Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance

Background

In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola.

Methods

We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction.

Results

The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa.

Conclusion

A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.

Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

Background

The vast majority of phylogenetic trees are inferred from molecular sequence data (nucleotides or amino acids) using time-reversible evolutionary models which assume that, for any pair of nucleotide or amino acid characters, the relative rate of X to Y substitution is the same as the relative rate of Y to X substitution. However, this reversibility assumption is unlikely to accurately reflect the actual underlying biochemical and/or evolutionary processes that lead to the fixation of substitutions. Here, we use empirical viral genome sequence data to reveal that evolutionary non-reversibility is pervasive among most groups of viruses. Specifically, we consider two non-reversible nucleotide substitution models: (1) a 6-rate non-reversible model (NREV6) in which Watson-Crick complementary substitutions occur at identical relative rates and which might therefor be most applicable to analyzing the evolution of genomes where both complementary strands are subject to the same mutational processes (such as might be expected for double-stranded (ds) RNA or dsDNA genomes); and (2) a 12-rate non-reversible model (NREV12) in which all relative substitution types are free to occur at different rates and which might therefore be applicable to analyzing the evolution of genomes where the complementary genome strands are subject to different mutational processes (such as might be expected for viruses with single-stranded (ss) RNA or ssDNA genomes).

Results

Using likelihood ratio and Akaike Information Criterion-based model tests, we show that, surprisingly, NREV12 provided a significantly better fit to 21/31 dsRNA and 20/30 dsDNA datasets than did the general time reversible (GTR) and NREV6 models with NREV6 providing a better fit than NREV12 and GTR in only 5/30 dsDNA and 2/31 dsRNA datasets. As expected, NREV12 provided a significantly better fit to 24/33 ssDNA and 40/47 ssRNA datasets. Next, we used simulations to show that increasing degrees of strand-specific substitution bias decrease the accuracy of phylogenetic inference irrespective of whether GTR or NREV12 is used to describe mutational processes. However, in cases where strand-specific substitution biases are extreme (such as in SARS-CoV-2 and Torque teno sus virus datasets) NREV12 tends to yield more accurate phylogenetic trees than those obtained using GTR.

Conclusion

We show that NREV12 should, be seriously considered during the model selection phase of phylogenetic analyses involving viral genomic sequences.

SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic

COVID-19 was first diagnosed in Egypt on 14 February 2020. By the end of November 2021, over 333,840 cases and 18,832 deaths had been reported. As part of the national genomic surveillance, 1027 SARS-CoV-2 near whole-genomes were generated and published by the end of July 2021. Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analyzed together with a representative set of global sequences within a phylogenetic framework. A single lineage, C.36, introduced early in the pandemic was responsible for most of the cases in Egypt. Furthermore, to remain dominant in the face of mounting immunity from previous infections and vaccinations, this lineage acquired several mutations known to confer an adaptive advantage. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and the need for enforcement of public health measures to prevent expansion of the existing lineages.

Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is adaptively evolving to ensure its persistence within human hosts. It is therefore necessary to continuously monitor the emergence and prevalence of novel variants that arise. Importantly, some mutations have been associated with both molecular diagnostic failures and reduced or abrogated next-generation sequencing (NGS) read coverage in some genomic regions. Such impacts are particularly problematic when they occur in genomic regions such as those that encode the spike (S) protein, which are crucial for identifying and tracking the prevalence and dissemination dynamics of concerning viral variants. Targeted Sanger sequencing presents a fast and cost-effective means to accurately extend the coverage of whole-genome sequences. We designed a custom set of primers to amplify a 401 bp segment of the receptor-binding domain (RBD) (between positions 22698 and 23098 relative to the Wuhan-Hu-1 reference). We then designed a Sanger sequencing wet-laboratory protocol. We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing. Finally, we developed SeqPatcher, a Python-based computational tool to analyse the trace files yielded by Sanger sequencing to generate consensus sequences, or take preanalysed consensus sequences in fasta format, and merge them with their corresponding whole-genome assemblies. We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples. Additionally, one sample had the Y508F mutation and four samples the S477N. Samples with RT-PCR Ct scores ranging from 13.85 to 37.47 (mean=25.70) could be Sanger sequenced efficiently. These results show that our method and pipeline can be used to improve the quality of whole-genome assemblies produced using NGS and can be used with any pairs of the most used NGS and Sanger sequencing platforms.

Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies

The mitogen-activated protein kinase (MAPK) pathways are crucial regulators of the cellular processes that fuel the malignant transformation of normal cells. The molecular aberrations which lead to cancer involve mutations in, and transcription variations of, various MAPK pathway genes. Here, we examine the genome sequences of 40,848 patient-derived tumours representing 101 distinct human cancers to identify cancer-associated mutations in MAPK signalling pathway genes. We show that patients with tumours that have mutations within genes of the ERK-1/2 pathway, the p38 pathways, or multiple MAPK pathway modules, tend to have worse disease outcomes than patients with tumours that have no mutations within the MAPK pathways genes. Furthermore, by integrating information extracted from various large-scale molecular datasets, we expose the relationship between the fitness of cancer cells after CRISPR mediated gene knockout of MAPK pathway genes, and their dose-responses to MAPK pathway inhibitors. Besides providing new insights into MAPK pathways, we unearth vulnerabilities in specific pathway genes that are reflected in the re sponses of cancer cells to MAPK targeting drugs: a revelation with great potential for guiding the development of innovative therapies.

Creating a model to predict time intervals from induction of labor to induction of anesthesia and delivery to coordinate workload

BACKGROUND

Induction of labor continues to become more common. We analyzed induction of labor and timing of obstetric and anesthesia work to create a model to predict the induction-anesthesia interval and the induction-delivery interval in order to co-ordinate workload to occur when staff are most available.

METHODS

Patients who underwent induction of labor at a single medical center were identified and multivariable linear regression was used to model anesthesia and delivery times. Data were collected on date of birth, race/ethnicity, body mass index, gestational age, gravidity, parity, indication for labor induction, number of prior deliveries, time of induction, induction agent, cervical dilation, effacement, and fetal station on admission, date and time of anesthesia administration, date and time of delivery, and delivery type.

RESULTS

A total of 1746 women met inclusion criteria. Associations which significantly influenced time from induction of labor to anesthesia and delivery included maternal age (anesthesia P <0.001, delivery P =0.002), body mass index (both P <0.001), prior vaginal delivery (both P <0.001), gestational age (anesthesia P <0.001, delivery P <0.018), simplified Bishop score (both P <0.001), and first induction agent (both P <0.001). Induction of labor of nulliparous women at 02:00 h and parous women at 04:00 or 05:00 h had the highest estimated probability of the mother having her first anesthesia encounter and delivering during optimally staffed hours when our institution's specialty personnel are most available.

CONCLUSIONS

Time to obstetric and anesthesia tasks can be estimated to optimize induction of labor start times, and shift anesthesia and delivery workload to hours when staff are most available.

Metabolic gene alterations impact the clinical aggressiveness and drug responses of 32 human cancers

Malignant cells reconfigure their metabolism to support oncogenic processes such as accelerated growth and proliferation. The mechanisms by which this occurs likely involve alterations to genes that encode metabolic enzymes. Here, using genomics data for 10,528 tumours of 32 different cancer types, we characterise the alterations of genes involved in various metabolic pathways. We find that mutations and copy number variations of metabolic genes are pervasive across all human cancers. Based on the frequencies of metabolic gene alterations, we further find that there are two distinct cancer supertypes that tend to be associated with different clinical outcomes. By utilising the known dose-response profiles of 825 cancer cell lines, we infer that cancers belonging to these supertypes are likely to respond differently to various anticancer drugs. Collectively our analyses define the foundational metabolic features of different cancer supertypes and subtypes upon which discriminatory strategies for treating particular tumours could be constructed.

Combined spinal/caudal catheter anesthesia: extending the boundaries of regional anesthesia for complex pediatric urological surgery

BACKGROUND

Spinal anesthesia (SA) is an established anesthetic technique for short outpatient pediatric urological cases. To avoid general anesthesia (GA) and expand regional anesthetics to longer and more complex pediatric surgeries, the authors began a program using a combined spinal/caudal catheter (SCC) technique.

STUDY DESIGN

The authors retrospectively reviewed the charts of all patients scheduled for surgery under SCC between December 2016 and April 2018 and recorded age, gender, diagnosis, procedure, conversion to GA/airway intervention, operative time, neuraxial and intravenous medications administered, complications, and outcomes. The SCC technique typically involved an initial intrathecal injection of 0.5% isobaric bupivacaine followed by placement of a caudal epidural catheter. At the discretion of the anesthesiologist, patients received 0.5 mg per kilogram of oral midazolam approximately 30 min prior to entering the operating room. One hour after the intrathecal injection, 3% chloroprocaine was administered via the caudal catheter to prolong the duration of surgical block. Intra-operative management included either continuous infusion or bolus dosing of dexmedetomidine, as needed, for patient comfort and to optimize surgical conditions. Prior to removal of caudal catheter in the post-anesthesia care unit, a supplemental bolus dose of local anesthesia was given through the catheter to provide prolonged post-operative analgesia.

RESULTS

Overall, 23 children underwent attempted SCC. SA was unsuccessful in three patients, and surgery was performed under GA. The remaining 20 children all had successful SCC placement. There were 11 girls and nine boys, with a mean age of 16.5 months (3.3-43.8). Surgeries performed under SCC included seven ureteral reimplantations, two ureterocele excisions/reimplantations, two megaureter repairs, four first-stage hypospadias repairs, one distal hypospadias repair, one second-stage hypospadias repair, two feminizing genitoplasties, and one open pyeloplasty. Average length of surgery was 109 min (range 63-172 min). Pre-operative midazolam was given in 13/20 (65%). All SCC patients were spontaneously breathing room air during the operation, and there were no airway interventions. Only one SCC patient received opioids intra-operatively. There were no intra-operative or perioperative complications.

DISCUSSION

This pilot study shows that the technique of SCC allows one to do more complex urologic surgery under regional anesthesia than what would be possible under pure SA alone. The main limitations of the study include the relatively small number of patients and the small median length of the operative procedures. As a proof of concept, however, this does show that complex genital surgery bladder level procedures such as ureteral reimplantation can be performed under regional anesthesia.

CONCLUSION

SCC allows for more complex surgeries to be performed exclusively under regional anesthesia, thus obviating the need for airway intervention, minimizing or eliminating the use of opioids, and thus avoiding known and potential risks associated with GA. The latter is of particular importance given current concerns regarding hypothetical neurocognitive effects of GA on children aged below 3 years.

Need for additional anesthesia after single injection spinal analgesia for labor: a retrospective cohort study

BACKGROUND

There is little information about the use and efficacy of single injection spinal blocks for labor analgesia; specifically, how frequently subsequent analgesia or anesthesia is needed. This study determined how frequently an additional anesthetic intervention was needed in women who received single injection spinal analgesia.

METHODS

This retrospective study examined electronic medical records to find all single injection spinal analgesic blocks for labor analgesia over a 14-year (2003-2016) period. Patient and block characteristics and patient outcomes were recorded. The primary outcome was need for an additional anesthetic intervention following single injection spinal for labor analgesia.

RESULTS

Four-hundred-and-twenty-eight patients received single injection spinal blocks for labor and 60 (14.0%) needed an additional anesthetic either for labor analgesia (n=49) or an unexpected procedure (n=11). Two of these (0.5%) required general anesthesia. Parity of zero (nulliparous), a low cervical dilation at the time of the spinal injection, and induction of labor status, were associated with an increased risk of needing an additional anesthetic intervention.

CONCLUSIONS

This retrospective review provides evidence that single injection spinal anesthesia may be used for multiparous women with spontaneous labor and more advanced cervical dilation.

Association between exposure to anaesthesia and surgery and long-term cognitive trajectories in older adults: report from the Mayo Clinic Study of Aging

BACKGROUND

The link between exposure to general anaesthesia and surgery (exposure) and cognitive decline in older adults is debated. We hypothesised that it is associated with cognitive decline.

METHODS

We analysed the longitudinal cognitive function trajectory in a cohort of older adults. Models assessed the rate of change in cognition over time, and its association with exposure to anaesthesia and surgery. Analyses assessed whether exposure in the 20 yr before enrolment is associated with cognitive decline when compared with those unexposed, and whether post-enrolment exposure is associated with a change in cognition in those unexposed before enrolment.

RESULTS

We included 1819 subjects with median (25th and 75th percentiles) follow-up of 5.1 (2.7-7.6) yr and 4 (3-6) cognitive assessments. Exposure in the previous 20 yr was associated with a greater negative slope compared with not exposed (slope: -0.077 vs -0.059; difference: -0.018; 95% confidence interval: -0.032, -0.003; P=0.015). Post-enrolment exposure in those previously unexposed was associated with a change in slope after exposure (slope: -0.100 vs -0.059 for post-exposure vs pre-exposure, respectively; difference: -0.041; 95% confidence interval: -0.074, -0.008; P=0.016). Cognitive impairment could be attributed to declines in memory and attention/executive cognitive domains.

CONCLUSIONS

In older adults, exposure to general anaesthesia and surgery was associated with a subtle decline in cognitive z-scores. For an individual with no prior exposure and with exposure after enrolment, the decline in cognitive function over a 5 yr period after the exposure would be 0.2 standard deviations more than the expected decline as a result of ageing. This small cognitive decline could be meaningful for individuals with already low baseline cognition.

Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes

Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients have remained poor. Besides being highly metastatic, pancreatic cancer is challenging to treat because it is caused by a heterogeneous array of somatic mutations that impact a variety of signaling pathways and cellular regulatory systems. Here we use publicly available transcriptomic, copy number alteration and mutation profiling datasets from pancreatic cancer patients together with data on disease outcomes to show that the three major pancreatic cancer subtypes each display distinctive aberrations in cell signaling and metabolic pathways. Importantly, patients afflicted with these different pancreatic cancer subtypes also exhibit distinctive survival profiles. Within these patients, we find that dysregulation of the phosphoinositide 3-kinase and mitogen-activated protein kinase pathways, and p53 mediated disruptions of cell cycle processes are apparently drivers of disease. Further, we identify for the first time the molecular perturbations of signalling networks that are likely the primary causes of oncogenesis in each of the three pancreatic cancer subtypes.

Increase in taxonomic assignment efficiency of viral reads in metagenomic studies

Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms. Here, based on published and original metagenomic datasets coming from virus-like particle enriched samples, we present and quantify the improvement of viral taxonomic assignment that is achievable with a new similarity-based approach. Indeed, prior to any use of similarity based taxonomic assignment methods, we propose assembling contigs from short reads as is currently routinely done in metagenomic studies, but then to further map unassembled reads to the assembled contigs. This additional mapping step increases significantly the proportions of taxonomically assignable sequence reads from a variety -plant, insect and environmental (estuary, lakes, soil, feces) - of virome studies.

Zika virus complete genome from Salvador, Bahia, Brazil

In May 2015 the first autochthonous Zika virus infection was reported in Brazil. Rapid and urgent measures are needed to contain the ongoing outbreak. Here we report the full-length ZIKV coding sequence from Bahia. Genetic analysis of outbreak sequences will be essential for characterizing the diversity of circulating strains, identifying hotspots of virus transmission and guiding public health control. Rapid and urgent measures are needed to contain the ongoing outbreak.

Biodegradable polymeric stents for vascular application in a porcine carotid artery model: English version

Over the past years the development of biodegradable polymeric stents has made great progress; nevertheless, essential problems must still be solved. Modifications in design and chemical composition should optimize the quality of biodegradable stents and remove the weaknesses. New biodegradable poly-L-lactide/poly-4-hydroxybutyrate (PLLA/P4HB) stents and permanent 316L stents were implantedendovascularly into both common carotid arteries of 10 domestic pigs. At 4 weeks following implantation, computed tomography (CT) angiography was carried out to identify the distal degree of stenosis. The PLLA/P4HB group showed a considerably lower distal degree of stenosis by additional oral application of atorvastatin (mean 39.81 ± 8.57 %) compared to the untreated PLLA/P4HB group without atorvastatin (mean 52.05 ± 5.80 %). The 316L stents showed no differences in the degree of distal stenosis between the group treated with atorvastatin (mean 44.21 ± 2.34 %) and the untreated group (mean 35.65 ± 3.72 %). Biodegradable PLLA/P4HB stents generally represent a promising approach to resolving the existing problems in the use of permanent stents. Restitutio ad integrum is only achievable if a stent is completely degraded.

Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011

Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

Differential disease phenotype of begomoviruses associated with tobacco leaf curl disease in Comoros

In the 2000s, tobacco plantations on the Comoros Islands were afflicted with a previously unobserved tobacco leaf curl disease characterised by symptoms of severe leaf curling and deformation. Previous molecular characterization of potential viral pathogens revealed a complex of African monopartite tobacco leaf curl begomovirus (TbLCVs). Our molecular investigation allowed the characterization of a new monopartite virus involved in the disease: tomato leaf curl Namakely virus (ToLCNamV). Agroinoculation experiments indicated that TbLCVs and tomato leaf curl viruses (ToLCVs) can infect both tomato and tobacco but that infectivity and symptom expression fluctuate depending on the virus and the plant cultivar combination.

Treatment of cavernous sinus tumors with linear accelerator radiosurgery

Since 1989, 79 patients with benign or malignant cavernous sinus tumors, have been treated at Stanford University with linear accelerator (linac) radiosurgery. Radiosurgery has been used as (1) a planned second-stage procedure for residual tumor following surgery, (2) primary treatment for patients whose medical conditions preclude surgery, (3) palliation of malignant lesions, and (4) definitive treatment for small, well-localized, poorly accessible tumors. Mean patient age was 52 years (range, 18 to 88); there were 28 males and 51 females. Sixty-one patients had benign tumors; 18 had malignant tumors. Mean tumor volume was 6.8 cm(3) (range 0.5 to 22.5 cm(3)) covered with an average of 2.3 isocenter (range, 1 to 5). Radiation dose averaged 17.1 Gy. Mean follow-up was 46 months. Tumor control or shrinkage, or both, varied with pathology. Radiographic tumor improvement was most pronounced in malignant lesions, with greater than 85% showing reduction in tumor size; benign tumors (meningiomas and schwannomas) had a 63% control rate and 37% shrinkage rate, with none enlarging. We concluded that stereotactic radiosurgery is a valuable tool in managing cavernous sinus tumors. There was excellent control and stabilization of benign tumors and palliation of malignant lesions.

NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments

SUMMARY

Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pair probabilities, alignment uncertainty, covarying sites and evolutionary conservation to identify biologically relevant secondary structures within multiple sequence alignments. Unique to NASP is the consideration of all this information together with a recursive permutation-based approach to progressively identify and list the most conserved probable secondary structures that are likely to have the greatest biological relevance. By focusing on identifying only evolutionarily conserved structures, NASP forgoes the prediction of complete nucleotide folds but outperforms various other secondary structure prediction methods in its ability to selectively identify actual base pairings.

AVAILABILITY

Downloable and web-based versions of NASP are freely available at http://web.cbio.uct.ac.za/~yves/nasp_portal.php

CONTACT

yves@cbio.uct.ac.za

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure

It is unresolved whether recently transmitted human immunodeficiency viruses (HIV) have genetic features that specifically favour their transmissibility. To identify potential "transmission signatures", we compared 20 full-length HIV-1 subtype C genomes from primary infections, with 66 sampled from ethnically and geographically matched individuals with chronic infections. Controlling for recombination and phylogenetic relatedness, we identified 39 sites at which amino acid frequency spectra differed significantly between groups. These sites were predominantly located within Env, Pol and Gag (14/39, 9/39 and 6/39 respectively) and were significantly clustered (33/39) within known immunoreactive peptides. Within 6 months of infection, we detected reversion-to-consensus mutations at 14 sites and potential CTL escape mutations at seven. Here we provide evidence that frequent reversion mutations probably allows the virus to recover replicative fitness which, together with immune escape driven by the HLA alleles of the new hosts, differentiate sequences from chronic infections from those sampled shortly after transmission.

Effects of Three Methods of Restraint on Intravenous Glucose Tolerance Testing in Rhesus and African Green Monkeys

The intravenous administration of 0.75 gm glucose per kg and the measurement of serum glucose pretest and at 10, 20, 30, 60, 90 and 120 minutes constitute a satisfactory protocol for intravenous glucose tolerance testing of Rhesus (Macaca mulatto) and African Green (Cercopithecus aethiops) monkeys. No significant differences were noted between animals restrained with ketamine hydrochloride and those restrained with sodium pentobarbital, but the African Green males and females and the male Rhesus monkeys yielded significantly different results while being manually restrained.

First Report of Maize streak virus Field Infection of Sugarcane in South Africa

Prior to the introduction of highly resistant sugarcane varieties, Sugarcane streak virus (SSV) caused serious sugar yield losses in southern Africa. Recently, sugarcane plants with streak symptoms have been identified across South Africa. Unlike the characteristic fine stippling and streaking of SSV, the symptoms resembled the broader, elongated chlorotic lesions commonly observed in wild grasses infected with the related Maize streak virus (MSV). Importantly, these symptoms have been reported on a newly released South African sugarcane cultivar, N44 (resistant to SSV). Following a first report from southern KwaZulu-Natal, South Africa in February 2006, a survey in May 2007 identified numerous plants with identical symptoms in fields of cvs. N44, N27, and N36 across the entire South African sugarcane-growing region. Between 0.04 and 1.6% of the plants in infected fields had streak symptoms. Wild grass species with similar streaking symptoms were observed adjacent to one of these fields. Potted stalks collected from infected N44 plants germinated in a glasshouse exhibited streak symptoms within 10 days. Virus genomes were isolated and sequenced from a symptomatic N44 and Urochloa plantaginea plants collected from one of the surveyed fields (1). Phylogenetic analysis determined that while viruses from both plants closely resembled the South African maize-adapted MSV strain, MSV-A₄ (>98.5% genome-wide sequence identity), they were only very distantly related to SSV (~65% identity; MSV-Sasri_S: EU152254; MSV-Sasri_G: EU152255). To our knowledge, this is the first confirmed report of maize-adapted MSV variants in sugarcane. In the 1980s, "MSV strains" were serologically identified in sugarcane plants exhibiting streak symptoms in Reunion and Mauritius, but these were not genetically characterized (2,3). There have been no subsequent reports on the impact of such MSV infections on sugarcane cultivation on these islands. Also, at least five MSV strains have now been described, only one of which, MSV-A, causes significant disease in maize and it is unknown which strain was responsible for sugarcane diseases on these islands in the 1980s (2,3). MSV-A infections could have serious implications for the South African sugar industry. Besides yield losses in infected plants due to stunting and reduced photosynthesis, the virus could be considerably more difficult to control than it is in maize because sugarcane is vegetatively propagated and individual plants remain within fields for years rather than months. Moreover, there is a large MSV-A reservoir in maize and other grasses everywhere sugarcane is grown in southern Africa. References: (1) B. E. Owor et al. J Virol. Methods 140:100, 2007. (2) M. S. Pinner and P. G. Markham. J. Gen. Virol. 71:1635, 1990. (3) M. S. Pinner et al. Plant Pathol. 37:74, 1998.

Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination

During the last few decades, many virus species have emerged, often forming dynamic complexes within which viruses share common hosts and rampantly exchange genetic material through recombination. Begomovirus species complexes are common and represent serious agricultural threats. Characterization of species complex diversity has substantially contributed to our understanding of both begomovirus evolution, and the ecological and epidemiological processes involved in the emergence of new viral pathogens. To date, the only extensively studied emergent African begomovirus species complex is that responsible for cassava mosaic disease. Here we present a study of another emerging begomovirus species complex which is associated with serious disease outbreaks in bean, tobacco and tomato on the south-west Indian Ocean (SWIO) islands off the coast of Africa. On the basis of 14 new complete DNA-A sequences, we describe seven new island monopartite begomovirus species, suggesting the presence of an extraordinary diversity of begomovirus in the SWIO islands. Phylogenetic analyses of these sequences reveal a close relationship between monopartite and bipartite African begomoviruses, supporting the hypothesis that either bipartite African begomoviruses have captured B components from other bipartite viruses, or there have been multiple B-component losses amongst SWIO virus progenitors. Moreover, we present evidence that detectable recombination events amongst African, Mediterranean and SWIO begomoviruses, while substantially contributing to their diversity, have not occurred randomly throughout their genomes. We provide the first statistical support for three recombination hot-spots (V1/C3 interface, C1 centre and the entire IR) and two recombination cold-spots (the V2 and the third quarter of V1) in the genomes of begomoviruses.

Modeling HIV transmission risk among Mozambicans prior to their initiating highly active antiretroviral therapy

Understanding sexual behavior and assessing transmission risk among people living with HIV-1 is crucial for effective HIV-1 prevention. We describe sexual behavior among HIV-positive persons initiating highly active antiretroviral therapy (HAART) in Beira, Mozambique. We present a Bernoulli process model (tool available online) to estimate the number of sexual partners who would acquire HIV-1 as a consequence of sexual contact with study participants within the prior three months. Baseline data were collected on 350 HAART-naive individuals 18-70 years of age from October 2004 to February 2005. In the three months prior to initiating HAART, 45% (n = 157) of participants had sexual relationships with 191 partners. Unprotected sex occurred in 70% of partnerships, with evidence suggesting unprotected sex was less likely with partners believed to be HIV-negative. Only 26% of the participants disclosed their serostatus to partners with a negative or unknown serostatus. Women were less likely to report concurrent relationships than were men (21 versus 66%; OR 0.13; 95%CI: 0.06, 0.26). Given baseline behaviors, the model estimated 23.2 infections/1,000 HIV-positive persons per year. The model demonstrated HAART along with syphilis and herpes simplex virus type 2 (HSV-2) treatment combined could reduce HIV-1 transmission by 87%; increasing condom use could reduce HIV-1 transmission by 67%.

Ascertainment of intimate partner violence using two abuse measurement frameworks

OBJECTIVE

To estimate prevalence of intimate partner violence (IPV) according to two abuse ascertainment tools, and agreement between the tools.

METHODS

2504 women randomly selected from a health maintenance organization were asked about IPV exposure in their most recent intimate relationship using five questions on physical and sexual abuse, and fear due to partner's threats and controlling behavior from the Behavioral Risk Factor Surveillance Survey (BRFSS) and 10 questions from the Women's Experience with Battering (WEB) scale. IPV prevalence was estimated according to the BRFSS and WEB, and the proportion of women who were WEB+/BRFSS+, WEB-/BRFSS-, WEB-/BRFSS+, and WEB+/BRFSS-.

RESULTS

In their most recent relationship, 14.7% of women reported abuse of any type on the BRFSS versus 7.0% on the WEB scale. In direct comparisons of the WEB and BRFSS questions, a higher percentage of abused women reported any IPV on the five BRFSS questions (88.4%) compared to the 10 WEB questions (42.0%). However, both the BRFSS and WEB identified some women as abused that would have been missed by the other instrument.

CONCLUSIONS

Intimate partner violence prevalence depends on how women are asked about abuse. Resources permitting, more than one abuse ascertainment strategy (for example, both the BRFSS and WEB questions) should be tried in order to broadly identify as many women as possible who interpret themselves as abused.

Genome analysis of a severe and a mild isolate of Papaya ringspot virus-type W found in Brazil

Papaya ringspot virus-type W (PRSV-W) is one of the most economically threatening viruses of cucurbits in Brazil. Premunization is one of the most effective PRSV control measures currently applied in squash and zucchini crops. PRSV-W-1, a mild and premunizing strain of PRSV has been successfully used to protect cucurbits against both the severe PRSV-W-C strain and other Brazilian PRSVs. To aid in understanding the mechanism by which PRSV-W-1 premunization operates, the complete genome sequences of PRSV-W-1 and PRSV-W-C were determined. PRSV-W-1 had a genome size of 10,332 nucleotides, whereas indels within the coat protein encoding gene meant that the genome size of PRSV-W-C was six nucleotides shorter than that of the mild strain. The genomes of the two strains shared 94.63% nucleotide sequence identity, with the 5' UTR and P1 being the most variable regions, and the coat protein and 3' UTR being the most conserved. Rigorous recombination analysis revealed that neither PRSV-W-1 nor PRSV-W-C was obviously recombinant, there was significant evidence that many other fully sequenced PRSV genomes were recombinant.

Coat protein gene diversity among Chrysanthemum virus B isolates from India

The complete coat protein (CP) sequences from 29 Indian isolates of Chrysanthemum virus B (CVB) were determined and analysed in relation to other previously characterized carlaviruses. The CP genes of the Indian CVB isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98%. Based on phylogenetic analyses, the isolates formed three groups potentially representing either two or three major CVB strain groupings. Recombination analysis revealed at least one definite recombination event involving the exchange of sequences between members of different groups. To our knowledge this is the first reported evidence of homologous recombination in carlaviruses.

ProteinChip system technology: a powerful tool to analyze expression differences in tissue-engineered blood vessels

At the time of implantation, tissue-engineered constructs should resemble native tissues as closely as possible. At present, histology and biochemical methods are commonly used to compare tissue-engineered constructs with native tissue. A ProteinChip system based on surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI) has been developed that allows visualization of complex protein profiles from biological samples. The aim of this study was to determine whether the ProteinChip system is a suitable tool with which to compare the protein expression profiles of tissue-engineered aortic blood vessels with native tissues. Tissue-engineered blood vessel substitutes were fabricated with poly-4-hydroxybutyrate scaffolds, ovine vascular cell seeding, and dynamic tissue culture conditions. Engineered, ovine aortic, and carotid tissues were homogenized and total protein was extracted. Samples were analyzed on ProteinChip arrays. Analysis yielded reproducible protein profiles from all samples. About 150 distinct protein peaks were detected. Comparative analysis with ProteinChip software revealed that the protein profiles from native aorta and native carotid arteries were similar whereas early tissue-engineered samples displayed more distinct deviations. In conclusion, ProteinChip system technology is rapid, reproducible, and highly sensitive in highlighting differentially expressed proteins in tissue-engineered blood vessel substitutes.

Widespread Recombination in Published Animal mtDNA Sequences1

Mitochondrial DNA (mtDNA) recombination has been observed in several animal species, but there are doubts as to whether it is common or only occurs under special circumstances. Animal mtDNA sequences retrieved from public databases were unambiguously aligned and rigorously tested for evidence of recombination. At least 30 recombination events were detected among 186 alignments examined. Recombinant sequences were found in invertebrates and vertebrates, including primates. It appears that mtDNA recombination may occur regularly in the animal cell but rarely produces new haplotypes because of homoplasmy. Common animal mtDNA recombination would necessitate a reexamination of phylogenetic and biohistorical inference based on the assumption of clonal mtDNA transmission. Recombination may also have an important role in producing and purging mtDNA mutations and thus in mtDNA-based diseases and senescence.

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints

We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant reference sequences. The algorithm is fast and includes a Bonferroni corrected statistical test of recombination to circumvent the multiple testing problems encountered when using the BOOTSCAN method to explore alignments for evidence of recombination. Using both simulated and real datasets we demonstrate that the modified algorithm is more powerful than other phylogenetic recombination detection methods and performs almost as well as one of the best substitution distribution recombination detection methods.

Characterisation of Potato virus Y nnp strain inducing veinal necrosis in pepper: a naturally occurring recombinant strain of PVY

The full-length genome of Potato virus Y (PVY) nnp strain, recovered from pepper showing veinal necrosis of leaves, was cloned and sequenced, finding an organisation typical for PVY species. It consists of 9699 nucleotides (nt) excluding the 3' terminal poly(A) tail and contains an open reading frame of 9186 nt, encoding the putative polyprotein of 3061 amino acids. In ELISA, the isolate reacted with a monoclonal antibody specific for PVY(C) but not with antibodies against PVY(N) or PVY(O). Sequence analysis strongly suggests that PVY-nnp originated from a recombination event involving a virus of the PVY(O) type and another parental virus, maybe resembling the PVY(NP) isolates, given the reasonably high similarity shared by PVY-nnp and Lye84.2 and Son41 isolates. The recombination event involved a breakpoint near the middle of the P1 gene, around position 603 of the viral genome. Proof for the existence of such a recombination comes from several lines of evidence, including similarity analysis, recombination analysis using six different methods and the different locations of nnp within phylogenetic trees constructed from genomic regions on either side of the identified recombination breakpoint.

A prospective study of household smoking bans and subsequent cessation related behaviour: the role of stage of change

OBJECTIVE

To assess the degree to which smokers living with a full household ban on smoking change their cessation related behaviour.

DESIGN, SETTING, AND PARTICIPANTS

Prospective cohort study; follow up of a population based cohort of 1133 smokers, identified from a 1997 telephone survey of adult Oregonians. After a median of 21 months, 565 were located and reinterviewed.

MAIN OUTCOME MEASURES

Quit attempts, time until relapse, and smoking cessation, defined as seven day and 90 day sustained abstinence at follow up.

RESULTS

A full ban at baseline was associated with a doubling of the odds of a subsequent quit attempt (odds ratio (OR) = 2.0, 95% confidence interval (CI), 1.0 to 3.9). Among respondents in the preparation stage at baseline (intention to quit in the next month with a quit attempt in the previous year), a full ban was associated with a lower relapse rate (hazard ratio = 0.5 (95% CI, 0.2 to 0.9)), while for those in precontemplation/contemplation (no intention to quit or intention to quit within the next six months, respectively), there was no significant association between full ban and relapse rate. For respondents in preparation, those with a full ban had over four times the odds of being in cessation for seven or more days before the follow up call (OR = 4.4 (1.1 to 18.7)), but for those in precontemplation/contemplation, full bans were unrelated to cessation.

CONCLUSIONS

Full household bans may facilitate cessation among smokers who are preparing to quit by increasing quit attempts. They may also prolong time to relapse among those smokers.

RDP2: recombination detection and analysis from sequence alignments

RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM chi(2), CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods.

AVAILABILITY

RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html)

CONTACT

darren@science.uct.ac.za

SUPPLEMENTARY INFORMATION

Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.

Tissue Engineering of Ovine Aortic Blood Vessel Substitutes Using Applied Shear Stress and Enzymatically Derived Vascular Smooth Muscle Cells

Compared to native blood vessels, all clinically available blood vessel substitutes perform suboptimally. Numerous approaches to tissue engineer (TE) blood vessels have been pursued using different scaffold materials, cell types, and culture conditions. Several limitations however remain to be overcome prior to the potential application in the arterial system. This study aimed at tissue engineering viable ovine blood vessels suitable for implantation into the systemic circulation of sheep. In recent studies vascular smooth muscle cells (vSMC) were derived by an explant technique. However, in this study we show that homogenous populations of differentiated vSMC were only obtained by enzymatic dispersion as characterized by immunostaining for specific vSMC marker proteins. In contrast the explant method yielded predominantly less differentiated myofibroblast-like cells. Enzymatically derived vSMC were seeded onto P-4-HB scaffolds and incubated either in a pulsatile flow bioreactor or under static conditions. Dynamically cultured TE blood vessel substitutes showed confluent layered tissue formation and were completely water resistant. They displayed significantly increased ECM synthesis, DNA, and protein content as well as vSMC marker expression. Mechanical properties of bioreactor cultured TE blood vessels approached those of native aorta. In conclusion ovine, aortic blood vessel substitutes were successfully created using enzymatically derived vSMC, bioabsorbable scaffolds, and applied shear stress.

Investigation of Maize streak virus pathogenicity determinants using chimaeric genomes

Genes and intergenic regions were reciprocally exchanged between a highly pathogenic Maize streak virus (MSV) isolate (MSV-MatA) and three less pathogenic isolates (MSV-Kom, MSV-R2, and MSV-VW) to determine the contribution of individual genome constituents to MSV pathogenicity in maize. Comparison of disease symptoms produced by the 54 resulting chimaeras and parental viruses enabled identification of genome constituents that are primarily responsible for the heightened pathogenicity of MSV-MatA in maize. Whereas pathogenicity determinants were detected in all of the MSV genomic regions examined, generally only chimaeras containing the MSV-MatA long intergenic region, coat protein gene, and/or movement protein gene were more pathogenic than the milder MSV isolates from which most of their genomes were derived. The pathogenicity of chimeras was strongly influenced by the relatedness of their parental viruses and evidence was found of nucleotide sequence-dependent interactions between both coding and intergenic regions.

Biological and Genomic Sequence Characterization of Maize streak virus Isolates from Wheat

ABSTRACT Maize streak virus (MSV) is best known as the causal agent of maize streak disease. However, only a genetically uniform subset of the viruses within this diverse species is actually capable of producing severe symptoms in maize. Whereas these "maize-type" viruses all share greater than 95% sequence identity, MSV strains isolated from grasses may share as little as 79% sequence identity with the maize-type viruses. Here, we present the complete genome sequences and biological characterization of two MSV isolates from wheat that share approximately 89% sequence identity with the maize-type viruses. Clonal populations of these two isolates, named MSV-Tas and MSV-VW, were leafhopper-transmitted to Digitaria sanguinalis and a range of maize, wheat, and barley genotypes. Whereas the two viruses showed some differences in their pathogenicity in maize, they were both equally pathogenic in D. sanguinalis and the various wheat and barley genotypes tested. Phylogenetic analyses involving the genome sequences of MSV-Tas and MSV-VW, a new maize-type virus also fully sequenced in this study (MSV-VM), and all other available African streak virus sequences, indicated that MSV-Tas and MSV-VW are close relatives that together represent a distinct MSV strain. Sequence analyses revealed that MSV-VM has a recombinant genome containing MSV-Tas/VW-like sequences within its movement protein gene.

Forced recombination between distinct strains of Maize streak virus

Recombination between divergent virus genomes is believed to be a major mechanism for generation of novel virus genotypes. We have examined the recombination process in geminiviruses by forcing recombination between two distinct isolates of Maize streak virus (MSV), MSV-Kom and MSV-Set. Heterodimeric agroinfectious constructs containing tandemly cloned mixtures of complete or partial MSV-Set and MSV-Kom genomes were used to simulate a circular dimeric form similar to that which would be expected to occur following a single intermolecular crossing-over event between MSV-Set and MSV-Kom replicative form DNAs at the long intergenic region (LIR)-movement protein gene (MP) interface. We isolated, analysed and biologically characterized many of the recombinant MSV genomes that were generated from the constructs in planta. Apart from having the same simulated breakpoint at the LIR-MP interface, all the genomes examined had a second breakpoint that had been generated through either intramolecular homologous recombination or a replicational release mechanism. The pathogenicities of six predominantly MSV-Kom-like recombinants were tested in maize. While all were capable of producing a symptomatic infection in this host, none was more virulent than MSV-Kom and only two were more virulent than MSV-Set. The two most virulent recombinants were leafhopper transmitted to a range of differentially MSV-resistant maize, wheat and barley genotypes and both were found to have unique biological properties.

Image-guided hypo-fractionated stereotactic radiosurgery to spinal lesions

OBJECTIVE

This article demonstrates the technical feasibility of noninvasive treatment of unresectable spinal vascular malformations and primary and metastatic spinal tumors by use of image-guided frameless stereotactic radiosurgery.

METHODS

Stereotactic radiosurgery delivers a high dose of radiation to a tumor volume or vascular malformation in a limited number of fractions and minimizes the dose to adjacent normal structures. Frameless image-guided radiosurgery was developed by coupling an orthogonal pair of x-ray cameras to a dynamically manipulated robot-mounted linear accelerator that guides the therapy beam to treatment sites within the spine or spinal cord, in an outpatient setting, and without the use of frame-based fixation. The system relies on skeletal landmarks or implanted fiducial markers to locate treatment targets. Sixteen patients with spinal lesions (hemangioblastomas, vascular malformations, metastatic carcinomas, schwannomas, a meningioma, and a chordoma) were treated with total treatment doses of 1100 to 2500 cGy in one to five fractions by use of image-guided frameless radiosurgery with the CyberKnife system (Accuray, Inc., Sunnyvale, CA). Thirteen radiosurgery plans were analyzed for compliance with conventional radiation therapy.

RESULTS

Tests demonstrated alignment of the treatment dose with the target volume within +/-1 mm by use of spine fiducials and the CyberKnife treatment planning system. Tumor patients with at least 6 months of follow-up have demonstrated no progression of disease. Radiographic follow-up is pending for the remaining patients. To date, no patients have experienced complications as a result of the procedure.

CONCLUSION

This experience demonstrates the feasibility of image-guided robotic radiosurgery for previously untreatable spinal lesions.

Sequence diversity and virulence in Zea mays of Maize streak virus isolates

Full genomic sequences were determined for 12 Maize streak virus (MSV) isolates obtained from Zea mays and wild grass species. These and 10 other publicly available full-length sequences were used to classify a total of 66 additional MSV isolates that had been characterized by PCR-restriction fragment length polymorphism and/or partial nucleotide sequence analysis. A description is given of the host and geographical distribution of the MSV strain and subtype groupings identified. The relationship between the genotypes of 21 fully sequenced virus isolates and their virulence in differentially MSV-resistant Z. mays genotypes was examined. Within the only MSV strain grouping that produced severe symptoms in maize, highly virulent and widely distributed genotypes were identified that are likely to pose the most serious threat to maize production in Africa. Evidence is presented that certain of the isolates investigated may be the products of either intra- or interspecific recombination.

The relative infectivities and genomic characterisation of three distinct mastreviruses from South Africa

The genomic nucleotide sequences of the cloned agroinfectious genomes of three South African mastreviruses obtained from Zea mays, a Setaria sp., and Panicum maximum (designated MSV-Kom, MSV-Set, and PanSV-Kar respectively), were determined. Additionally, their relative infectivities and virulence were analysed in a range of differentially susceptible wheat, maize, and barley genotypes. MSV-Kom produced moderate to severe streak symptoms in all maize genotypes tested, but only moderate to very mild symptoms in the wheat and barley genotypes. MSV-Set infected only the susceptible to tolerant maize genotypes, but was generally more severe in the barley and wheat genotypes than MSV-Kom. PanSV-Kar was incapable of infecting any of the wheat and barley genotypes and only produced very mild symptoms on the three most sensitive maize genotypes. Genomic characteristics in common with related mastreviruses were identified. Phylogenetic analysis indicated that while MSV-Kom was closely related to previously sequenced MSV isolates, MSV-Set and PanSV-Kar represented distinctly novel strains of MSV and PanSV respectively. In the case of MSV-Set, this is the most distantly related MSV strain yet characterised.

Risk of uterine rupture during labor among women with a prior cesarean delivery

BACKGROUND

Each year in the United States, approximately 60 percent of women with a prior cesarean delivery who become pregnant again attempt labor. Concern persists that a trial of labor may increase the risk of uterine rupture, an uncommon but serious obstetrical complication.

METHODS

We conducted a population-based, retrospective cohort analysis using data from all primiparous women who gave birth to live singleton infants by cesarean section in civilian hospitals in Washington State from 1987 through 1996 and who delivered a second singleton child during the same period (a total of 20,095 women). We assessed the risk of uterine rupture for deliveries with spontaneous onset of labor, those with labor induced by prostaglandins, and those in which labor was induced by other means; these three groups of deliveries were compared with repeated cesarean delivery without labor.

RESULTS

Uterine rupture occurred at a rate of 1.6 per 1000 among women with repeated cesarean delivery without labor (11 women), 5.2 per 1000 among women with spontaneous onset of labor (56 women), 7.7 per 1000 among women whose labor was induced without prostaglandins (15 women), and 24.5 per 1000 among women with prostaglandin-induced labor (9 women). As compared with the risk in women with repeated cesarean delivery without labor, uterine rupture was more likely among women with spontaneous onset of labor (relative risk, 3.3; 95 percent confidence interval, 1.8 to 6.0), induction of labor without prostaglandins (relative risk, 4.9; 95 percent confidence interval, 2.4 to 9.7), and induction with prostaglandins (relative risk, 15.6; 95 percent confidence interval, 8.1 to 30.0).

CONCLUSIONS

For women with one prior cesarean delivery, the risk of uterine rupture is higher among those whose labor is induced than among those with repeated cesarean delivery without labor. Labor induced with a prostaglandin confers the highest risk.

Delivery method and self-reported postpartum general health status among primiparous women

Despite nearly four million deliveries in the United States each year, minimal information exists on unintended health consequences following childbirth, particularly in relation to delivery method. The purpose of this study was to assess the association between method of delivery and the general health status, sexual, bowel and urinary functioning of primiparous women as measured at 7 weeks postpartum. Data from the Statewide Obstetrical Review of Quality System (StORQS) Survey of Maternity Care in Washington State were analysed. Participants included all primiparous women with a delivery of a singleton infant discharged alive between August and December 1991 from 10 non-federal short-stay hospitals who responded to the StORQS Survey of Maternity Care (n = 971). The main outcome measures included the modified Medical Outcomes Study 36-Item Short-Form Health Survey and self-reported sexual, bowel and urinary functioning. At 7 weeks postpartum, women who had caesarean or assisted vaginal deliveries reported significantly lower postpartum general health status scores than women with unassisted vaginal delivery. Additionally, women with assisted vaginal delivery reported significantly worse sexual, bowel and urinary functioning. Our results suggest that more careful attention to the postpartum general health and sexual functioning of women with caesarean and assisted vaginal delivery may be merited.

Pro- and Anti-inflammatory Cytokine Gene Expression in Rat Sciatic Nerve Chronic Constriction Injury Model of Neuropathic Pain

Cytokines may be pathophysiologically involved in hyperalgesia. Uncertainty exists about the types of cytokines and their site of action. To study the role of key pro- and anti-inflammatory cytokines in a chronic constriction model of neuropathic pain, mRNA expression of TNF, IL-1beta, IL-6, and IL-10 was quantified using competitive RT-PCR. Each cytokine mRNA in rat sciatic nerve was examined at days 3, 7, 14, and 45 after chronic constriction injury (CCI). We also undertook behavioral testing of these rats. Thermal warming and touch thresholds were significantly reduced at days 3, 7, and 14 in the CCI group, compared with the sham-operated group. Cytokine gene expression in sciatic nerve was significantly increased at day 7 for IL-1beta and IL-6 and at day 14 for TNF. Expression of IL-10 underwent a gradual and progressive increase, reaching statistical significance at day 45.

First-birth cesarean and placental abruption or previa at second birth(1)

OBJECTIVE

To assess the association between first-birth cesarean delivery and second-birth placental abruption and previa.

METHODS

We conducted a population-based, retrospective cohort analysis using data from the Washington State Birth Events Record Database. The study cohort included all primiparas who gave birth to live singleton infants in nonfederal short-stay hospitals from January 1, 1987, through December 31, 1996, and who had second singleton births during the same period (n = 96,975). Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for placental abruption or previa at second births associated with first-birth cesareans.

RESULTS

Among our study cohort, abruptio placentae complicated 11.5 per 1000 and placenta previa 5.2 per 1000 singleton deliveries at second births. In logistic regression analyses adjusted for maternal age, women with first-birth cesareans had significantly increased risk of abruptio placentae (OR 1.3, 95% CI 1.1, 1.5), and placenta previa (OR 1.4, 95% CI 1.1, 1.6) at second births, compared with women with prior vaginal deliveries.

CONCLUSION

We found moderately increased risk of placental abruption and previa as a long-term effect of prior cesarean delivery on second births.