A comparison of New World alphaviruses in the western equine encephalomyelitis complex by immunochemical and oligonucleotide fingerprint techniques

Identification of salivary gland escape barriers to western equine encephalitis virus in the natural vector, Culex tarsalis

Herein we describe a previously uninvestigated salivary gland escape barrier (SEB) in Culex tarsalis mosquitoes infected with two different strains of Western equine encephalitis virus (WEEV). The WEEV strains were originally isolated either from mosquitoes (IMP181) or a human patient (McMillan). Both IMP181 and McMillan viruses were fully able to infect the salivary glands of Culex tarsalis after intrathoracic injection as determined by expression of mCherry fluorescent protein. IMP181, however, was better adapted to transmission as measured by virus titer in saliva as well as transmission rates in infected mosquitoes. We used chimeric recombinant WEEV strains to show that inclusion of IMP181-derived structural genes partially circumvents the SEB.

Continued Evidence of Decline in the Enzootic Activity of Western Equine Encephalitis Virus in Colorado

Western equine encephalitis (WEE) was once prevalent and routinely isolated from mosquitoes in Colorado; however, isolations of Western equine encephalitis virus (WEEV) have not been reported from mosquito pools since the early 1990s. The objective of the present study was to test pools of Culex tarsalis (Coquillett) mosquitoes sampled from Weld County, CO, in 2016 for evidence of WEEV infection. Over 7,000 mosquitoes were tested, but none were positive for WEEV RNA. These data indicate that WEEV either was not circulating enzootically in Northern Colorado, was very rare, and would require much more extensive mosquito sampling to detect, or was heterogeneously distributed spatially and temporally and happened to not be present in the area sampled during 2016. Even though the reported incidence of WEE remains null, screening for WEEV viral RNA in mosquito vectors offers forewarning toward the detection and prevention of future outbreaks.

Complete genomic RNA sequence of western equine encephalitis virus and expression of the structural genes

The complete nucleotide sequence of the 71V-1658 strain of western equine encephalitis virus (WEE) was determined (minus 25 nucleotides from the 5' end). A 5' RACE reaction was used to sequence the 5' terminus from WEE strain CBA87. The deduced WEE genome was 11508 nucleotides in length, excluding the 5' cap nucleotide and 3' poly(A) tail. The nucleotide composition was 28% A, 25% C, 25% G and 22% U. Comparison with partial WEE sequences of strain 5614 (nsP2-nsP3 of the nonstructural region) and strain BFS1703 (26S structural region) revealed comparatively little variation; a total of 149 nucleotide differences in 8624 bases (1.7% divergence), of which only 28% (42 nucleotides) altered the encoded amino acids. Comparison of deduced nsP1 and nsP4 amino acid sequences from WEE with the corresponding proteins from eastern equine encephalitis virus (EEE) yielded identities of 84.9 and 83.8%, respectively. Previously uncharacterized stem-loop structures were identified in the nontranslated terminal regions. A cDNA clone of the 26S region encoding the structural polyprotein of WEE strain 71V-1658 was placed under the control of a cytomegalovirus promoter and transfected into tissue culture cells. The viral envelope proteins were functionally expressed in tissue culture, as determined by histochemical staining with monoclonal antibodies that recognize WEE antigens, thus, forming the initial step in the investigation of subunit vaccines to WEE.

Recombinational history and molecular evolution of western equine encephalomyelitis complex alphaviruses

Western equine encephalomyelitis (WEE) virus (Togaviridae: Alphavirus) was shown previously to have arisen by recombination between eastern equine encephalomyelitis (EEE)- and Sindbis-like viruses (C. S. Hahn, S. Lustig, E. G. Strauss, and J. H. Strauss, Proc. Natl. Acad. Sci. USA 85:5997-6001, 1988). We have now examined the recombinational history and evolution of all viruses belonging to the WEE antigenic complex, including the Buggy Creek, Fort Morgan, Highlands J, Sindbis, Babanki, Ockelbo, Kyzylagach, Whataroa, and Aura viruses, using nucleotide sequences derived from representative strains. Two regions of the genome were examined: sequences of 477 nucleotides from the C terminus of the E1 envelope glycoprotein gene which in WEE virus was derived from the Sindbis-like virus parent, and 517 nucleotide sequences at the C terminus of the nsP4 gene which in WEE virus was derived from the EEE-like virus parent. Trees based on the E1 region indicated that all members of the WEE virus complex comprise a monophyletic group. Most closely related to WEE viruses are other New World members of the complex: the Highlands J, Buggy Creek, and Fort Morgan viruses. More distantly related WEE complex viruses included the Old World Sindbis, Babanki, Ockelbo, Kyzylagach, and Whataroa viruses, as well as the New World Aura virus. Detailed analyses of 38 strains of WEE virus revealed at least 4 major lineages; two were represented by isolates from Argentina, one was from Brazil, and a fourth contained isolates from many locations in South and North America as well as Cuba. Trees based on the nsP4 gene indicated that all New World WEE complex viruses except Aura virus are recombinants derived from EEE- and Sindbis-like virus ancestors. In contrast, the Old World members of the WEE complex, as well as Aura virus, did not appear to have recombinant genomes. Using an evolutionary rate estimate (2.8 x 10(-4) substitutions per nucleotide per year) obtained from E1-3' sequences of WEE viruses, we estimated that the recombination event occurred in the New World 1,300 to 1,900 years ago. This suggests that the alphaviruses originated in the New World a few thousand years ago.

The alphaviruses: gene expression, replication, and evolution

The alphaviruses are a genus of 26 enveloped viruses that cause disease in humans and domestic animals. Mosquitoes or other hematophagous arthropods serve as vectors for these viruses. The complete sequences of the +/- 11.7-kb plus-strand RNA genomes of eight alphaviruses have been determined, and partial sequences are known for several others; this has made possible evolutionary comparisons between different alphaviruses as well as comparisons of this group of viruses with other animal and plant viruses. Full-length cDNA clones from which infectious RNA can be recovered have been constructed for four alphaviruses; these clones have facilitated many molecular genetic studies as well as the development of these viruses as expression vectors. From these and studies involving biochemical approaches, many details of the replication cycle of the alphaviruses are known. The interactions of the viruses with host cells and host organisms have been exclusively studied, and the molecular basis of virulence and recovery from viral infection have been addressed in a large number of recent papers. The structure of the viruses has been determined to about 2.5 nm, making them the best-characterized enveloped virus to date. Because of the wealth of data that has appeared, these viruses represent a well-characterized system that tell us much about the evolution of RNA viruses, their replication, and their interactions with their hosts. This review summarizes our current knowledge of this group of viruses.

Medically important arboviruses of the United States and Canada

Of more than 500 arboviruses recognized worldwide, 5 were first isolated in Canada and 58 were first isolated in the United States. Six of these viruses are human pathogens: western equine encephalitis (WEE) and eastern equine encephalitis (EEE) viruses (family Togaviridae, genus Alphavirus), St. Louis encephalitis (SLE) and Powassan (POW) viruses (Flaviviridae, Flavivirus), LaCrosse (LAC) virus (Bunyaviridae, Bunyavirus), and Colorado tick fever (CTF) virus (Reoviridae, Coltivirus). Their scientific histories, geographic distributions, virology, epidemiology, vectors, vertebrate hosts, transmission, pathogenesis, clinical and differential diagnoses, control, treatment, and laboratory diagnosis are reviewed. In addition, mention is made of the Venezuelan equine encephalitis (VEE) complex viruses (family Togaviridae, genus Alphavirus), which periodically cause human and equine disease in North America. WEE, EEE, and SLE viruses are transmitted by mosquitoes between birds; POW and CTF viruses, between wild mammals by ticks; LAC virus, between small mammals by mosquitoes; and VEE viruses, between small or large mammals by mosquitoes. Human infections are tangential to the natural cycle. Such infections range from rare to focal but are relatively frequent where they occur. Epidemics of WEE, EEE, VEE, and SLE viruses have been recorded at periodic intervals, but prevalence of infections with LAC and CTF viruses typically are constant, related to the degree of exposure to infected vectors. Infections with POW virus appear to be rare. Adequate diagnostic tools are available, but treatment is mainly supportive, and greater efforts at educating the public and the medical community are suggested if infections are to be prevented.

Immunogens of encephalitis viruses

The equine encephalitis viruses are members of the genus Alphavirus, in the family Togaviridae. Three main virus serogroups represented by western (WEE), eastern (EEE) and Venezuelan equine encephalitis (VEE) viruses cause epizootic and enzootic infection of horses throughout the western hemisphere. All equine encephalitis viruses are transmitted through the bite of an infected mosquito. The first equine encephalitis virus vaccines were produced by virus inactivation. Problems with inadequate inactivation, which may have caused a major epidemic/epizootic of VEE in central America and Texas in the 1970s, led to the development of a live attenuated VEE virus vaccine (TC-83) derived by cell culture passage. Inactivated vaccines are still used to prevent equine infections with WEE and EEE viruses. Alphaviruses are small single stranded, positive sense RNA viruses. The 12000 nucleotide genome is enclosed in an icosahedral nucleocapsid composed of multiple copies of the capsid (C) protein. The virion is enveloped. The membrane is modified by the insertion of heterodimers of two glycoproteins: E1 and E2. Monoclonal antibody analysis of the surface glycoproteins have provided a detailed understanding of important protective antigens. Recent studies comparing gene sequences from virulent and avirulent VEE viruses have begun to delineate mechanisms of alphavirus attenuation.

Genetic heterogeneity among isolates of Ross River virus from different geographical regions

The RNase T1 maps of 80 isolates of Ross River virus from different regions of mainland Australia and the Pacific Islands were compared. Four different clusters of isolates with greater than an estimated 5 to 6% diversity at the nucleotide level were found. There was a pattern of differences between eastern and western Australian strains; however, the pattern was disturbed by overlaps and incursants. Pacific Islands isolates belonged to the eastern Australian topotype. Our findings suggest that certain genetic types of Ross River virus predominate in different geographical regions. In contrast, populations of other important Australian arboviruses (Murray Valley encephalitis, Kunjin, and Sindbis viruses) are distributed across the Australian continent as minor variants of one strain. Our data also show that in one region, strains of Ross River virus with identical RNase T1 maps circulate during both years when epidemics occur and years when they do not. This finding suggests that Ross River virus epidemics are not dependent on the introduction or evolution of new strains of the virus. Two strains, belonging to the eastern Australian topotype, were isolated in Western Australia. It is likely that viremic humans or possibly domestic livestock travelling by aircraft were responsible for this movement.

Genomic variability among globally distributed isolates of equine arteritis virus

Equine arteritis virus (EAV), a non-arthropod borne togavirus, has been shown to have a global distribution. To date, no major antigenic variation has been demonstrated between EAV isolates from different geographic origins. In this study, the genomic RNA of EAV isolates obtained from horses of different breeds in various countries around the world was oligonucleotide fingerprinted. Comparisons of these fingerprints were used to determine the extent of genomic variation among such isolates. Comparisons among isolates from North American horses revealed, for the most part, oligonucleotide homologies of less than 60%. Only 29 of the 98 comparisons revealed greater than 60% oligonucleotide homology. Nonetheless, several comparisons indicated a close epidemiologic relationship between isolates from horses of different breeds located in different states. Though all European isolates were of Standardbred origin and were from horses located in northern European countries, the majority had oligonucleotide homologies of less than 60%. Where oligonucleotide homology was apparent, it was, with one exception, greater than 70%. The two isolates from New Zealand had 93.2% oligonucleotide homology. This is indicative of an extremely close epidemiologic relationship. Comparisons between EAV isolates from around the world revealed oligonucleotide homologies between viruses from North America, Europe and New Zealand. In several instances, this homology was greater than 70% and in one case greater than 80%. No oligonucleotide homology was evident in comparisons involving the virus from South Africa. The high level of genomic conservation between certain EAV isolates of disparate geographic origins may reflect dissemination of the virus associated with the international movement of horses. The extent of genomic variation demonstrated between most of the EAV isolates used in this study confirms the need for further investigation of genomic heterogeneity among strains of this virus before techniques that rely upon nucleic acid hybridization can be effectively applied as diagnostic procedures.

Molecular evolution of eastern equine encephalomyelitis virus in North America

We examined the rate and spatial pattern of eastern equine encephalomyelitis virus (EEEV) evolution in North America using primer-extension sequencing of viral RNA. Nucleotide sequences of the entire 26 S structural gene region of four EEEV strains revealed remarkable conservation between 1933 and 1985, with an estimated 0.7% divergence or 1.4 x 10(-4) nucleotide substitutions per site per year. Sequences from smaller 26 S regions of nine additional strains suggested that EEEV evolves in North America in a single lineage, with genetic exchange regularly occurring among enzootic transmission foci. In these limited 26 S genome regions, only synonymous nucleotide substitutions became fixed between 1933 and 1988, implying a high degree of conservation in protein structure. Short nucleotide sequences from a Panamanian, South American variety isolate revealed a relatively distant relationship to North American serotype viruses. This suggested genetic divergence between antigenic varieties, and independent evolution of EEEV in North and South America. Factors related to replication and epidemiology of EEEV, which may constrain its evolution in nature, are discussed. Possible mechanisms of genetic exchange among enzootic foci are also considered.

Detection of dengue viral RNA in mosquito vectors by mixed phase and solution hybridization

A mixed phase hybridization technique was developed to detect dengue virus type 2 (DEN-2) RNA in pools of infected Aedes albopictus mosquitoes using radiolabelled RNA probes. This technique used a guanidine thiocyanate extraction procedure to simplify analyte preparation. The probes contained sequences complementary to portions of the NS-1 or NS-5 genes of the DEN-2 viral genome. One infected mosquito in a pool of 25 could be detected in approximately 48 h. RNAs from DEN serotypes 1-4 were extracted from cultured mosquito (C6/36) cells. The NS-1 RNA probe was highly specific for DEN-2 RNA. The NS-5 RNA probe detected both DEN-2 and DEN-4 RNA. DEN-2 RNA was also detected by molecular hybridization in concentrated solutions of guanidine thiocyanate using the NS-1 probe. Solution hybridization was 10-fold more sensitive when detecting RNA from purified DEN-2 virus than the mixed phase assay and could detect one infected mosquito in a pool of 25 within 6-8 h. Solution hybridizations were performed in 2-3 h vs 16-20 h for mixed phase hybridizations, and solution hybridizations required 5-10 times less mosquito RNA than mixed phase hybridizations to attain comparable sensitivities. However, solution hybridizations did result in a broader probe specificity than mixed phase hybridizations.

Vesicular stomatitis New Jersey virus glycoprotein gene sequence and neutralizing epitope stability in an enzootic focus

Vesicular stomatitis New Jersey (VS NJ) virus is capable of undergoing rapid evolution in nature and therefore has the potential for antigenic variation. We selected an area of Costa Rica where VS NJ virus is enzootic to study whether this virus used the mechanism of antigenic variation to persist in nature. Three sentinel herds and three nonsentinel herds were observed from 1986 to 1988. Eleven VS NJ virus isolates were collected from naturally infected cattle. Remarkably, nine animals that were bled prior to reinfection with VS NJ virus had neutralizing antibody titers up to 1: 102,400 yet virus was isolated from, and disease was observed in, these animals. Sequence analysis of the portion of the glycoprotein gene coding for the neutralizing epitopes demonstrated that all virus isolates were 98-100% similar with no indication of specific genetic variation. The 3' end of the glycoprotein gene also remained stable in that all isolates were again 98-100% similar in nucleotide sequence. Each isolate was neutralized to equivalent titers with monoclonal antibodies directed against four neutralizing epitopes on the glycoprotein. Additionally, preisolation sera from each animal were able to neutralize the virus that caused the subsequent disease. These results provide evidence that antigenic variation is not a mechanism used by VS NJ virus to persist in an enzootic focus of Costa Rica.

Genetic variation and microevolution of dengue 2 virus in Southeast Asia

Dengue 2 (DEN 2) virus strains collected from dengue hemorrhagic fever (DHF) patients and Aedes aegypti mosquitoes in Thailand, Burma, and Vietnam over a 25-year period have been analyzed by computer assisted T1-RNase-resistant oligonucleotide fingerprinting. Fifty-seven DEN 2 virus strains of the Thailand topotype were separated into four major clusters by phylogenetic analysis of 97 unique oligonucleotides identified in a common well-resolved region of the fingerprints. Similarities in the 57 fingerprints indicated that DEN 2 virus of a single, continually evolving genetic population has been involved in endemic transmission of the disease. Virus isolates from DHF cases and mosquitoes are genetically very similar, indicating that different genetic topotypes are not selectively the cause of severe DEN disease in Thailand. Microevolution of the DEN 2 virus genome from 1962-1986 was gradual with detectable changes in the pattern of oligonucleotides through time. Segregation of the DEN 2 virus fingerprints into the three decades (1960s, 1970s, and 1980s) revealed the rate of genetic change to be one consensus oligonucleotide per year. Based on average association coefficient (Sab) values between the consensus fingerprints for each decade, the similarity between the consensus fingerprints decreased by 1.4% per year. Genetic variation during each of the three decades was found to be essentially the same (0.866 +/- 0.053). Constancy in the microevolutionary rate and genetic variability suggests that a balance of genetic drift and natural selection acting on the viral population did not significantly change throughout the 25-year period.

Monoclonal antibodies that cross-react with the E1 glycoprotein of different alphavirus serogroups: characterization including passive protection in vivo

A panel of four monoclonal antibodies (mAb) were produced that cross-react with representatives of two different togavirus serogroups, namely sindbis (SIN) and Semliki Forest (SF) viruses, by ELISA and ADCMC assays. Three of these mAb, IgG2a and IgG2b isotypes, passively protected C3H/Hej mice against 10 and 100 LD50 of SF challenge and one, IgM, did not protect against either challenge dose, or even at 1 LD50. All these mAb were cross-reactive with the E1 glycoprotein of the viruses by immunoblotting in which three different patterns of reactivity were evident, suggesting that three epitopes were involved. The patterns depended upon whether the mAb recognized E1 extracted from purified virions or infected cells and whether SDS-PAGE and immunoblotting were done in the presence or absence of beta-mercaptoethanol. One mAb (IgM) reacted with nonreduced or reduced E1 from either virions or cells suggesting recognition of a linear epitope. The other three mAb reacted with nonreduced but not reduced E1 from virions suggesting that recognition depends upon conformational epitopes. These three mAb reacted also with nonreduced E1 extracted from SF-infected cells whereas only one reacted with nonreduced E1 extracted from SIN-infected cells.

RNA virus evolution and the control of viral disease

RNA viruses and other RNA genetic elements must be viewed as organized distributions of sequences termed quasi-species. This means that the viral genome is statistically defined but individually indeterminate. Stable distributions may be maintained for extremely long time periods under conditions of population equilibrium. Perturbation of equilibrium results in rapid distribution shifts. This genomic organization has many implications for viral pathogenesis and disease control. This review has emphasized the problem of selection of viral mutants resistant to antiviral drugs and the current difficulties encountered in the design of novel synthetic vaccines. Possible strategies for antiviral therapy and vaccine development have been discussed.

Impact of climate on western equine encephalitis in Manitoba, Minnesota and North Dakota, 1980-1983

Information was collected on confirmed outbreaks of western equine encephalitis (WEE) in North America east of the Rockies for 1981 and 1983 (epidemic years) and 1980 and 1982 (non-epidemic years). The initial pattern of outbreaks in Manitoba, Minnesota and North Dakota was determined for each year. Backward (and in some instances forward) wind trajectories were computed for each day 4-15 days (incubation period) before the initial outbreaks of WEE in a given area of province or state. During these years the timing and location of WEE outbreaks in horses and man, seroconversion in chickens, the maximum Culex tarsalis counts at Winnipeg and first isolation of WEE virus from C. tarsalis could be correlated with trajectories of winds from states further south within acceptable intervals. It is suggested that C. tarsalis mosquitoes infected with WEE virus are carried on the wind from Texas on the Gulf of Mexico, where they continue to breed during the northern winter months, to northern Texas and Oklahoma in the spring. In May, June and July C. tarsalis are carried north on southerly winds from these states through Kansas and Nebraska to North Dakota, Minnesota, Wisconsin and Manitoba. Distances of 1250-1350 km are traversed in 18-24 h at heights up to 1.5 km with temperatures greater than or equal to 13 degrees C. Landing takes place where the warm southerly winds meet cold fronts associated with rain. Convergence leads to concentration of C. tarsalis and determines where outbreaks occur. It is possible that return of new generations of C. tarsalis to the south may occur later in the year. The development of an epidemic of WEE in the northern states and provinces would appear to depend on (i) suitable trajectories from the south in June and July with temperatures greater than or equal to 13 degrees C meeting cold fronts with rain, (ii) sufficient C. tarsalis infected with WEE virus at source, carried on the wind and locally, (iii) C. tarsalis biting horses and man, (iv) maintenance of local mosquito populations in August and (v) susceptible hosts (birds) at source and susceptible hosts (horses and man) locally. Possible methods of prediction involving determination of trajectories, identification of C. tarsalis blood meals, measuring seroconversion in calves are discussed in addition to the methods already in use.

Geographic classification of dengue-2 virus strains by antigen signature analysis

Dengue-2 virus strains from different locations were compared by T1-RNAse-resistant oligonucleotide fingerprinting and antigen signature analysis. The latter technique involved construction of radioimmunoassays using monoclonal antibodies that recognize nine distinct dengue-2 type-specific and flavivirus cross-reactive epitopes over a range of antigen concentrations. A statistical method was used to align unknown dengue antigen concentrations in different strain preparations, allowing comparison of binding profiles. Twenty-six dengue-2 virus strains were separated into five distinct groups (topotypes) on the basis of unique RNA fingerprints. Two of these were represented by New Guinea C, the prototype virus isolated in 1944, and a Philippine strain; others were segregated on the basis of greater than or equal to 80% shared oligonucleotides into similarity groups representing Burma/Thailand (8 strains), Puerto Rico (12 strains), and Jamaica (4 strains). Signature analysis of the prototype and four geographic topotype strains revealed striking antigenic differences. In contrast, a high degree of antigenic similarity was found among strains from the same geographic region. Variation between antigenically distinct strains occurred at both type-specific and group-reactive epitopes, but the widest differences appeared at group-reactive determinants. Signature analysis provides a more rapid and simpler means than RNA fingerprinting of monitoring changes or new introductions of dengue virus populations in a geographic region.

Purification of small oligonucleotides by polyacrylamide gel electrophoresis and transfer to diethylaminoethyl paper

The application of polyacrylamide gel electrophoresis with subsequent electroelution onto DEAE paper for the purification of small oligonucleotides is described. We demonstrate that synthetic DNAs and hydrolyzed RNAs as small as three nucleotides in length can be purified by this technique. The product is undegraded and homogeneous in length.

Recent vesicular stomatitis virus infection detected by immunoglobulin M antibody capture enzyme-linked immunosorbent assay

We developed an enzyme-linked immunosorbent assay (ELISA) that was capable of detecting immunoglobulin M (IgM) antibody to vesicular stomatitis virus (VSV) in the sera of experimentally and naturally infected cattle and horses. The detection of IgM in the sera of these animals permitted an estimate of the recency of infection by VSV serotype New Jersey. A VSV serotype New Jersey epizootic strain isolated from a horse and passed once in an Aedes albopictus cell line was used to infect a horse and a calf. Sera from these animals were used to standardize the ELISA. This assay was used to test sera from cattle and horses involved in the 1982 VSV epizootic. Comparative antibody titrations were performed by three systems: the serum-dilution plaque-reduction neutralization, complement fixation, and indirect immunofluorescent tests. The antibody titers by neutralization and the ELISA were comparable for the period that IgM was present; when IgM ELISA titers diminished, the neutralization titers remained high. The complement fixation and indirect immunofluorescent antibody titers followed closely the IgM pattern determined by the ELISA. The capture IgM ELISA is applicable for the rapid detection of IgM antibody to VSV in cattle and horses and is a useful assay of recent infection.

Determination of human IgG and IgM class antibodies to West Nile virus by enzyme linked immunosorbent assay (ELISA)

An enzyme-linked immunosorbent assay (ELISA) was developed and used for the detection of IgG and IgM antibodies to West Nile virus in human sera. Thirteen paired sera of clinical cases and 24 control sera taken randomly from a blood bank repository were tested. The sera were reacted in microtiter plates coated with PEG-treated WNV antigen. IgG or IgM antibodies were quantitated by the use of alkaline-phosphatase-conjugated anti-human IgG or IgM antibodies. Of the 24 randomly collected serum samples, 7 were positive in the IgG-ELISA test. One positive by the IgM-ELISA was found to contain rheumatoid factor. In 12 of 13 paired sera of clinical cases, IgM as well as IgG antibodies were detected in the second serum sample taken about 3 wk after the onset of clinical signs. The IgM positive sera were screened for rheumatoid factor (RF) on IgG-coated plates. None of them contained RF. Antibody titers obtained by ELISA showed a good correlation with titers obtained by hemagglutination inhibition, complement fixation, and neutralization tests. The ELISA tests for detection of IgM and IgG antibodies to WNV therefore can replace the other serological methods for epidemiological surveillance and diagnostic purposes.

Analysis of Ross River virus genomic RNA using HaeIII digests of single-stranded cDNA to infected-cell RNA and virion RNA

To study genetic relationships between isolates of Ross River virus (RRV), an alphavirus with a chromosome of approximately 12,000 nucleotides, total high-molecular-weight RNA from RRV-infected baby hamster kidney (BHK) cells was transcribed into 32P-labeled, complementary DNA using reverse transcriptase and random calf-thymus DNA primers. The cDNA was digested with HaeIII or TaqI (restriction nucleases which cleave single-stranded DNA), and the restriction fragments separated on a standard DNA sequencing gel. The resulting HaeIII or TaqI restriction digest profiles mainly comprised virus-specific bands; cell RNAs were transcribed poorly. In reconstruction experiments, purified 49 S RRV genomic RNA and a 10-fold mass excess of mock-infected-cell RNA were reverse transcribed in the same reaction mix. Under these conditions there was no interference with the transcription of viral RNA sequences. When the level of viral RNA was lowered to one-hundredth that of cell RNA in the reaction mix, there was no qualitative change in restriction digest profiles. The procedure is rapid, simple, uses small amounts of 32P, does not require purification of virus or viral RNA, and permits cross-comparison between several virus strains on a single one-dimensional gel. The method should be applicable to other single-stranded RNA viruses of moderate genome complexity.

An evolutionary tree relating eight alphaviruses, based on amino-terminal sequences of their glycoproteins

The NH2-terminal amino acid sequences of both structural glycoproteins of each of eight alphaviruses have been obtained. These sequences demonstrate that the alphaviruses are all closely related and have in all probability descended from a common ancestor. Cysteines are conserved as well as several other residues important for secondary structure, suggesting that the three-dimensional conformations of the alphavirus glycoproteins are conserved while considerable variation in the primary sequence has evolved. Secondary structure predictions based upon the amino acid sequences are consistent with this hypothesis. An evolutionary tree for these eight alphaviruses has been constructed from the amino acid sequence data and, at many positions in the sequence, the amino acids present in the ancestral glycoproteins have been deduced.

Applications of Oligonucleotide Fingerprinting to the Identification of Viruses

This chapter focuses on applications of oligonucleotide fingerprinting to the identification of viruses. Fingerprinting is a technique by which oligonucleotides, produced by cleavage of RNA molecules with specific ribonucleases, are separated in two dimensions. It is a definitive method of identifying RNA viruses according to their genotypes. It is not subject to the problems of antigenic drift or antigenic convergence that complicate serological identification. Furthermore, it provides a semiquantitative means of following the evolution of viral genomes in nature. Because all regions of the genome are represented by the large diagnostic oligonucleotides, a survey of the total genomic changes can be monitored. Fingerprinting has two limitations as a diagnostic tool. First, although highly definitive, fingerprinting is not as rapid or inexpensive as serological techniques and cannot be as easily scaled up for routine identification of a large number of samples. Second, the evolutionary range of fingerprinting is short and relationships may not be evident for isolates of rapidly evolving viruses obtained over long intervals. However, these limitations are not large, compared to the full benefits offered to the virologist by the fingerprinting method.

Genetic variation among dengue 2 viruses of different geographic origin

Genetic variation in dengue 2 isolates from various geographic areas was examined by oligonucleotide fingerprinting of the 40 S genome RNA. Oligonucleotide maps of geographically isolated and epidemiologically unrelated viruses were very distinct. Direct comparison of the oligonucleotide map of the dengue 2 prototype New Guinea 2 virus, isolated in 1944, with the fingerprints of more recent isolates from the South Pacific indicated that the genome of dengue 2 virus had undergone extensive change although the viruses are serologically indistinguishable. The oligonucleotide map of an isolate from a recent case in Jamaica and a mosquito isolate from Upper Volta, Africa, were recognized to be almost identical, suggesting that virus may have been introduced into the Caribbean from West Africa. Likewise, the fingerprints of isolates from Puerto Rico and the South Pacific shared 80 to 95% of their large oligonucleotides, suggesting that the virus involved in these epidemics may have spread throughout Tahiti, American Samoa, Fiji, and to Puerto Rico in the Caribbean or vice versa. On the basis of these studies, five genetic variants or topotypes of dengue 2 virus have been established: (1) Puerto Rico-South Pacific, (2) Burma-Thailand, (3) the Seychelles, (4) the Philippines, and (5) Jamaica-West Africa. Oligonucleotide fingerprinting offers a highly sensitive and reproducible technical approach to the investigation of dengue 2 virus intratypic variation and possibly to the understanding of the biological variation associated with dengue fever and hemorrhagic disease.

A variant of western equine encephalitis virus with nonglycosylated E3 protein

A variant clone (At/A125) of western equine encephalitis virus was isolated from a line of mosquito cells persistently infected with a temperature-sensitive parent strain, A125. Variant-infected cells produced an altered form of PE2 protein which migrated with a higher electrophoretic mobility than wild type or A125 PE2. The altered PE2, like PE2 of wild type, was precipitated by anti-envelope proteins serum but not by anti-E1 serum. In pulse-chase experiments the altered PE2 protein was shown to yield E2 of normal electrophoretic mobility in SDS-polyacrylamide gel electrophoresis. The unglycosylated form of the altered PE2 synthesized in the presence of tunicamycin migrated at the same position as the unglycosylated PE2 obtained from tunicamycin-treated, parent strain-infected cells. This suggested that migration difference might be ascribable to incomplete glycosylation of PE2, possibly of its E3 component. E3 is released into culture fluid of wild-type-infected cells as an approximately 11-kd glycoprotein, while variant-infected culture fluid yielded a smaller, apparently virus-specific protein. The protein could not be labeled with [3H]mannose, suggesting that the polypeptide moiety of E3 in the variant infected cells failed to be glycosylated. The parent strain, A125, and a revertant of the variant, At/A125/rev, did not synthesize such altered PE2 and E3 proteins. The growth of At/A125 in mosquito cells was similar to that of parent or wild type but depressed in vertebrate cells.

Rubella virion polypeptides: characterization by polyacrylamide gel electrophoresis, isoelectric focusing and peptide mapping

Four polypeptides with molecular weights of 55 K, 47 K, 45 K, and 33 K have been resolved by polyacrylamide gel electrophoresis of immune precipitated rubella virus. The 47 K and 45 K components have similar peptide maps but different isoelectric points so that the same polypeptide may exist in more than one charged form. The 55 K and 45 K components have similar isoelectric points but different peptide maps showing that similarity of isoelectric point is not evidence of identity.