Mika Salminen

DNA Sequence of the Long Terminal Repeat of Human Immunodeficiency Virus Type 1 Subtype A through G

485 THE RAPID ACCUMULATION of mutations and recombination occurs by processes that actively contribute to the evolution of HIV-1 and its genetic diversity. At least 10 distinct genetic subtypes of HIV-1 have been identified on the basis of the phylogenetic analysis of nucleotide sequences in the envV3 and gagp17 regions.1,2 According to an analysis of the 1993 Los Alamos HIV Database, 10% of the reported sequences were V3/p17 recombinants. Intersubtype mosaic forms of HIV-1 have been reported in geographic areas where multiple HIV-1 subtypes cocirculate. While many studies have been focused on phylogenetic analysis of the structural genes,1,2,5 relatively little attention has been paid to the genetic variation in the HIV1 long terminal repeat (LTR) region. Here we have characterized a collection of the LTR sequences from seven different HIV-1 subtypes and intersubtype recombinants representing different geographic origins. HIV-1 DNA was extracted from peripheral blood mononuclear cells (PBMCs) of 28 randomly chosen HIV-1-infected patients (21 African and 7 Swedish patients), as previously described. HIV-1 was subtyped by direct sequencing of the V3 and p17 regions of all of the patients, followed by phylogenetic analyses, as previously described. Full-length HIV genomic sequences (subtypes A±H), as presented in the 1997 Los Alamos HIV Database, were used as reference sequences in the alignments for V3 and p17 regions. For some subtypes unpublished full-length sequences (subtype H: VI991-3, VI997-2; subtype F: BZ126, F9363, ITM850; subtype A: SE8538, SE8131-3, SE8891, SE7253, SE7535; and subtype J: SE91733, SE9280-9) were available. The LTR was amplified by a nested polymerase chain reaction (PCR), using the previously described primers BJLTR1, BJLTR3, and BJLTR4.8 After cloning of the PCR fragments into the pCR2.1 vector (Invitrogen, San Diego, CA) the double-stranded (ds) DNA was used as a template for sequencing. The sequencing reactions were primed with CY5-labeled universal (or reverse) primers, provided in the Sequenase version 2.0 kit (United States Biochemical, Cleveland, OH), according to the protocol of the manufacturer. Multiple LTR clones (3±10 clones per patient) for each of the 28 HIV-1 strains were sequenced from both directions. The LTR sequences (nucleotides 2 382 to 1 113 relative to transcription start) were then aligned using Omiga 1.01 (ClustalW Oxford Molecular, Ltd., Oxford, UK) and DNASIS sequence analysis software (Hitachi Software Engineering America, San Bruno, CA). The LTR sequences presented in this study were aligned with the various subtype LTR sequences from the Los Alamos HIV Database of 1997 (data not shown). The alignment was optimized manually. On the basis of the LTR, p17, and V3 phylogenetic analyses 1 of the samples was classified as subtype A, 10 as B, 6 as C, and 1 as G (Fig. 1A, B, and C, respectively2,9). A discrepant topology was observed in the V3, p17, or LTR phylogenetic tree in 5 of the 28 HIV-1 strains (marked with asterisks in Fig. 1). The HIV-1 strains that gave discrepant clustering in the phylogenetic trees were therefore putatively classified as recombinant strains (SO5549, A/C; GM6139, A/G; IC5381, A/G; GM6452, E/A; and TH6098, E/A). On the basis of the LTR analysis five of the strains were classified as subtype D (UG6476, UG6083, UG4696, UG6357, and UG5609); however, a clear subtype classification based on p17 and V3 (except for patient UG6476) could not be obtained for those strains (marked with double asterisks in Fig. 1B and C). A possible explanation may be that in those strains these regions contain a recombination point so that one part of the sequence belong to one subtype and one part to another, leading to unclear classification of those isolates. Interestingly, all of these strains are from Uganda, where a high frequency of HIV-1 hybrid genomes can be expected owing to the cocirculation of multiple divergent HIV-1 strains, mainly subtypes A and D.1 The LTR analysis revealed a distinction between the LTR region of subtype C and that of all the other subtypes studied (A, B, D, E, F, and G), in that subtype C isolates (except the sample SO5549) contained an additional potential NFk B-binding site (NFk B1) (GGGCGKTCY). Such a unique pattern for the LTR region of HIV-1 clade C has previously been reported from Ethiopia,

Should Europe have a universal hepatitis B vaccination programme

WHO recommends that hepatitis B virus should be included in childhood vaccination programmes. Pierre Van Damme and colleagues argue that universal immunisation is essential to stop people becoming carriers but Tuija Leino and colleagues think that a targeted approach is a better use of resources in countries with low endemicity

Respiratory diphtheria in an asylum seeker from Afghanistan arriving to Finland via Sweden, December 2015.

In December 2015, an asylum seeker originating from Afghanistan was diagnosed with respiratory diphtheria in Finland. He arrived in Finland from Sweden where he had already been clinically suspected and tested for diphtheria. Corynebacterium diphtheriae was confirmed in Sweden and shown to be genotypically and phenotypically toxigenic. The event highlights the importance of early case detection, rapid communication within the country and internationally as well as preparedness plans of diphtheria antitoxin availability.

Analysis of results from the Joint External Evaluation: examining its strength and assessing for trends among participating countries

Background The Joint External Evaluation (JEE) is part of the World Health Organization’s (WHO) new process to help countries assess their ability to prevent, detect and respond to public health threats such as infectious disease outbreaks, as specified by the International Health Regulations (IHR). How countries are faring on these evaluations is not well known and neither is there any previous assessment of the performance characteristics of the JEE process itself. Methods We obtained JEE data for 48 indicators collectively across 19 technical areas of preparedness for 55 countries. The indicators are scored on a 1 to 5 scale with 4 indicating demonstrated capacity. We created a standardized JEE index score representing cumulative performance across indicators using principal components analysis. We examined the state of performance across all indicators and then examined the relationship between this index score and select demographic and health variables to better understand potential drivers of performance. Results Among our study cohort, the median performance on 43 of the 48 (89.6%) indicators was less than 4, suggesting that countries were failing to meet demonstrated capacity on these measures. The two weakest indicators were related to antimicrobial resistance (median scoreu2009=u20091.0, interquartile rangeu2009=u20091.0-2.0) and biosecurity response (median scoreu2009=u20092.0, interquartile rangeu2009=u20092.0-3.0). JEE index scores correlated with various metrics of health outcomes (life expectancy, under-five year mortality rate, disability-adjusted life years lost to communicable diseases) and with standard measures of social and economic development that enable public health system performance in the total sample, but in stratified analyses, these relationships were much weaker in the AFRO region. Conclusions We find large variations in JEE scores among countries and WHO regions with many nations still unprepared for the next disease outbreak with pandemic potential The strong correlations between JEE performance and metrics of both health outcomes and health systems’ performance suggests that the JEE is likely accurately measuring the strength of IHR-specific, public health capabilities.

P4: Epidemiology of hepatitis C virus infections in Finland between the years 1995 and 2011

PURPOSE OF THE STUDY: Recent studies have identified a seroprevalence of hepatitis C of 1.6% in the United States and 0.7% in Germany. A significant variation has, however, been detected between rural and metropolitan areas. Identification of hepatitis C virus (HCV)-positive persons for appropriate counseling and management is the major focus of national prevention programs. Currently, routine testing is recommended for persons most likely to have HCV infection. Our aim was to assess the prevalence of hepatitis C in the German Ruhr region, which is one of the largest and most densely populated metropolitan areas in Europe. METHODS: Between 06/2009 and 07/2010 8435 consecutive patients (46.4% male, 53.6% female) who were admitted to the emergency unit of a tertiary care center (St. Josef Hospital, Ruhr-University Bochum, Germany) were investigated. Tests included analysis of antibodies to HCV (anti-HCV), ASTand ALT-levels and HCV RNA, if applicable. Thirty patients with known replicative hepatitis C infection served as internal control. SUMMARY OF RESULTS: The seroprevalence of anti-HCV was 3.45% (291/8435 patients). 194/291 (66.67%) seropositive individuals were amendable for further evaluation. Viral replication was detected in 70.62% of these patients (137/194) equating to a prevalence of replicative and chronic hepatitis C of 1.62% in this population. Age and sex distribution did not differ between anti-HCV positive patients and negative controls. Following analysis of liver transaminases, significant differences in AST levels between anti-HCV positive patients and negative controls (AST antiHCV positive = 60.8 4.2 U/L; AST controls = 37.7 4.5 U/L; p < 0.01) were detected. No differences were shown between ALT levels between these groups (ALT anti-HCV positive = 51.5 4.1 U/L; ALT controls = 49.5 13.9 U/L; p > 0.05). CONCLUSIONS: The prevalence of hepatitis C in densely populated metropolitan areas seems to be higher than previously expected (3.45% versus 0.4–0.7%). Revisiting the risk stratification and a more extensive screening might contribute to more effective prevention programs. The mere evaluation of transaminases is not suitable for predicting either seroprevalence of anti-HCV antibodies or chronic hepatitis C. Furthermore, the pre-clinical identification of HCV-positive individuals might significantly reduce the risk of accidental hepatitis C transmission among healthcare workers and would lead to an increase of the early hepatitis C diagnosis targeting to an early lead-in of the antiviral therapy avoiding late complications.