Monica M. Parker

Sequence comparison of the N genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein

Abstract To obtain information about the structure and evolution of the nucleocapsid (N) protein of the coronavirus mouse hepatitis virus (MHV), we determined the entire nucleotide sequences of the N genes of MHV-A59, MHV-3, MHV-S, and MHV-1 from cDNA clones. At the nucleotide level, the N gene sequences of these viral strains, and that of MHV-JHM, were more than 92% conserved overall. Even higher nucleotide sequence identity was found in the 3′ untranslated regions (3′ UTRs) of the five strains, which may reflect the role of the 3′ UTR in negative-strand RNA synthesis. All five N genes were found to encode markedly basic proteins of 454 or 455 residues having at least 94% sequence identity in pairwise comparisons. However, amino acid sequence divergences were found to be clustered in two short segments of N, putative spacer regions that, together, constituted only 11% of the molecule. Thus, the data suggest that the MHV N protein is composed of three highly conserved structural domains connected to each other by regions that have much less constraint on their amino acid sequences. The first two conserved domains contain most of the excess of basic amino acid residues; by contrast, the carboxy-terminal domain is acidic. Finally, we noted that four of the five N genes contain an internal open reading frame that potentially encodes a protein of 207 amino acids having a large proportion of basic and hydrophobic residues.

Detecting Acute Human Immunodeficiency Virus Infection Using 3 Different Screening Immunoassays and Nucleic Acid Amplification Testing for Human Immunodeficiency Virus RNA, 2006-2008

BACKGROUND The yield of nucleic acid amplification testing (NAAT) after routine screening for human immunodeficiency virus (HIV) antibody to detect acute HIV infection (AHI) may vary with different HIV-antibody assays. METHODS From April 24, 2006, through March 28, 2008, patients underwent routine HIV-antibody screening using a first-generation assay at 14 county sexually transmitted disease (STD) clinics and 1 community clinic serving homosexual patients in Los Angeles; using a second-generation rapid test at 3 municipal STD clinics in New York; and using a third-generation assay at 80 public health clinics in Florida. To identify AHI, seronegative specimens were pooled for NAAT, followed by individual NAAT of specimens with positive findings. All AHI samples screened by first- and second-generation assays also underwent third-generation testing. RESULTS We screened 37 012 persons using NAAT after first-generation testing; 35 AHIs were identified, increasing HIV case detection by 8.2%. After a second-generation rapid test, 6547 persons underwent NAAT; 7 AHIs were identified, increasing HIV case detection by 24.1%. After third-generation testing, 54 948 persons underwent NAAT; 12 AHI cases were identified, increasing HIV case detection by 1.4%. Overall, pooled NAAT after negative third-generation test results detected 26 AHI cases, increasing HIV case detection by 2.2%. Most of the AHI cases from Los Angeles (26 of 35 [74%]) were identified at the community clinic where NAAT after third-generation testing increased HIV case detection by 11.9%. CONCLUSIONS Pooled NAAT after third-generation testing increases HIV case detection, especially in venues of high HIV seropositivity. Therefore, targeted AHI screening using pooled NAAT after third-generation testing may be most effective, warranting a cost-benefit analysis.

Rapid HIV screening: Missed opportunities for HIV diagnosis and prevention

BACKGROUND Although rapid HIV tests increase the number of persons who are aware of their HIV status, they may fail to detect early HIV infection. OBJECTIVES To evaluate the sensitivity for early HIV infection of several rapid tests and third- and fourth-generation assays compared with nucleic acid amplification testing (NAAT). STUDY DESIGN Sensitivity for early HIV infection was evaluated using 62 NAAT-positive/WB-negative or indeterminate specimens from the CDC Acute HIV Infection study. Specimens underwent third-generation testing with Genetic Systems 1/2+O(®) and rapid testing with Multispot HIV-1/HIV-2. A subset was also tested with four FDA-approved rapid tests and Determine HIV-1 Antigen/Antibody Rapid Test(®) and Architect HIV Antigen/Antibody Combo(®), both fourth-generation tests. RESULTS Of 99,111 specimens screened from April 2006 to March 2008, 62 met the definition for early HIV infection (60 NAAT-positive/seronegative and 2 NAAT-positive/Western blot indeterminate). Third-generation testing correctly detected antibody in 34 specimens (55%; 95% confidence interval (CI): 42-67); Multispot detected antibody in 16 (26%; 95% CI: 16-38). Of the 62 specimens, 33 (53%) had sufficient quantity for further testing. Rapid test sensitivities for early HIV infection ranged from 22-33% compared with 55-57% for the third-generation assay and 76-88% for the fourth-generation tests. CONCLUSIONS Many rapid HIV tests failed to detect half of the early HIV infection cases in whom antibody was present. Programs that screen high-incidence populations with rapid tests should consider supplemental testing with NAAT or other antigen-based tests. These data support the need for more sensitive antigen-based point-of-care screening tests for early HIV infection.

Evaluation of dried blood spot specimens for HIV-1 drug-resistance testing using the Trugene HIV-1 genotyping assay.

BACKGROUND Efforts to simplify the collection and shipping of specimens for HIV drug-resistance testing in resource-limited settings are needed as antiretroviral therapy increases worldwide. OBJECTIVE To evaluate the reliability and practicality of using dried blood spots (DBS) for HIV-1 drug-resistance testing with the Trugene HIV-1 genotyping assay. STUDY DESIGN Nucleic acids from 33 DBS and counterpart plasma specimens were extracted using the Nuclisens MiniMAG system and genotyped using the Trugene HIV-1 genotyping assay. Results were evaluated for sensitivity, accuracy, and reproducibility. RESULTS A genotype was obtained for 33 (100%) plasma specimens and 26 (78.8%) DBS specimens, including 19 of 21 (90.5%) DBS specimens with a viral load greater than 6000 copies/mL. The mean nucleotide sequence concordance for the 940-nucleotide region evaluated was 99.3% for 26 DBS and plasma pairs, and 99.2% for 15 replicate DBS pairs. All 58 resistance-associated mutations detected in plasma specimens were detected in the corresponding DBS specimens. CONCLUSIONS We show that DBS can be reliably and accurately genotyped using standard clinical assay methods, offering a practical alternative to plasma. This method is well suited for pre-treatment resistance testing and has potential for use in monitoring drug resistance in ART-treated individuals.

Multiple Clusters of Hepatitis Virus Infections Associated With Anesthesia for Outpatient Endoscopy Procedures

BACKGROUND & AIMS Hepatitis B virus (HBV) and hepatitis C virus (HCV) can be transmitted during administration of intravenous anesthesia when medication vials are used for multiple patients using incorrect technique. We investigated an outbreak of acute HBV and HCV infections among patients who received anesthesia during endoscopy procedures from the same anesthesiologist (anesthesiologist 1), in 2 different gastroenterology clinics. METHODS Chart reviews, patient interviews, clinic site visits and infection control assessments, and molecular sequencing of patient isolates were performed. Patients treated by anesthesiologist 1 on specific procedure days were offered testing for blood-borne pathogens. Endoscopy and anesthesia procedures were reviewed; HCV quasispecies analysis was performed. RESULTS Six cases of outbreak-associated HCV infection and 6 cases of outbreak-associated HBV infection were identified in clinic 1. One outbreak-associated HCV infection was identified in clinic 2. HCV quasispecies sequences from the patients were nearly identical (96.9%-100%) to those from source patients with chronic viral hepatitis. All affected patients in both clinics received propofol from anesthesiologist 1, who inappropriately used a single-patient-use vial of propofol for multiple patients. Reuse of syringes to redose patients, with resulting contamination of medication vials used for subsequent patients, likely resulted in viral transmission. CONCLUSIONS Twelve persons acquired HBV and HCV infections (6 hepatitis C, 5 hepatitis B, and 1 coinfection) in 2 separate offices as a result of receiving anesthesia from anesthesiologist 1. Gastroenterologists are urged to review carefully the injection, medication handling, and other infection control practices of all staff under their supervision, including providers of anesthesia services.

Prevalence of drug-resistance mutations and non-subtype B strains among HIV-infected infants from New York state

Summary: Prevalence studies indicate that transmission of drug-resistant HIV has been rising in the adult population, but data from the perinatally infected pediatric population are limited. In this retrospective study, we sequenced the pol region of HIV from perinatally infected infants diagnosed in New York State in 2001-2002. Analyses of drug resistance, subtype diversity, and perinatal antiretroviral exposure were conducted, and the results were compared with those from a previous study of HIV-infected infants identified in 1998-1999. Eight of 42 infants (19.1%) had provirus carrying at least 1 drug-resistance mutation, an increase of 58% over the 1998-1999 results. Mutations conferring resistance to nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors were detected in 7.1%, 11.9%, and 2.4% of specimens, respectively. Consistent with previous results, perinatal antiretroviral exposure was not associated with drug resistance (P = 0.70). Phylogenetic analysis indicated that 16.7% of infants were infected with a non-subtype B strain of HIV. It seems that drug-resistant and non-subtype B strains of HIV are becoming increasingly common in the perinatally infected population. Our results highlight the value of resistance testing for all HIV-infected infants upon diagnosis and the need to consider subtype diversity in diagnostic and treatment strategies.

Prevalence of genotypic drug resistance among a cohort of HIV-infected newborns.

A retrospective, blinded study was conducted to examine the prevalence of antiretroviral drug resistance among a cohort of HIV-infected infants born in 1998 and 1999 in New York State. The earliest available HIV-positive specimen was tested. Most samples were from infants younger than 60 days of age. Genotype data were generated for the protease and reverse transcriptase genes of HIV-1 proviral DNA from 91 infected infants. Eleven infants (12.1%) had provirus with mutations associated with drug resistance, with all three classes of antiretroviral drugs represented. Two infants (2.2%) had mutations associated with resistance to two classes of antiretrovirals. Perinatal antiretroviral drug exposure was examined; it was not found to be significantly associated with the presence of resistance mutations. However, for those infants who had perinatal antiretroviral exposure and genotypic evidence of drug resistance to HIV, the mutations that were detected correlated with at least one antiretroviral from the perinatal period. The prevalence of genotypic drug resistance among this infant cohort is comparable with that found among recently infected adults. These results suggest that resistance testing should be strongly considered for perinatally infected infants, at the earliest possible time point, to avoid use of antiretroviral drugs to which the infant has preexisting resistance.

Accessory Protein 5a Is a Major Antagonist of the Antiviral Action of Interferon against Murine Coronavirus

ABSTRACT The type I interferon (IFN) response plays an essential role in the control of in vivo infection by the coronavirus mouse hepatitis virus (MHV). However, in vitro, most strains of MHV are largely resistant to the action of this cytokine, suggesting that MHV encodes one or more functions that antagonize or evade the IFN system. A particular strain of MHV, MHV-S, exhibited orders-of-magnitude higher sensitivity to IFN than prototype strain MHV-A59. Through construction of interstrain chimeric recombinants, the basis for the enhanced IFN sensitivity of MHV-S was found to map entirely to the region downstream of the spike gene, at the 3′ end of the genome. Sequence analysis revealed that the major difference between the two strains in this region is the absence of gene 5a from MHV-S. Creation of a gene 5a knockout mutant of MHV-A59 demonstrated that a major component of IFN resistance maps to gene 5a. Conversely, insertion of gene 5a, or its homologs from related group 2 coronaviruses, at an upstream genomic position in an MHV-A59/S chimera restored IFN resistance. This is the first demonstration of a coronavirus gene product that can protect that same virus from the antiviral state induced by IFN. Neither protein kinase R, which phosphorylates eukaryotic initiation factor 2, nor oligoadenylate synthetase, which activates RNase L, was differentially activated in IFN-treated cells infected with MHV-A59 or MHV-S. Thus, the major IFN-induced antiviral activities that are specifically inhibited by MHV, and possibly by other coronaviruses, remain to be identified.

Progress in prevention of mother-to-child transmission of HIV in New York State: 1988-2008.

OBJECTIVES To assess the outcomes of efforts to prevent mother-to-child transmission (MTCT) of human immunodeficiency virus (HIV) made over the last 2 decades in New York State (NYS), through review of data from multiple sources. METHODS Using available surveillance, laboratory, and program monitoring data, the following were examined for NYS: (1) the rate of prenatal HIV testing, (2) HIV prevalence among childbearing women, (3) maternal prenatal and delivery care, (4) care of HIV-exposed infants, and (5) the rate of MTCT. Trends over time and comparisons among groups were assessed. RESULTS In NYS, HIV prevalence in childbearing women has declined 70% since its peak in 1989. Rates of prenatal HIV testing have been more than 95% in recent years. Rates of MTCT have decreased significantly; since 2003, transmission in HIV-exposed births has ranged from 1.2% to 2.6% annually. On bivariate analysis, MTCT is more likely to occur with breastfeeding or absence of antiretroviral administration in the prenatal, labor/delivery, and newborn periods. CONCLUSIONS Mother-to-child HIV transmission has declined dramatically in all groups in NYS. Universal newborn screening data have provided the foundation for identifying HIV-exposed births and for initiating follow-up to track all aspects of MTCT in NYS. Remaining challenges include universal prenatal care, prevention of acquisition of HIV infection during pregnancy, and adherence to antiretroviral therapy.

Evolution and recombination of genes encoding HIV-1 drug resistance and tropism during antiretroviral therapy.

Characterization of residual plasma virus during antiretroviral therapy (ART) is a high priority to improve understanding of HIV-1 pathogenesis and therapy. To understand the evolution of HIV-1 pol and env genes in viremic patients under selective pressure of ART, we performed longitudinal analyses of plasma-derived pol and env sequences from single HIV-1 genomes. We tested the hypotheses that drug resistance in pol was unrelated to changes in coreceptor usage (tropism), and that recombination played a role in evolution of viral strains. Recombinants were identified by using Bayesian and other computational methods. High-level genotypic resistance was seen in approximately 70% of X4 and R5 strains during ART. There was no significant association between resistance and tropism. Each patient displayed at least one recombinant encompassing env and representing a change in predicted tropism. These data suggest that, in addition to mutation, recombination can play a significant role in shaping HIV-1 evolution.