Analysis of the survival of Venezuelan equine encephalomyelitis virus and possible viral simulants in liquid suspensions.

AIMS: To compare the inactivation rate of Venezuelan equine encephalomyelitis (VEE) virus in liquids to that of Sindbis virus (SV, another alphavirus) and to a bacteriophage (MS2) generally used as a viral simulant in the development of countermeasures in biodefense. METHODS AND RESULTS: Viruses were inoculated into liquids and viral titres were determined at various times postinoculation. The viruses were stable in distilled-deionized (dd) water at 4 degrees C during the 21 days of the study. The inactivation rates of VEE and SV in dd water at 21 and 30 degrees C were very similar (between 0.12 and 0.14 log(10) per day), while MS2 was three-fold slower. In tap water (chlorine content between 4 and 5 ppm) at 21 degrees C, VEE and SV were inactivated at twice the rate measured in dd water. CONCLUSIONS: The inactivation rates of VEE and SV were similar to each other and faster than MS2 in all liquids tested. SIGNIFICANCE AND IMPACT OF THE STUDY: VEE is likely to remain viable for many days after release into water, snow, or even chlorinated tap water. SV can be used to estimate the persistence of VEE in liquids, but using MS2 as a simulant would overestimate of the stability of VEE.

Emergence of drug resistance mutations in a group of HIV-infected children taking nelfinavir-containing regimens.

HIV-1-infected children are often treated with therapy regimens including protease inhibitors (PIs). We monitored the virologic response in a small group of pediatric patients undergoing therapy with regimens including the PI nelfinavir and determined whether new drug resistance mutations were present immediately after virologic failure. Seventeen reverse transcriptase inhibitor (RTI)-experienced children starting nelfinavir-containing therapy regimens were studied. After virologic failure, HIV-1 protease (PR) and RT sequences were examined for drug resistance mutations. Viral load levels decreased to <400 HIV RNA copies/ml in six patients and remained at <400 HIV RNA copies/ml in four patients. Three patients did not respond virologically; all three had mutations specific for one or more of their regimen drugs either before or soon after nelfinavir initiation. The virologic response was transient in eight patients whose viral loads did not decrease to <400 HIV RNA copies/ml. Genotypic data from seven of the eight patients revealed mutations specific for one or more of their regimen drugs after virologic rebound. PI resistance mutations occurred in eight patients: D30N in six, and L90M in three. In three patients, the only new mutation after failure was the RT mutation M184V. Despite virologic failure, sustained increases in CD4+ lymphocyte counts were noted in eight patients. We conclude that in this small group of pediatric patients, virologic failure occurred in all patients whose viral loads did not become undetectable after the switch to a nelfinavir-containing regimen. After failure, new drug resistance mutations were found in either PR or RT. Studies of larger cohorts are warranted to determine whether HIV-1 genotypic data can help in the formulation of effective salvage therapies in children.

Sequence analysis of dru regions from methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates.

Methicillin-resistance in staphylococci results from expression of mecA, which occurs in a larger region of DNA (the mec region) lacking counterpart in susceptible cells. The mec region harbors in addition a highly polymorphic element, the dru (direct repeat unit) segment, which in an early S. aureus strain, BB270, was found to contain 10 imperfect 40 base-pair repeats. We have explored the utility of direct sequencing of dru segments for discriminating among strains of methicillin-resistant S. aureus (MRSA) and coagulase-negative staphylococci (MRCNS). We sequenced dru segments of 24 clinical isolates of MRSA, and 15 of MRCNS, and reexamined strain BB270. Six S. aureus and 2 S. epidermidis isolates were found to have deletions which removed all drus. The other strains were found to have multiple contiguous dru repeats of precisely 40 bp. Analysis of these strains plus dru segment sequence from 4 recent reports yielded 18 unique dru segment sequences (designated "dru types") differing in numbers of repeats and/or sequences of particular repeats. Dru typing was more discriminating than sequencing of non-mec region genes, including a repeat-containing segment (spa Xr) of the S. aureus protein A gene. Yet dru type was sufficiently stable to register epidemiological clusters. Dru sequencing is a useful tool for tracking methicillin-resistant lineages of S. aureus and CNS.

HIV-1 reverse transcriptase mutations found in a drug-experienced patient confer reduced susceptibility to multiple nucleoside reverse transcriptase inhibitors.

HIV-1 reverse transcriptase (RT) genotypes were obtained from 13 patients treated with stavudine. No previously-reported mutations indicative of stavudine resistance were found in these patients and no novel mutations occurred in more than two patients. One patient, treated with stavudine for 1 month and treated previously with zidovudine, zalcitabine and lamivudine, carried a mutation at codon 75 of the RT (V75M). A chimeric virus, including the patient's RT sequence from codon 25 to codon 220, which carried the resistance mutations M41 L, D67N, T69D, K70R, L210W and T215Y in addition to V75M, displayed reduced susceptibility to multiple nucleoside RT inhibitors (NRTIs). Removal of V75M from this RT background resulted in a return of susceptibility to didanosine and lamivudine. Our data are in agreement with previous studies demonstrating the rarity of stavudine resistance mutations in stavudine-treated patients. However, we describe a new set of mutations, found in the RT of a heavily-treated patient, that can confer reduced susceptibility to multiple NRTIs. These results underscore the importance of increased vigilance for possible multiple-drug resistance in patients who have been heavily treated with NRTIs.

A sequence variant of Staphylococcus hominis with a high prevalence of oxacillin and fluoroquinolone resistance.

A newly identified subspecies of Staphylococcus hominis, S. hominis subsp. novobiosepticus, was found to be the cause of several invasive infections at a hospital in New Jersey. This subspecies differs from classical S. hominis, now S. hominis subsp. hominis, by the phenotypic characteristics of novobiocin resistance and the inability to ferment trehalose. DNA sequences of segments of 16S rRNA, DNA gyrase (gyrA), and DNA topoisomerase IV (grlA) genes were determined for the type strains of the 2 subspecies, and for 34 S. hominis clinical isolates. The 16S rRNA sequences of the type strains differed at 3 positions over 410 bp; the grlA sequences differed at 6 positions over 119 bp. These sequence differences define S. hominis subsp. novobiosepticus and S. hominis subsp. hominis "sequevars." Of 34 S. hominis clinical isolates, 31 were S. hominis subsp. novobiosepticus sequevars, 28 of which were resistant to both oxacillin and ciprofloxacin. The clinical microbiology laboratory, using a MicroScan system, identified 7 of the 31S. hominis subsp. novobiosepticus sequevars as S. hominis subsp. hominis on the basis of phenotypic characteristics. Three S. hominis subsp. hominis sequevars were all identified phenotypically as S. hominis subsp. hominis and were oxacillin- and ciprofloxacin-susceptible. Although the precise relationship between the S. hominis sequevars and their phenotypic subspecies remains to be determined, our results indicate that antibiotic-resistant clinical isolates of S. hominis belong almost exclusively to the S. hominis subsp. novobiosepticus sequevar.

A new contained human immunodeficiency virus type 1 host cell system for evaluation of antiviral activities of interferons and other agents in vitro.

HIV-host infection systems in vitro are important in the pre-clinical assessment of anti-retroviral drug activity. The present report describes the development of a new HIV-host model comprised of an epithelial cell line of HeLa lineage (HeLa-1), transfected with expression vectors bearing tat and rev (TART) genes of HIV-1 as well as the CD4 receptor gene, and HIV-1(delta Tat/Rev), a biologically contained strain of HIV-1 deleted in tat and rev. Measurement of infectivity, by syncytium formation and reverse transcriptase assay, revealed that HeLa-1 is infected with HIV-1(deltaTat/Rev). This virus failed to productively infect the TART-deficient CD4-positive HeLa cells, confirming its contained, non-infectious nature. The HeLa-1/HIV-1deltaTat/Rev system was used to measure the anti-retroviral activity of a human leukocyte-derived interferon (IFN-alphan3) preparation, several nucleoside analogs, and protease inhibitors. The HeLa-1/ HIV-1(deltaTat/Rev model provides a biologically contained system for the study of the HIV pathogenesis and the relative and combined therapeutic effects of anti-retroviral agents in vitro.

Topoisomerase sequences of coagulase-negative staphylococcal isolates resistant to ciprofloxacin or trovafloxacin.

Coagulase-negative staphylococcal isolates (n = 188) were screened for susceptibility to oxacillin, ciprofloxacin, and trovafloxacin, a new fluoroquinolone. At an oxacillin concentration of >/=4 microg/ml, 43% were methicillin resistant; of these, 70% were ciprofloxacin resistant (MIC, >/=4 microg/ml). Of the methicillin-resistant, ciprofloxacin-resistant isolates, 46% were susceptible to /=8 microg/ml) and increased trovafloxacin MICs (0.25 to 2 microg/ml) could be conferred by the combined presence of single mutations in each gyrA and grlA gene. Trovafloxacin MICs of >/=8 microg/ml also occurred, but these required an additional mutation in grlA.

Topoisomerase mutations in trovafloxacin-resistant Staphylococcus aureus.

A total of 201 Staphylococcus aureus isolates were surveyed for susceptibility to ciprofloxacin and trovafloxacin. Of 66 methicillin-resistant isolates, 89% were ciprofloxacin resistant and 6% were also trovafloxacin resistant. Trovafloxacin-resistant strains had unusual patterns of quinoline resistance mutations in DNA topoisomerase genes, including two mutations in the A subunit (encoded by grlA) of topoisomerase IV.

Effect of the HIV-1 syncytium-inducing phenotype on disease stage in vertically-infected children.

The syncytium-inducing (SI) capability of HIV-1 isolates from 48 HIV-infected children was determined in order to examine the association of the SI phenotype with an AIDS diagnosis and/or with other clinical parameters in HIV-infected children. In a retrospective cross-sectional analysis, phenotypic data were linked to clinical and immunologic data from each patient. Multiple longitudinal samples were analyzed from 14 patients. Children with SI viruses were older than children with nonsyncytium-inducing (NSI) strains. Twelve of 13 children less than 2 years old carried NSI viruses, seven of the 12 already had a diagnosis of AIDS. Two children under 2 years of age died within 1 month of NSI virus isolation. Although plasma p24 antigen levels tended to be higher in the NSI group, the difference appeared to reflect high p24 levels in children under 2 years old with AIDS. When children under 2 were omitted, differences in age, CD4+ cell counts, p24 antigenemia, and clinical parameters were not significant. The SI phenotype of HIV-1 did not occur more frequently in children with an AIDS diagnosis. Four children remained stable with SI isolates overtime periods of 16 to 31 months. Three children's isolates converted from NSI to SI and 2 converted from SI to NSI. These data indicate that SI viruses do not play a significant role in progression to AIDS during the first 2 years of life. Furthermore, for children above the age of 2, the association between advanced disease stage and the SI phenotype in adults may not apply.

Transmission from one child to another of human immunodeficiency virus type 1 with a zidovudine-resistance mutation.

BACKGROUND AND METHODS. We describe a child who apparently acquired human immunodeficiency virus type 1 (HIV-1) infection in the home setting. The suspected source of infection was a child with the acquired immunodeficiency syndrome who had received zidovudine and whose virus contained a mutation associated with in vitro zidovudine resistance. The children were born to different HIV-1-infected mothers, but they lived in the same home between the ages of two and five years. Child 1 was infected perinatally; Child 2 was not and was repeatedly found to be seronegative. Child 2 was examined because of acute lymphadenopathy and had seroconverted to HIV-1 positivity. HIV-1 proviral DNA was amplified from peripheral-blood mononuclear cells and subjected to sequence analysis. Sequences from Child 2 were compared with those from Child 2's mother, Child 1, and local HIV-1-infected control children.

Human immunodeficiency virus type 1 pol gene mutations in an AIDS patient treated with multiple antiretroviral drugs.

Multiple mutations were found in the human immunodeficiency virus pol gene following treatment of an AIDS patient with antiretroviral drugs. After approximately 2.5 years of monthly alternating therapy with 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxycytidine (ddC), most of the pol sequences amplified from the patient's peripheral blood mononuclear cell DNA contained known AZT resistance mutations at codons 41, 67, and 215 and a putative ddC resistance mutation at codon 69 as well as other novel mutations. These mutations persisted for 6 months after the patient was switched to 2',3'-dideoxyinosine monotherapy. Mutations known to be associated with 2',3'-dideoxyinosine resistance did not occur during this time. Antiviral susceptibility testing of point mutants, introduced into the genetic background of laboratory strain NL4-3, showed that the codon 41 mutation antagonized ddC resistance when present with the codon 69 mutation. However, this antagonism was not found with a chimeric mutant containing the patient's pol gene sequence from codons 25 to 218, implying that other mutations compensated for the antagonism. Thus, alternating therapy with AZT and ddC resulted in the selection of viruses resistant to both drugs.

A new type of G-->A hypermutation affecting human immunodeficiency virus.

A form of G-->A hypermutation preferentially affecting GA dinucleotides of genomic RNA has been found to occur in retroviral systems ("type 1"). In a detailed longitudinal study of an AIDS patient we have observed a new type of G-->A hypermutation, which preferentially affects one or more 5' G residues in runs of G's. HIV-1 proviral DNA samples obtained at widely separate times during this patient's course contained representatives of this type of G-->A hypermutation, designated "type 2." We propose that G-->A hypermutation is caused by a mutated form of the HIV-1 reverse transcriptase; and that hypermutated DNA may persist for long periods in infected patients, perhaps as proviral DNA in long-lived cell lineages. Like type 1 G-->A hypermutation, type 2 G-->A hypermutation may contribute to the heterogeneity of replicating pools of HIV by recombination.

Human immunodeficiency virus type 1 pol gene mutations which cause decreased susceptibility to 2',3'-dideoxycytidine.

To investigate whether human immunodeficiency virus type 1 pol gene mutations are selected during prolonged 2',3'-dideoxycytidine (ddC) therapy, we used the polymerase chain reaction to amplify a portion of the reverse transcriptase segment of the pol gene from the peripheral blood mononuclear cell DNA of a patient with AIDS before and after an 80-week course of ddC therapy. The consensus sequence from the second sample contained a unique double mutation (ACT to GAT) in the codon for reverse transcriptase amino acid 69, causing substitution of aspartic acid (Asp) for the wild-type threonine (Thr). A mutation (ACA to ATA) also occurred in the codon for position 165, causing substitution of isoleucine (Ile) for Thr. The GAT (Asp) codon was introduced into the pol gene of a molecular clone of human immunodeficiency virus via site-directed mutagenesis. Following transfection, mutant and wild-type viruses were tested for susceptibility to ddC by a plaque reduction assay. The mutant virus was fivefold less susceptible to ddC than the wild type; cross-resistance to 3'-azido-3'-deoxythymidine or 2'3'-dideoxyinosine was not found. The Ile-165 mutation did not confer additional ddC resistance. The Asp-69 substitution may have contributed to the generation of resistant virus in this patient.

In vivo sequence variation of the human immunodeficiency virus type 1 env gene: evidence for recombination among variants found in a single individual.

To assess in vivo sequence heterogeneity of the human immunodeficiency virus type 1 (HIV-1) env gene, we used the polymerase chain reaction to amplify proviral sequences present in peripheral blood mononuclear cell DNA of a patient with acquired immunodeficiency syndrome (AIDS). The amplified env gene fragment (575 bp) contains the first hypervariable region and part of the first conserved region. Eleven and twelve clones were sequenced, respectively, from specimens collected two months apart. Notable heterogeneity was observed among sequences recovered from both specimens. Also, the proviral population recovered from the first specimen varied significantly from that found in the second specimen. Both specimens contained forms with and without an 18 bp duplication. The presence or absence of this duplication, in addition to several point mutations, appear to define two molecular groups evolving in parallel within this patient. Several genotypes which had sequences characteristic of both groups occurred primarily in the second specimen; these can best be explained by multiple recombinational events between representatives of the two groups during reverse transcription. This study demonstrates that recombination may contribute significantly to the generation of diversity among HIV variants within a single individual.

In vivo prevalence of azidothymidine (AZT) resistance mutations in an AIDS patient before and after AZT therapy.

In order to examine the in vivo prevalence of AZT resistance mutations in AID patients after long-term therapy we amplified, by polymerase chain reaction (PCR), a 654 bp pol gene fragment from peripheral blood mononuclear cell DNA samples from a patient before, and 19 months after, the start of AZT therapy. PCR products from each sample were cloned and 9 clones from each sample were sequenced. Seven of 9 clones from the post-AZT sample, but none from the pre-AZT sample, contained an amino acid substitution (Thr215 to Tyr) requiring two nucleotide changes within the same codon (ACC to TAC). This change had previously been shown by Larder and Kemp (Science, 246:1155-1158, 1989) to correlate with partial AZT resistance of virus isolates. In colony hybridizations using synthetic oligonucleotides corresponding to the mutant and wild-type sequences, 22 of 22 clones from the pre-AZT sample hybridized only to the wild-type probe while 21 of 26 clones from the post-AZT sample hybridized only to the mutant. Clinically, this patient remains well, indicating that while Tyr215 may be the first amino acid substitution leading to resistance, it alone does not appear to have significantly influenced the clinical status of this patient.

Cloning of a gene from Pseudomonas sp. strain PG2982 conferring increased glyphosate resistance.

A plasmid carrying a 2.4-kilobase-pair fragment of DNA from Pseudomonas sp. strain PG2982 has been isolated which was able to increase the glyphosate resistance of Escherichia coli cells. The increase in resistance was dependent on the presence of a plasmid-encoded protein with a molecular weight of approximately 33,000, the product of a translational fusion between a gene on the vector, pACYC184, and the insert DNA. An overlapping region of the PG2982 chromosome carrying the entire gene (designated igrA) was cloned, and a plasmid (pPG18) carrying the gene was also able to increase glyphosate resistance in E. coli. A protein with a molecular weight of approximately 40,000 was encoded by the PG2982 DNA contained in pPG18. This plasmid was not able to complement a mutation in the gene for 5-enolpyruvylshikimate-3-phosphate synthase (aroA) in E. coli, and modification of glyphosate by E. coli cells containing the plasmid could not be demonstrated. The nucleotide sequence of the PG2982 DNA contained an open reading frame able to encode a protein with a calculated molecular weight of 39,396.