Quasispecies Sequences Research Articles

QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.

The existence of quasispecies in the viral population causes difficulties for disease prevention and treatment. High-throughput sequencing provides opportunity to determine rare quasispecies and long sequencing reads covering full genomes reduce quasispecies determination to a clustering problem. The challenge is high similarity of quasispecies and high error rate of long sequencing reads. We developed QuasiSeq using a novel signature-based self-tuning clustering method, SigClust, to profile viral mixtures with high accuracy and sensitivity. QuasiSeq can correctly identify quasispecies even using low-quality sequencing reads (accuracy <80%) and produce quasispecies sequences with high accuracy (≥99.55%). Using high-quality circular consensus sequencing reads, QuasiSeq can produce quasispecies sequences with 100% accuracy. QuasiSeq has higher sensitivity and specificity than similar published software. Moreover, the requirement of the computational resource can be controlled by the size of the signature, which makes it possible to handle big sequencing data for rare quasispecies discovery. Furthermore, parallel computation is implemented to process the clusters and further reduce the runtime. Finally, we developed a web interface for the QuasiSeq workflow with simple parameter settings based on the quality of sequencing data, making it easy to use for users without advanced data science skills. QuasiSeq is open source and freely available at https://github.com/LHRI-Bioinformatics/QuasiSeq. The current release (v1.0.0) is archived and available at https://zenodo.org/badge/latestdoi/340494542. Supplementary data are available at Bioinformatics online.

Viral quasispecies quantitative analysis: a novel approach for appraising the immune tolerant phase of chronic hepatitis B virus infection

ABSTRACT Few non-invasive models were established for precisely identifying the immune tolerant (IT) phase from chronic hepatitis B (CHB). This study aimed to develop a novel approach that combined next-generation sequencing (NGS) and machine learning algorithms using our recently published viral quasispecies (QS) analysis package. 290 HBeAg positive patients from whom liver biopsies were taken were enrolled and divided into a training group (n = 148) and a validation group (n = 142). HBV DNA was extracted and QS sequences were obtained by NGS. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) based on viral operational taxonomic units (OTUs) were performed to explore the correlations among QS and clinical phenotypes. Three machine learning algorithms, including K-nearest neighbour, support vector machine, and random forest algorithm, were used to construct diagnostic models for IT phase classification. Based on histopathology, 90 IT patients and 200 CHB patients were diagnosed. HBsAg titres for IT patients were higher than those of CHB patients (p < 0.001). HCA and PCA analysis grouped IT and CHB patients into two distinct clusters. The relative abundance of viral OTUs differed mainly within the BCP/precore/core region and was significantly correlated with liver inflammation and fibrosis. For the IT phase classification, all machine-learning models showed higher AUC values compared to models based on HBsAg, APRI, and FIB-4. The relative abundance of viral OTUs reflects the severity of liver inflammation and fibrosis. The novel QS quantitative analysis approach could be used to diagnose IT patients more precisely and reduce the need for liver biopsy.

Analysis of HBV X gene quasispecies characteristics by next-generation sequencing and cloning-based sequencing and its association with hepatocellular carcinoma progression.

This study aimed to describe the differences between next-generation sequencing (NGS) and cloning-based sequencing (CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and hepatocellular carcinoma (HCC). A total of 12 serum samples were collected. Serum hepatitis B virus (HBV) DNA was extracted, and the HBV X-region (HBX) was amplified by nested polymerase chain reaction (PCR). The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX. A total of 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity, it was found that the quasispecies complexity value of HBV X-region obtained by NGS was higher than CBS (P < 0.05). The diversity values, including d, dS, dN, an d d N/ dS obtained by NGS were lower than by CBS (all of P < 0.01). The relativity of Spearman(rs) in d, dS, and dN were statistically significant (rs_ d = 0.865, P = 0.001; rs_ dS = 0.722, P = 0.014; and rs_ dN = 0.738, P = 0.011, respectively). There were 21 different bases between the HBX quasispecies of case A and control B. The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high-risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration.

CRISPR/Cas9 Genome Editing to Disable the Latent HIV-1 Provirus.

HIV-1 infection can be successfully controlled with anti-retroviral therapy (ART), but is not cured. A reservoir of cells harboring transcriptionally silent integrated provirus is able to reestablish replicating infection if ART is stopped. Latently HIV-1 infected cells are rare, but may persist for decades. Several novel strategies have been proposed to reduce the latent reservoir, including DNA sequence targeted CRISPR/Cas9 genome editing of the HIV-1 provirus. A significant challenge to genome editing is the sequence diversity of HIV-1 quasispecies present in patients. The high level of quasispecies diversity will require targeting of multiple sites in the viral genome and personalized engineering of a CRISPR/Cas9 regimen. The challenges of CRISPR/Cas9 delivery to the rare latently infected cells and quasispecies sequence diversity suggest that effective genome editing of every provirus is unlikely. However, recent evidence from post-treatment controllers, patients with controlled HIV-1 viral burden following interruption of ART, suggests a correlation between a reduced number of intact proviral sequences and control of the virus. The possibility of reducing the intact proviral sequences in patients by a genome editing technology remains intriguing, but requires significant advances in delivery to infected cells and identification of effective target sites.

Identification of a new hepatitis B virus recombinant D2/D3 in the city of São Paulo, Brazil.

Two hundred forty million people are chronically infected with hepatitis B virus (HBV) worldwide. The rise of globalization has facilitated the emergence of novel HBV recombinants and genotypes. We evaluated HBV genotypes and recombinants, mutations associated with resistance to antivirals (AVs), progression of hepatic illness, and inefficient hepatitis B vaccination responses in chronically infected individuals in the city of São Paulo, Brazil. Forty-five full-length and 24 partial-length sequences were obtained. The genotype distribution was as follows: A (66.7%), D (15.9%), F (11.6%) and C (4.3%). We describe a new recombinant (D2/D3), confirmed through next-generation sequencing (NGS) and reconstruction of the quasispecies sequences in silico. Primary resistance and major vaccine escape mutations were not found. We did, however, find mutations in the S region that might may be related to HBV antigenicity changes, as well as Pre-S deletions. The precore/core mutations A1762T+G1764A (40.9%) were found mostly in genotypes A and D, and G1896A (29.55%) was more frequent in genotype D than in genotype A. The genotypic distribution reflects the history of Brazilian immigration. This is the first description of recombination between genotypes D2 and D3 in Brazil. It is also the first confirmation through NGS and reconstruction of the quasispecies in silico. However, little is known about the response to treatment of recombinants. This demonstrates the need for molecular epidemiology studies involving the analysis of full-length HBV sequences.

Multi-layered Gag-specific immunodominant responses contribute to improved viral control in the CRF01_AE subtype of HIV-1-infected MSM subjects.

BackgroundThe purpose of this study was to characterize specific cytotoxic T-cell (CTL) responses in men who have sex with men (MSM) subjects infected with the human immunodeficiency virus type 1 (HIV-1) CRF01_AE subtype during the first year of infection and impacts on viral control and evolution.ResultsFifteen HIV-1 primary infected cases were recruited from Liaoning MSM prospective cohort. CTL responses to Gag, Pol and Nef proteins at 3 month and 1 year post infection were detected with Gamma interferon enzyme-linked immunospot (ELISPOT) assay using optimized consensus overlapping peptides, as well as the viral quasispecies sequences from the synchronous plasma. Gag and Nef proteins were the main targets of CTL responses during the first year of HIV-1 infection, and this was evident from the data after adjusting for the length of amino acids by dividing the amino acids number of the corresponding protein and multiplying by 100. Additionally, relative magnitudes of Gag at both 3 months and 1 year post infection were significantly negatively correlated with the viral set point (p = 0.002, r = −0.726; p = 0.025, r = −0.574). While the relative magnitude of Nef at 1 year post infection were significantly positively correlated with viral set point (p = 0.004, r = 0.697). Subjects with multi-layered Gag immunodominant responses during the first year of infection had significantly lower viral set points than subjects without such responses (p = 0.002).ConclusionMulti-layered Gag immunodominant responses during the first year of infection were correlated with viral control, which provides a theoretical basis for vaccine design targeting MSM subjects with the CRF01_AE subtype.Electronic supplementary materialThe online version of this article (doi:10.1186/s12865-016-0166-8) contains supplementary material, which is available to authorized users.

Naturally occurring deletion/insertion mutations within HBV whole genome sequences in HBeAg-positive chronic hepatitis B patients are correlated with baseline serum HBsAg and HBeAg levels and might predict a shorter interval to HBeAg loss and seroconversion during antiviral treatment

ObjectivesDeletion/insertion (Del/Ins) throughout hepatitis B virus (HBV) genome has not been well studied for HBeA-positive chronic hepatitis B (CHB) patients. This study aimed to characterize the HBV Del/Ins mutations in full-length genome quasispecies sequences in such patients at antiviral baseline and to reveal their potential impacts on HBV serological markers and responses to nucleos(t)ide analogue (NUC) treatment. Materials and methodsA total of 30 HBeAg-positive CHB patients with genotype C infection receiving a 104-week lamivudine (LMV) and adefovir dipivoxil (ADV) combination therapy were enrolled. HBV whole genome sequences in serum samples at baseline were clone sequenced and analyzed using bioinformatics tools. ResultsAmong 306 unspliced clone sequences, 61.8% (189/306) had Del/Ins mutations, 38.2% (117/306) were full-length genomes without any Del/Ins. Due to different combinations of 125 deletion types and 45 insertion types, we identified 55 Del/Ins-harboring HBV genome patterns, which affected a single or several functional genomic regions. Importantly, the proportion of Del/Ins-harboring clones was found to be significantly negatively correlated with HBsAg (r=−0.3985, P=0.0292) and HBeAg (r=−0.3878, P=0.0342) at baseline. Higher percentage of Del/Ins-harboring clones at baseline was found to predict a shorter interval to HBeAg loss and seroconversion. ConclusionDel/Ins mutations within HBV whole genome were prevalent in HBeAg-positive CHB patients prior to antiviral treatment. A higher detection rate of these mutations at baseline might correlate with a better response to LMV and ADV combination therapy.

Outbreak of hepatitis C virus infection associated with narcotics diversion by an hepatitis C virus–infected surgical technician

Drug diversion by health care personnel poses a risk for serious patient harm. Public health identified 2 patients diagnosed with acute hepatitis C virus (HCV) infection who shared a common link with a hospital. Further investigation implicated a drug-diverting, HCV-infected surgical technician who was subsequently employed at an ambulatory surgical center. Patients at the 2 facilities were offered testing for HCV infection if they were potentially exposed. Serum from the surgical technician and patients testing positive for HCV but without evidence of infection before their surgical procedure was further tested to determine HCV genotype and quasi-species sequences. Parenteral medication handling practices at the 2 facilities were evaluated. The 2 facilities notified 5970 patients of their possible exposure to HCV, 88% of whom were tested and had results reported to the state public health departments. Eighteen patients had HCV highly related to the surgical technician's virus. The surgical technician gained unauthorized access to fentanyl owing to limitations in procedures for securing controlled substances. Public health surveillance identified an outbreak of HCV infection due to an infected health care provider engaged in diversion of injectable narcotics. The investigation highlights the value of public health surveillance in identifying HCV outbreaks and uncovering a method of drug diversion and its impacts on patients.

Automated sequence analysis and editing software for HIV drug resistance testing

BackgroundAccess to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. ObjectivesTo develop an automated sequence analysis and editing software to support high throughput automated sequencing. Study designThe ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. ResultsThe ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR–RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. ConclusionsThe ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

BackgroundRNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.ResultsIn this paper, we introduce a new Viral Spectrum Assembler (ViSpA) method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons), and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at http://alla.cs.gsu.edu/~software/VISPA/vispa.html.ConclusionsViSpA enables accurate viral quasispecies spectrum reconstruction from 454 pyrosequencing reads. We are currently exploring extensions applicable to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.

QColors: an algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads.

Next generation sequencing technologies have recently been applied to characterize mutational spectra of the heterogeneous population of viral genotypes (known as a quasispecies) within HIV-infected patients. Such information is clinically relevant because minority genetic subpopulations of HIV within patients enable viral escape from selection pressures such as the immune response and antiretroviral therapy. However, methods for quasispecies sequence reconstruction from next generation sequencing reads are not yet widely used and remains an emerging area of research. Furthermore, the majority of research methodology in HIV has focused on 454 sequencing, while many next-generation sequencing platforms used in practice are limited to shorter read lengths relative to 454 sequencing. Little work has been done in determining how best to address the read length limitations of other platforms. The approach described here incorporates graph representations of both read differences and read overlap to conservatively determine the regions of the sequence with sufficient variability to separate quasispecies sequences. Within these tractable regions of quasispecies inference, we use constraint programming to solve for an optimal quasispecies subsequence determination via vertex coloring of the conflict graph, a representation which also lends itself to data with non-contiguous reads such as paired-end sequencing. We demonstrate the utility of the method by applying it to simulations based on actual intra-patient clonal HIV-1 sequencing data.

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

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. 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. 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. 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.

Establishment of an end-point limiting-dilution PCR assay for detection of human immunodeficiency virus type 1 quasispecies

Objective To establish a novel end-point limiting-dilution PCR (EPLD-PCR) assay to detect human immunodeficieney virus type 1 (HIV-1) quasispecies and evaluate its application value. Methods The multiplex limiting-dilution nested PCR base on the second round TaqMan real time PCR ( N-RT PCR) and regular PCR, end-point PCR and sequencing technology were used for detection of the sequences of HIV-1 quasispecies env gene c2-v3-c3 region and gag gene p17 region from the PBMCs of 3 HIV-1 infected patients with low level viral load. All sequences of c2-v3-c3 and p17 were confirmed by sequencing. Phylogenetic tree analysis for nucleetide sequences and alignment analysis for amino acid sequences were performed to evaluate the result of HIV-1 quasispecies assay. The HIV-1 DNA copy number in per million PBMCs was calculated by QUALITY program. Results Total 1 207 N-RT PCRs were carried out for all 3 patients' samples from different visiting time points. Sixty-five sequences of c2-v3-c3 and 101 sequences of p17 were obtained from regular nested second round PCRs; the quantification of HIV-1 DNA in per million PBMCs from 3 patients was between 1.34 copies to 53.76 copies. Phylogenetic tree analysis for all nucleotide sequences showed that the sequences in different patients were separated and they got together specially in the same patient. Amino acid sequences alignment analysis showed that HIV-1 quasispecies sequences were simplex at early stage of infection and became more complex alone with increase of infected time. Conclusions The end-point limiting-dilution real-time PCR technology described in this study is a novel, sensitive, specific and high throughput PCR assay to detect human immunedeficiency virus type 1 quasispecies. This PCR assay could be applied for detection of HIV-1 quasispecies in HIV-1 infected populations with low level viral load. Key words: HIV-1 ; Polymerase chain reaction

Seroconversion to hepatitis C virus alternate reading frame protein during acute infection #

The existence of hepatitis C virus (HCV) proteins encoded by alternate reading frames overlapping the core-encoding region has been suggested. Several mechanisms of production have been postulated, and the functions of these proteins in the HCV life cycle remain unknown. We analyzed cases of seroconversion to an alternate reading frame protein in a group of 17 patients infected by one of the two HCV genotype 1b strains during an outbreak in a hemodialysis unit. Three patients seroconverted, and antibodies were transiently detected in another patient. Three of these patients were infected by one of the two HCV strains, whereas the strain infecting the remaining patient could not be identified. Quasispecies sequence analysis of the core-coding region showed no differences in the core or +1 reading frame sequences that could explain alternate reading frame protein seroconversion in some but not all of the patients infected by one of the HCV strains, and no such difference was found between the two strains. Because differences in the structure of RNA elements could play a role in frameshift events, we conducted a predictive analysis of RNA folding. No difference was found between the patients who did and did not seroconvert to alternate reading frame protein. Our findings prove that alternate reading frame proteins can be produced during acute HCV infection. However, seroconversion does not occur in all patients for unknown reasons. Alternate reading frame protein could be generated by minority quasispecies variants or variants that occur transiently.

The Nonstructural 5A Protein of Hepatitis C Virus Genotype 1b Does Not Contain an Interferon Sensitivity–Determining Region

The nonstructural (NS) 5A protein of hepatitis C virus (HCV) has been suggested to contain an interferon (IFN) sensitivity-determining region (ISDR). We studied whether the degree of viral decline on day 1 is associated with differences in NS5A amino acid sequences among patients receiving IFN- alpha. Phylogenetic analyses of the full-length protein and of functional domains showed no relationship between the baseline protein sequence and the antiviral response. NS5A quasispecies sequences showed no differences in the number of mutations in the putative ISDR relative to a prototype sequence between responders and nonresponders or according to IFN- alpha antiviral efficacy. No relationship was found between antiviral efficacy at 24 h and the baseline sequence of any NS5A region. Amino acid changes were observed in a few cases at 24 h in both responders and nonresponders, but no consistent pattern of amino acid shifts was observed, ruling out the possibility that IFN- alpha selected IFN-resistant variants. Our findings show that there is no ISDR in the HCV genotype 1 NS5A protein and that the NS5A sequence does not influence the capacity of IFN- alpha to block viral replication. The findings do not rule out a role for NS5A in subsequent viral clearance.

Hepatitis C Virus Infections From a Contaminated Radiopharmaceutical Used in Myocardial Perfusion Studies

Nuclear pharmacies prepare radiopharmaceutical products for use in common diagnostic procedures, including myocardial perfusion studies. Hepatitis C virus (HCV) transmission has not been reported previously in the setting of nuclear imaging studies. To investigate an outbreak of acute HCV infection identified among patients who underwent myocardial perfusion studies on October 15, 2004, using an injected radiopharmaceutical. Outbreak investigation including molecular epidemiology and pharmacy site investigation at outpatient cardiology clinics and a nuclear pharmacy in Maryland. Ninety patients who received injections drawn from select radiopharmaceutical vials prepared on October 14-15, 2004, at a single nuclear pharmacy were offered testing for bloodborne pathogens. Pharmacy procedures were reviewed and HCV quasi species analysis was performed. Hepatitis C virus infection and quasispecies sequence similarity. Sixteen patients with acute HCV infection were identified from 3 separate clinics. All patients received radiopharmaceutical injections drawn from a single pharmacy vial (vial 1). None of the 59 tested patients who received doses from 6 other vials had acute HCV infection. Blood from a potential source patient with HCV and human immunodeficiency virus (HIV) infection was processed for a radiolabeled white blood cell study in the pharmacy 12 hours before vial 1 was prepared. The HCV quasispecies sequences from this potential source patient were nearly identical to those from cases (97.8%-98.5% similarity). No acute HIV infections were identified. Pharmacy practices that could have led to blood cross-contamination included reuse of needles and syringes during dilutions and use of common flow hoods for some steps in the preparation of sterile and blood-derived products. Sixteen persons acquired HCV infection from a blood-contaminated radiopharmaceutical. The source and practices that could have facilitated breaks in aseptic technique were identified at the pharmacy. Nuclear pharmacies that handle biological products should follow appropriate aseptic technique to prevent contamination of sterile radiopharmaceuticals.

SIVsm Quasispecies Adaptation to a New Simian Host

Despite the potential for infectious agents harbored by other species to become emerging human pathogens, little is known about why some agents establish successful cross-species transmission, while others do not. The simian immunodeficiency viruses (SIVs), certain variants of which gave rise to the human HIV-1 and HIV-2 epidemics, have demonstrated tremendous success in infecting new host species, both simian and human. SIVsm from sooty mangabeys appears to have infected humans on several occasions, and was readily transmitted to nonnatural Asian macaque species, providing animal models of AIDS. Here we describe the first in-depth analysis of the tremendous SIVsm quasispecies sequence variation harbored by individual sooty mangabeys, and how this diverse quasispecies adapts to two different host species—new nonnatural rhesus macaque hosts and natural sooty mangabey hosts. Viral adaptation to rhesus macaques was associated with the immediate amplification of a phylogenetically related subset of envelope (env) variants. These variants contained a shorter variable region 1 loop and lacked two specific glycosylation sites, which may be selected for during acute infection. In contrast, transfer of SIVsm to its natural host did not subject the quasispecies to any significant selective pressures or bottleneck. After 100 d postinfection, variants more closely representative of the source inoculum reemerged in the macaques. This study describes an approach for elucidating how pathogens adapt to new host species, and highlights the particular importance of SIVsm env diversity in enabling cross-species transmission. The replicative advantage of a subset of SIVsm variants in macaques may be related to features of target cells or receptors that are specific to the new host environment, and may involve CD4-independent engagement of a viral coreceptor conserved among primates.

Transmissions nosocomiales de l'h�patite C de patient � patient, li�es � l'anesth�sie g�n�rale dans l'inter-r�gion Nord en 2001?2002

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.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.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.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.

Interferon resistance of hepatitis C virus genotype 1b: relationship to nonstructural 5A gene quasispecies mutations.

A 40-amino-acid sequence located in the nonstructural 5A (NS5A) protein of hepatitis C virus genotype 1b (HCV-1b) was recently suggested to be the interferon sensitivity-determining region (ISDR), because HCV-1b strains with an ISDR amino acid sequence identical to that of the prototype strain HCV-J were found to be resistant to alpha interferon (IFN-alpha) whereas strains with amino acid substitutions were found to be sensitive (N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, N. Izumi, F. Marumo, and C. Sato, J. Clin. Invest. 96:224-230, 1995; N. Enomoto, I. Sakuma, Y. Asahina, M. Kurosaki, T. Murakami, C. Yamamoto, Y. Ogura, N. Izumi, F. Marumo, and C. Sato, N. Engl. J. Med. 334:77-81, 1996). We used single-strand conformation polymorphism (SSCP) analysis, combined with cloning and sequencing strategies, to characterize NS5A quasispecies in HCV-1b-infected patients and determine the relationships between pre- and posttreatment NS5A quasispecies mutations and the IFN-alpha sensitivity of HCV-1b. The serine residues involved in phosphorylation of NS5A protein were highly conserved both in the various patients and in quasispecies in a given patient, suggesting that phosphorylation is important in NS5A protein function. A hot spot for amino acid substitutions was found at positions 2217 to 2218; it could be the result of either strong selection pressure or tolerance to these amino acid replacements. The proportion of synonymous mutations was significantly higher than the proportion of nonsynonymous mutations, suggesting that genetic variability in the region studied was the result of high mutation rates and viral replication kinetics rather than of positive selection. Sustained HCV RNA clearance was associated with low viral load and low nucleotide sequence entropy, suggesting (i) that the replication kinetics when treatment is started plays a critical role in HCV-1b sensitivity to IFN-alpha and (ii) that HCV-1b resistance to IFN-alpha could be conferred by numerous and/or related mutations that could be patient specific and located at different positions throughout the viral genome and could allow escape variants to be selected by IFN-alpha-stimulated immune responses. No NS5A sequence appeared to be intrinsically resistant or sensitive to IFN-alpha, but the HCV-J sequence was significantly more frequent in nonresponder quasispecies than in sustained virological responder quasispecies, suggesting that the balance between NS5A quasispecies sequences in infected patients could have a subtle regulatory influence on HCV replication.

Molecular Epidemiology of HIV-1 Based on Phylogenetic Analysis of in Vivo gag p7/p9 Direct Sequences

Viruses of different geographical origin are circulating in Finland. We wanted to test whether phylogenetic analysis of patient lymphocyte proviral quasispecies sequences could be used to group different strains into genetic lineages. The gag p7/p9 coding region was analyzed using solid-phase direct sequencing from 30 patients in Finland and Estonia. Proviral sequences were found to represent at least four, possibly even five, different, highly diverged major lineages. Different methods of phylogenetic analysis resulted in the same conclusion. Serial samples from the same patients, taken over a period of several years showed limited variation over time. Cases of potential patient-to-patient transmission or common source of infection were identified based on the sequence analysis. Compared to similar analyses of longer genome segments, the gag p7/p9 nucleic acid binding protein coding region produces analogous results in phylogenetic analysis. The method can be used as a rapid way of determining the genetic subtype of HIV-1 strains circulating in populations.