1 (13) by using the Kimura-2 distance-parameter and a bootstrap See boot.
(operating system, compiler) bootstrap - To load and initialise the operating system on a computer. Normally abbreviated to "boot". From the curious expression "to pull oneself up by one's bootstraps", one of the legendary feats of Baron von Munchhausen. confidence level of a 1,000 replicates. Nucleotide and amino acid p-distances (the number of pairwise nucleotide or amino acid differences divided by the total number of nucleotides or amino acids in the sequenced region) were calculated by using MEGA version 3.1. Signalase cleavage predicted scores were calculated with AnalyzeSignalase 2.03 (14).
Four lineage 2 WNV strains isolated from patients in South Africa who had mild or severe WNV infections were selected for genome sequencing. Phenotypic pathogenicity data for these strains (H442, SPU116/89, SA93/01, SA381/00) in humans and mice are summarized in Table 1. Detailed clinical data for all 4 strains have been described by Burt et al. (3), and mouse neuroinvasive experiments and gene expression data for H442, SPU 116/89, and SA381/00 have been described by Venter venter /ven·ter/ (ven´ter) pl. ven´tres [L.]
1. a fleshy contractile part of a muscle.
3. a hollowed part or cavity.
n. et al. (4). Strain SA93/01 has been shown to be highly neuroinvasive in a mouse model (M. Venter, unpub, data), similar to SPUl16/89 and H442 strains, whereas SA381/00 has been classified as being of low neuroinvasive phenotype in mice. H442 and SA381/00 caused fever, rash, myalgia myalgia /my·al·gia/ (mi-al´jah) muscular pain.myal´gic
epidemic myalgia see under pleurodynia.
n. , and arthralgia arthralgia /ar·thral·gia/ (ahr-thral´jah) pain in a joint.
Severe pain in a joint. Also called arthrodynia. in human patients; SA93/01 caused nonfatal encephalitis in 2, and SA116/89 caused fatal hepatitis (3).
The 4 South African strains were compared with strains that were known to be highly or less neuroinvasive in mice or that had been reported to be highly pathogenic or attenuated Attenuated
Alive but weakened; an attenuated microorganism can no longer produce disease.
Mentioned in: Tuberculin Skin Test
having undergone a process of attenuation. . Lineage 2 strains for which both full genome sequences and neuronvirulence data in mice were available included isolate B956D117B3 (21) and Madagascar strain AnMg798. B956Dl17B3 is a passaged clone of reduced virulence (7) of the prototype strain (B956), which was originally associated with fever in a patient and was neurotropic neurotropic
pertaining to or emanating from neurotrophy, e.g. neurotropic osteopathy. in mice (22); AnMg798 is not neuroinvasive (2). Lineage 1 strains included the highly pathogenic and neuroinvasive NY385-99 strain (2), the attenuated non-neuroinvasive strain TM 171-03 isolated in Mexico in 2003 (19), hamster-passaged attenuated clones of NY-385-99 (clone TYP-9376 and clone 9317B) (18), and a non-neuroinvasive Kunjin virus strain MRM MRM Marketing Resource Management
MRM Mobile Resource Management
MRM Metabolic Response Modifiers
MRM Multiple Reaction Monitoring (mass spectrometry)
MRM Mormonism Research Ministry
MRM Mechanically Recovered Meat 61C (Table 1).
Phylogenetic analysis confirmed that the South African strains described here belong within lineage 2 (Figure 1). SA93/01 and SPU116/89 clustered together; H442 and SA381/00 were on separate branches within lineage 2 with respect to the full genome sequences or with respect to individual E, NS3, and NS5 genes (data not shown). Although the Indian strain clustered with lineage 1, p-distance analysis suggested that it was as distant to the lineage 1 strains (20% differences) as to the lineage 2 strains (21%-22%) relative to <5% differences within lineage 1C and 12% differences between 1A and 1B. It was therefore termed lineage 5, as suggested by Bondre et al. (23).
Genome Sequences and Distance Analysis
The complete genome sequences of strains H442, SPU116/89, SA381/00, and SA93/01 were deposited in GenBank (accession nos. EF429197-200). The termini were amplified with primers designed from other lineage 2 full genome sequences. If one assumes that the 5' and 3' termini are identical in length to other published strains, these genomes were 11052 nt (SPU116/89, SA381/00, and SA93/01) and 11051 nt (H442) long. South African strains had overall nucleotide p-distances of 0.0278 (97.2% similarity) to each other (Table 2), with <1% amino acid differences over the complete genome despite having been isolated as many as 50 years apart. The highest percentage of amino acid differences in the individual proteins of the lineage 2 strains were in the NS proteins, especially the NS5 protein. Table 3 shows the differences between individual proteins of the South African lineage 2 strains.
[FIGURE 1 OMITTED]
The 2 strains from North America North America, third largest continent (1990 est. pop. 365,000,000), c.9,400,000 sq mi (24,346,000 sq km), the northern of the two continents of the Western Hemisphere. , New York New York, state, United States
New York, Middle Atlantic state of the United States. It is bordered by Vermont, Massachusetts, Connecticut, and the Atlantic Ocean (E), New Jersey and Pennsylvania (S), Lakes Erie and Ontario and the Canadian province of (NY385-99) and Mexico (TM171-03), were similarly conserved. In contrast, the Madagascar strain, AnMg798, differed by >3% at the amino acid level from all lineage 2 strains from South Africa or Uganda B956D117B3, and the lineage 1 and 2 strains differed by >6% amino acids from each other.
Amino Acid Differences between Highly and Less Neuroinvasive Strains
Few amino acid differences were observed between the structural proteins of the South African strains (Figure 2). SA381/00 had only 1 difference in the premembrane (prM) protein at position 105 relative to the highly neuroinvasive strains (Alal05Val) (Figure 2). Two differences, (Ala54Gly and Thr70Pro) could result in structural changes in the E protein of H442, which was isolated 50 years earlier than strains SPU 116/89, SA93/01, and SA381/00. The attenuated lineage 2 strain B956D117B3 and the nonneuroinvasive Madagascar strain AnMg798 contained differences in the glycosylation site of the E protein relative to the South African strains (residues 154-157 deleted in B956Dl17B3, and Ser156Pro in AnMg798). Either of these changes would prevent glycosylation. Further substitutions of hydrophilic amino acids for proline and glycine residues with potentially structural implications were found in AnMg798 at positions 156, 199, and 230.
The NS3, NS4A/B A/B Airborne
A/B Afterburner (jet engines)
A/B Air Blast
A/B Air Bus
A/B Afterburning , and NS5 proteins were the most variable viral proteins. In strain SA381/00, the least virulent of the 4 strains, a hydrophobic amino acid in contrast to a hydrophilic amino acid (Ser160Ala) and Arg298Gly could alter the structure of the SA381/00 NS3 protein. In the highly pathogenic strain SPU 116/89, a hydrophobic-tohydrophilic mutation (Ala79Thr) in NS4B is found relative to the other strains. Other amino acid changes with potential structural implications were for strain B956D117B3 at positions 18 and 145 of the NS4A gene and 14 of the NS4B gene and for strain AnMg798 at positions 14 and 27 in the NS4B gene of (Figure 2).
The NS5 protein was the most variable. Several positions were identified where the South African strains associated with mild infections (SA381/00 and H442) and the 2 other lineage 2 strains (AnMg798,B956D117B3) associated with reduced virulence in mice had the same amino acid changes relative to strains that caused severe disease (SPU116/89 and SPU93/01). These included hydrophilic versus hydrophobic amino acids in position 614 and hydrophobic (mild) versus hydrophilic (pathogenic) in positions 625 and 626 of the NS5 protein. SPU116/89, isolated from a patient with necrotic hepatitis, was found to have amino acid changes that affect the hydrophobicity of the NS5 protein relative to all other strains in positions 197, 623, 635, 641, and 643.
Approximately 98.6% identity existed between the 5' noncoding regions of SA381/00 and the 3 remaining South African strains; the other strains were 100% conserved. For the 3' noncoding regions, the overall identity was 98.5% (99% between SPU381/00 and H442 and 98% between SPU 116/89 and SA381/00). Noteworthy nucleotide differences in the 3' noncoding regions were a 2-nt deletion at nt 10439 and nt 10440 in strain H442 and a 76-bp deletion in the 3' noncoding region from nt 10404 through nt 10479 in the attenuated strain B956D117B3, which was not present in the prototype strain (B956) or in any of the South African strains. Strain AnMg798 had deletions overlapping those of strain B956D117B3 at position 10411 to 10487 and from 10501 to 10512 and 10951 (Figure 2, panel B). The sequence of the AnMg798 strain is incomplete in GenBank and ended at position 10866 (16).
Envelope-Protein Glycosylation Motif
The E protein glycosylation motif previously identified in lineage 1 at positions 154-156 (NYS 1. Is not. See Nis. )(6) was present in all 4 South African strains. However, as a result of a proline substitution at position 156, the site was not predicted to be glycosylated in strain AnMg798. The glycosylation motif is deleted completely in strains B956 and B956D117B3 (Table 1).
Signalase prediction algorithms were used to analyze the signal peptidase peptidase /pep·ti·dase/ (pep´ti-das) any of a subclass of proteolytic enzymes that catalyze the hydrolysis of peptide linkages; it comprises the exopeptidases and endopeptidases.
n. cleavage sites (14); no differences were found in cleavage efficiency between the highly and less pathogenic strains (Table 4). The only meaningful difference was observed in the capsid capsid /cap·sid/ (kap´sid) the shell of protein that protects the nucleic acid of a virus; it is composed of structural units, or capsomers.
n. (C)-PrM cleavage region, as indicated by the Student t test probability calculated in Table 4, where the lineage 2 strains were predicted to be cleaved cleaved (klevd) split or separated, as by cutting. more efficiently than lineage 1 stains. Only slight differences were apparent in the PrM-E site; no differences were apparent in any other cleavage regions between lineage 1 and 2 strains.
Phylogenetic and p-distance analyses suggested that relationships between WNV strains were influenced by geographic rather than temporal factors (Figure 1, Tables 2, 3). Four South African strains isolated over 50 years differed from each other by an average of only 3% of nucleotides but from the AnMg798 (Madagascar) strain by 21%.
The WNV genome consists of a 5' noncoding region, a single open reading frame coding for 3 viral structural proteins (C, M, and E) and 7 NS proteins, and a 3' noncoding region. The E and membrane (M) proteins are associated with host range, tissue tropism Tissue Tropism
Tissue tropism is a term most often used in virology to define the cells and tissues of a host which support growth of a particular virus. Bacteria and other parasites may also be referred to as having a tissue tropism. , replication, assembly, and the stimulation of the B- and T-cell immune responses; replication functions are associated with the NS proteins, which may also modulate responses to viral infection viral infection,
n an infection by a pathogenic virus. A virus acts on the cell nucleus, taking over the genetic material within the nucleus and replicating itself. (6). The E protein is the viral hemagglutinin hemagglutinin /he·mag·glu·ti·nin/ (-gloo´ti-nin) an antibody that causes agglutination of erythrocytes.
cold hemagglutinin one which acts only at temperatures near 4° C. that mediates virus-host cell binding and elicits most of the virus neutralizing antibodies and serotype serotype /se·ro·type/ (ser´o-tip) the type of a microorganism determined by its constituent antigens; a taxonomic subdivision based thereon.
v. specificity of the virus (1, 24, 25).
In this study, differences between highly and less neuroinvasive lineage 2 stains were identified in the noncoding regions, which may potentially affect enzyme binding sites and replication efficiency (Figure 2, panel B). It has been postulated that the 3' stem loop structure may function as a translation suppressor sup·pres·sor
1. or sup·press·er One that suppresses: a suppressor of free speech.
2. A gene that suppresses the phenotypic expression of another gene, especially of a mutant gene. (26) and that nucleotide sequence variation in the 3' noncoding region of different dengue dengue
or breakbone fever or dandy fever
Infectious, disabling mosquito-borne fever. Other symptoms include extreme joint pain and stiffness, intense pain behind the eyes, a return of fever after brief pause, and a characteristic rash. strains may have evolved as a function of transmission or replication ability in different mosquito and nonhuman primate/human host cycles (27). A 76-bp deletion in the 3' noncoding region is present in strains B956Dl17B3 and AnMg798 relative to the South African strains. This deletion is not present in the original neurotropic mouse brain isolate of the B956 Uganda strain, which has recently been resequenced (7). Strain B956D117B3, a descendent of the original B952 isolate, has been shown to be less virulent than the original B956 strain. The absence of this deletion in all of the neuroinvasive lineage 2 strains isolated from clinical cases warrants further investigation of the role of the region in the pathogenicicty of WNV.
The genetic stability observed in the surface E and M proteins of lineage 2 strains suggests an absence of immune-driven selection. Only the H442 strain, isolated 50 years before the other strains, had 2 substitutions in the E gene with potential structural implications (Figure 2). The absence of a putative E protein glycosylation site at positions 154-156 of the E protein (NYS) has previously been associated with reduced virulence in mice (19). This glycosylation motif was present in all the South African strains, including the less neuroinvasive strain SA381/00. However, the prototype lineage 2 strain B956D117B3 and the non-neuroinvasive lineage 1 and 2 strains MRM61C and AnMg798 were not glycosylated. This finding further emphasizes that glycosylation of the E protein is not the only determining factor for virulence.
Most substitutions were found in the NS proteins, in particular NS3, NS4A/B, and NS5. The NS3 protein is part of the protease protease /pro·te·ase/ (pro´te-as) endopeptidase.
Any of various enzymes, including the proteinases and peptidases, that catalyze the hydrolytic breakdown of proteins. complex, which is important for cleavage of the polyprotein and may affect virulence; it has been suggested that less efficient cleavage results in delayed virus assembly and release, enabling the host immune system immune system
Cells, cell products, organs, and structures of the body involved in the detection and destruction of foreign invaders, such as bacteria, viruses, and cancer cells. Immunity is based on the system's ability to launch a defense against such invaders. to clear infection (28). The NS3 protein of the less neuroinvasive strain, SA381/00, manifested hydrophobic and hydrophilic changes, which could lead to structural changes that affect function and, by implication, virulence. The highly neuroinvasive strain SPU 116/89 had mutations that may alter the hydrophobicity of the NS4B protein (Ala79Thr) relative to the other strains and may have potential structural and functional implications for the viral replicase replicase /rep·li·case/ (rep´li-kas)
1. a polymerase synthesizing RNA from an RNA template.
2. more generically, any enzyme that replicates nucleic acids, i.e., a DNA or RNA polymerase. complex of which NS4B is a component (25).
[FIGURE 2 OMITTED]
Most amino acid differences occurred in the NS5 protein, which is associated with cytoplasmic cytoplasmic
pertaining to or included in cytoplasm.
include secretory inclusions (enzymes, acids, proteins, mucosubstances), nutritive inclusions (glycogen, lipids), pigment granules (melanin, lipofuscin, RNA replication because it contains an RNA-dependent RNA polymerase RNA polymerase
A polymerase that catalyzes the synthesis of RNA from a DNA or RNA template. , S-adenosylmethionine methyltransferase, and importin [beta]-binding motifs (28). Deletions in the NS5 protein abolish replication (29), which suggests that amino acid substitutions may effect replication efficiency and, hence, virulence. Temperature-sensitive strains with reduced virulence for mice, isolated in Texas, also contained mutations in the NS proteins (30). In addition, organ tropism tropism (trōp`ĭzəm), involuntary response of an organism, or part of an organism, involving orientation toward (positive tropism) or away from (negative tropism) one or more external stimuli. of strains has been associated with mutations in the NS5, NS2, and E proteins (18). The 2 lineage 2 strains that caused mild disease in patients (H442 and SA381/00) had several substitutions of hydrophobic to hydrophilic amino acids relative to the other 2 strains in the NS5 protein. SPU 116/89, isolated from a patient with necrotic hepatitis, had several amino acid changes that may affect its hydrophobicity and result in structural and functional changes that have implications for altered replication efficiency, tissue tropism, and pathogenicity.
Flavivirus polyproteins are cleaved either by a host signal peptidase or a viral-encoded serine protease In biochemistry, serine proteases or serine endopeptidases (newer name) are a class of peptidases (enzymes that cleave peptide bonds in proteins) that are characterised by the presence of a serine residue in the active site of the enzyme. consisting of the NS3 protease and the NS2B cofactor cofactor
An atom, organic molecule, or molecular group that is necessary for the catalytic activity (see catalysis) of many enzymes. A cofactor may be tightly bound to the protein portion of an enzyme and thus be an integral part of its functional structure, or it may (NS2BNS Noun 1. BNS - a bachelor's degree in naval science
Bachelor of Naval Science
bachelor's degree, baccalaureate - an academic degree conferred on someone who has successfully completed undergraduate studies 3) (29). Proteolytic pro·te·o·lyt·ic
Relating to, characterized by, or promoting proteolysis.
adj processing of the C-prM and NS4A/ B proteins occurs efficiently only after upstream cleavage of the signal sequence by cytoplasmic viral protease. Efficiency of signal peptidase cleavage at the [NH.sub.2] termini of prM and NS4 proteins is increased by coexpression of the viral NS2B-NS3 protease and the structural polyprotein region (31). Mutagenesis mutagenesis /mu·ta·gen·e·sis/ (mu?tah-jen´e-sis)
1. the production of change.
2. the induction of genetic mutation.
n. pl. analysis of the signal sequence of yellow fever virus yellow fever virus
An arbovirus of the genus Flavivirus that causes yellow fever and is transmitted by mosquitoes. prM protein indicated that mutations that enhance cleavage by the signal peptidase almost totally suppress production of infectious virions (31). Signal peptidase cleavage of prM protein results in the production of membrane-anchored forms of the C protein, which may be deleterious for replication if it functions poorly as a substrate for viral protease. The signal peptidase-mediated cleavage at the [NH.sub.2] terminus of prM protein does not occur efficiently, whereas cleavage at the [NH.sub.2] terminus of the E protein does. Inadequate prM protein production in turn affects production and lowers the secretion of prM-E heterodimers. When these constructs are used in vaccination studies, a lack of immunogenicity immunogenicity /im·mu·no·ge·nic·i·ty/ (-je-nis´it-e) the property enabling a substance to provoke an immune response, or the degree to which a substance possesses this property. is noted (32).
In the present study, all highly and less pathogenic lineage 2 strains as well as lineage 1 strains were predicted to be cleaved with the same efficiency. At the C-prM site, lineage 2 strains are cleaved slightly more efficiently than lineage 1 strains; at prM-E, the reverse is true. How these differences in cleavage efficiency affect pathogenicity is unclear and may warrant further investigation.
The high number of cases of neurologic infections in recent epidemics in the United States United States, officially United States of America, republic (2005 est. pop. 295,734,000), 3,539,227 sq mi (9,166,598 sq km), North America. The United States is the world's third largest country in population and the fourth largest country in area. may be attributed to the rapid distribution of a single highly neuroinvasive strain in a highly susceptible population. The comparatively low number of WNV fever or neurologic cases reported in South Africa, despite the wide distribution of the virus and the presence of neuroinvasive strains, may reflect inadequate surveillance and a lack of medical awareness of the disease potential of arboviruses arboviruses (ar´bōvī´rsz),
n. . Moreover, the importance of WNV in South Africa may be overshadowed by the presence and effect of other diseases such as HIV/AIDS HIV/AIDS Human Immunodeficiency Virus/Acquired Immune Deficiency Syndrome . Nevertheless, the epidemic potential and effect that WNV may have on a large population of immunocompromised immunocompromised /im·mu·no·com·pro·mised/ (-kom´pro-mizd) having the immune response attenuated by administration of immunosuppressive drugs, by irradiation, by malnutrition, or by certain disease processes (e.g., cancer). HIV-infected persons necessitates improved surveillance of arbovirus arbovirus
Any of a large group of viruses that develop in arthropods (chiefly mosquitoes and ticks). The name derives from “arthropod-borne virus.” The spheroidal virus particle is encased in a fatty membrane and contains RNA; it causes no apparent harm to the infections of persons in southern Africa.
In conclusion, these full genome sequences provide insight into the molecular factors that may differentiate pathogenic from mild lineage 2 WNV strains. Mutations in the NS proteins encoding viral replication and protein cleavage mechanisms are the most likely determinants of differences in pathogenicity.
We thank A.A. Grobbelaar for assisting with the RNA extractions.
The study was funded by the National Research Foundation, South Africa.
Ms Botha is pursuing a master of science degree in microbiology at the University of Pretoria. She is conducting research on the epidemiology and pathogenicity of lineage 2 WNV.
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Address for correspondence: Marietjie Venter, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria/NHLS Tswhane Academic Division, PO Box 2034, Pretoria, 0001 South Africa; email: email@example.com
Elizabeth M. Botha, * Wanda Markotter, * Mariaan Wolfaardt, * Janusz T. Paweska, ([dagger]) Robert Swanepoel, ([dagger]) Gustavio Palacios, ([double dagger double dagger
A reference mark () used in printing and writing. Also called diesis.
Noun 1. ]) Louis H. Nel, * and Marietjie Venter *
* University of Pretoria, Pretoria, South Africa; ([dagger]) National Institute for Communicable Diseases, Sandringham, South Africa; and ([double dagger]) Columbia University, New York, New York, USA
Table 1. Characteristics and origin of West Nile virus strains included in this investigation * Strain, year of isolation Passage Source Location SPU 116/89, Mouse 3 Human SA 1989 SA93/01, 2001 Mouse 1 Human SA SA381/00, 2000 Mouse 1 Human SA H442, 1958 Mouse 2 Human SA B956, 1937 Mouse 2 Human Uga B956D117B3, Unknown Human Uga ([double dagger]) 1937 Madagascar- Unknown Parrot Mad AnMg798, 1978 ([section]) NY 385-99, Vero 2 Human USA 1999 NY-385-99 Hamster Hamster USA Clone TYP-9376, 2005 NY-385-99 Hamster Hamster USA Clone 9317B, 2005 TIM171-03,2003 Vero 1 Common Mex raven MRM61C, 1960 NA Mosquito (#) Aus Strain, year of isolation Syndrome Outcome L SPU 116/89, Necrotic Died 2 1989 hepatitis SA93/01, 2001 Fever, rash, Survived 2 myalgia, encephalitis SA381/00, 2000 Fever, rash, Survived 2 myalgia, arthralgia H442, 1958 Fever, rash, Survived 2 myalgia, arthralgia B956, 1937 Febrile Survived 2 disease B956D117B3, Febrile Survived 2 ([double dagger]) disease 1937 Madagascar- NA Died 2 AnMg798, 1978 NY 385-99, Unknown Unknown 1 1999 NY-385-99 NA NA 1 Clone TYP-9376, 2005 NY-385-99 NA NA 1 Clone 9317B, 2005 TIM171-03,2003 Unknown Died 1 MRM61C, 1960 NA NA 1 Strain, year of isolation Neuro Glyco Ref SPU 116/89, High NYS This 1989 ([dagger]) study SA93/01, 2001 High NYS This ([dagger]) study SA381/00, 2000 Mild NYS This ([dagger]) study H442, 1958 High NYS This ([dagger]) study B956, 1937 Mild Deletion (7) of entire motif B956D117B3, Less Deletion (15) ([double dagger]) than of entire 1937 B956 motif Madagascar- None NYP (16) AnMg798, 1978 NY 385-99, High NYS (17) 1999 ([dagger]) NY-385-99 None NYS (18) Clone TYP-9376, ([paragraph]) ([dagger]) 2005 NY-385-99 None NYS (18) Clone 9317B, ([paragraph]) ([dagger]) 2005 TIM171-03,2003 None NYP (19) ([paragraph]) MRM61C, 1960 None NYF (20) Strain, year of isolation GenBank SPU 116/89, EF429197 1989 SA93/01, 2001 EF429198 SA381/00, 2000 EF429199 H442, 1958 EF429200 B956, 1937 AY532665 B956D117B3, M12294 ([double dagger]) 1937 Madagascar- DQ176636 AnMg798, 1978 NY 385-99, DQ211652 1999 NY-385-99 AY848697 Clone TYP-9376, 2005 NY-385-99 D066423 Clone 9317B, 2005 TIM171-03,2003 AY660002 MRM61C, 1960 D00246 * L, lineage; Neuro, neuroinvasiveness in mice; Glyco, glycosylation of envelope protein; Ref, reference no.; GenBank, GenBank accession no.; SA, South Africa; Uga, Uganda; Mad, Madagascar; NA, not applicable; USA, United States; Mex, Mexico; Aus, Australia. ([dagger]) Strains that are glycosylated in the envelope protein positions 154-156. ([double dagger]) A descendant of B956. ([section]) Coracopsis vasa. ([paragraph]) Attenuated laboratory strains. (#) Culex annulirostris. Table 2. Percentage of amino acid and nucleotide differences when comparing the entire genome of selected West Nile virus strains * Strain SA381/00 H442 SPU116/89 SA93/01 SA381/00 2.4 3.6 3.7 H442 0.7 2.7 3.0 SPU116/89 0.9 0.7 1.3 SA93/01 0.8 0.7 0.6 B956D117B3 1.0 0.8 1.0 0.9 B956 0.7 0.6 0.7 0.7 AnMg798 3.4 3.3 3.5 3.4 NY-385-99 6.0 5.9 6.1 6.1 NY-385-99 6.1 6.0 6.2 6.2 Clone TYP- 9376 NY-385-99 6.1 6.0 6.2 6.2 Clone 9317B TM171-03 6.0 5.9 6.1 6.1 MRM61C 6.5 6.5 6.7 6.6 B956D1 Strain 17B3 B956 ANMg798 NY-385-99 SA381/00 3.1 2.9 15.8 20.6 H442 1.8 1.6 15.6 20.5 SPU116/89 2.0 1.9 16.0 20.8 SA93/01 2.3 2.2 15.7 20.8 B956D117B3 0.3 15.7 20.7 B956 0.7 15.8 20.7 AnMg798 3.5 3.4 21.5 NY-385-99 6.1 6.0 6.6 NY-385-99 6.2 6.1 6.7 0.1 Clone TYP- 9376 NY-385-99 6.2 6.1 6.7 0.1 Clone 9317B TM171-03 6.1 6.0 6.7 0.1 MRM61C 6.6 6.5 7.1 2.4 NY-385-99 NY-385-99 Clone Clone Strain TYP-9376 9317B TM171-03 MRM61C SA381/00 20.6 20.6 20.6 20.5 H442 20.6 20.6 20.5 20.6 SPU116/89 20.9 20.9 20.8 20.7 SA93/01 20.9 20.9 20.8 20.6 B956D117B3 20.7 20.7 20.7 20.6 B956 20.7 20.7 20.7 20.6 AnMg798 21.5 21.5 21.4 21.2 NY-385-99 0.1 0.1 0.4 11.7 NY-385-99 0.0 0.5 11.8 Clone TYP- 9376 NY-385-99 0.0 0.5 11.8 Clone 9317B TM171-03 0.2 0.2 11.8 MRM61C 2.4 2.4 2.4 * The lower left matrix corresponds to amino acid sequences, and the upper right matrix corresponds to nucleotide sequences. Table 3. Percentage amino acid and nucleotide differences when comparing individual proteins of selected West Nile virus strains * Strain SA381 /00 H442 SPU116/89 SA93/01 Capsid SA381/00 H442 0 SPU116/89 0 0 SA93/01 0 0 0 Envelope SA381/00 H442 0.8 SPU116/89 0.2 0.6 SA93/01 0.2 0.6 0 NS2A/B SA381/00 H442 0.6 SPU116/89 0.3 0.8 SA93/01 0.3 0.8 0 NS4A/B SA381/00 H442 0.2 SPU116/89 0.2 0.5 SA93/01 0 0.2 0.2 prM SA381/00 H442 0.6 SPU116/89 0.6 0 SA93/01 0.6 0 0 NS1 SA381/00 H442 0.9 SPU116/89 0.9 0 SA93/01 1.1 0.3 0.3 NS3 SA381/00 H442 0.8 SPU116/89 0.6 0.5 SA93/01 0.6 0.5 0 NS5 SA381/00 H442 0.8 SPU116/89 2.1 1.5 SA93/01 1.9 1.3 2.0 * prM, premembrane; NS, nonstructural. Table 4. Summary of cleavage scores predicted for cleavage junctions of proteins of West Nile virus strains * SA381/ SPU116/ 0 H442 89 SA93/01 Between capsid and premembrane proteins G +3.69 +3.69 +3.69 +3.69 A ([double dagger]) +9.37 +9.37 +9.37 +9.37 V -9.14 -9.14 -9.14 -9.14 Between premembrane and envelope proteins Y -10.15 -10.15 -10.15 -10.15 S ([double dagger]) +11.27 +11.27 +11.27 +11.27 F -5.37 -5.37 -5.37 -5.37 Between envelope protein and nonstructural protein 1 H -9.01 -9.01 -9.01 -9.01 A ([double dagger]) +4.26 +4.26 +4.26 +4.26 D -11.05 -11.05 -11.05 -11.05 Between nonstructural proteins 4B and 5 R -16.05 -16.05 -16.05 -16.05 G ([double dagger]) -13.19 -13.19 -13.19 -13.19 G -19.54 -19.54 -19.54 -19.54 NY-385-- 99 clone B956D1 AnMg79 NY-385-- TYP- 17B3 8 99 9376 Between capsid and premembrane proteins G +3.69 +4.00 -0.49 -0.49 A ([double dagger]) +9.37 +8.01 +5.93 +5.93 V -9.14 -7.8 -9.52 -9.52 Between premembrane and envelope proteins Y -10.15 -9.12 -9.12 -9.12 S ([double dagger]) +11.27 +12.42 +12.42 +12.42 F -5.37 -4.78 -4.78 -478 Between envelope protein and nonstructural protein 1 H -9.01 -9.71 -9.01 -9.01 A ([double dagger]) +4.26 +4.04 +4.26 +4.26 D -11.05 -11.15 -11.05 -11.05 Between nonstructural proteins 4B and 5 R -16.05 -16.05 -16.05 -16.05 G ([double dagger]) -13.19 -13.19 -13.19 -13.19 G -19.54 -19.54 -19.54 -19.54 NY-385-- 99 clone TM171 p value 9317B -03 MRM61C ([dagger]) Between capsid and premembrane proteins G -0.49 -0.49 -1.85 0.00005 A ([double dagger]) +5.93 +5.93 +7.37 0.00004 V -9.52 -9.52 -10.32 0.02235 Between premembrane and envelope proteins Y -9.12 -9.12 -9.45 0.00433 S ([double dagger]) +12.42 +12.42 +11.50 0.01728 F -4.78 -4.78 -5.27 0.01977 Between envelope protein and nonstructural protein 1 H -9.01 -9.01 -9.01 0.36322 A ([double dagger]) +4.26 +4.26 +4.26 0.36322 D -11.05 -11.05 -11.05 0.36322 Between nonstructural proteins 4B and 5 R -16.05 -15.83 -16.05 0.37390 G ([double dagger]) -13.19 -13.08 -13.19 0.37390 G -19.54 -19.66 -19.54 0.37390 * Signal cleavage predicted scores were calculated with AnalyzeSignalase 2.03 (14). The table indicates only the last amino acid of the first protein and the first 2 amino acids of the following protein. ([dagger]) Two-tailed Student t test results, indicating the probability of significance of observed differences between lineage 2 and lineage 1 strains. ([double dagger]) Exact cleavage site.