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Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.

International audience; Background: Global HIV-1 genetic diversity and evolution form a major challenge to treatment and prevention efforts. An increasing number of distinct HIV-1 recombinants have been identified worldwide, but their contribution to the global epidemic is unknown. We aimed to estimate the global and regional distribution of HIV-1 recombinant forms during 1990-2015.Methods: We assembled a global HIV-1 molecular epidemiology database through a systematic literature review and a global survey. We searched the PubMed, Embase (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) databases for HIV-1 subtyping studies published from Jan 1, 1990, to Dec 31, 2015. Unpublished original HIV-1 subtyping data were collected through a survey among experts in the field who were members of the WHO-UNAIDS Network for HIV Isolation and Characterisation. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. Countries were grouped into 14 regions and analyses were done for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV in each country to generate regional and global estimates of numbers and proportions of HIV-1 recombinants in each time period. The systematic review is registered with PROSPERO, CRD42017067164.Findings: Our global data collection yielded an HIV-1 molecular epidemiology database of 383 519 samples from 116 countries in 1990-2015. We found that the proportion of recombinants increased over time, both globally and in most regions, reaching 22·8% (7 978 517 of 34 921 639) of global HIV-1 infections in 2010-15. Both the proportion and the number of distinct CRFs detected increased over time to 16·7% and 57 CRFs in 2010-15. The global and regional distribution of HIV-1 recombinants was diverse and evolved over time, and we found large regional variation in the numbers (0-44 CRFs), types (58 distinct CRFs), and proportions (0-80·5%) of HIV-1 recombinants. Globally, CRF02_AG was the most prevalent recombinant, accounting for 33·9% (2 701 364 of 7 978 517) of all recombinant infections in 2010-15. URFs accounted for 26·7% (2 131 450 of 7 978 517), CRF01_AE for 23·0% (1 838 433), and other CRFs for 16·4% (1 307 270) of all recombinant infections in 2010-15. Although other CRFs accounted for small proportions of infections globally (

PurposeThe Finnish HIV Quality of Care Register (FINHIV) was created to: (1) estimate the number of people living with HIV (PLWH) in Finland, (2) evaluate the national level of antiretroviral medication use and viral suppression, (3) examine the change in the HIV epidemic in Finland to pinpoint issues to address and (4) enable evaluation of the health of the PLWH by combining the FINHIV data with other national healthcare data.ParticipantsThe FINHIV includes all people diagnosed or being treated for HIV infection in Finland since 1984. The register was formed in 2020 by combining data from the National Infectious Diseases Register (information from time of diagnosis, data from 1984) and from the 21 HIV Clinics that treat HIV-positive patients in Finland (earliest data from 1998). The register population forms a nationwide, open cohort with yearly updates; currently it consists of 4218 PLWH (including 718 deceased) with HIV diagnosed or treated in Finland 1984–2019. Current rate of new cases is 150 cases/year.Findings to dateFrom the FINHIV data, we can confirm that Finland has reached the Joint United Nations Programme for HIV/AIDS (UNAIDS) 90-90-90 targets set for 2020, and that the proportion of virally suppressed is constant between all 21 HIV Clinics in Finland, despite their varying size. Linkage to care is estimated at 94.3% of those diagnosed. In contrast to the treatment results, more than half of the PLWH have been diagnosed at a late stage, and the proportion has increased since 2000.Future plansCombinations of FINHIV data with other national healthcare register data in Finland will provide further information on other aspects of the health of the PLWH in a high-resource setting (eg, comorbidities, sexual health and use of healthcare resources). Additionally, implementation of patient-reported experience and outcome measures within the FINHIV is ongoing.

The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection diagnosis is reverse transcription (RT)-PCR from a nasopharyngeal swab specimen (NPS). Its collection involves close contact between patients and health care workers, requiring a significant amount of workforce and putting them at risk of infection. We evaluated self-collection of alternative specimens and compared their sensitivity and cycle threshold (CT) values to those of NPS. We visited acute coronavirus disease 2019 (COVID-19) outpatients to collect concomitant NPS and gargle specimens and had patients self-collect gargle and either sputum or spit specimens the next morning. We included 40 patients and collected 40 concomitant NPS and gargle specimens, as well as 40 gargle, 22 spit, and 16 sputum specimens the next day (2 patients could not produce sputum). All specimens were as sensitive as NPS. Gargle specimens had a sensitivity of 0.97 (95% confidence interval [CI], 0.92 to 1.00), whether collected concomitantly with NPS or the next morning. Next-morning spit and sputum specimens showed sensitivities of 1.00 (95% CI, 1.00 to 1.00) and 0.94 (95% CI, 0.87 to 1.00]), respectively. The gargle specimens had significantly higher mean CT values of 29.89 (standard deviation [SD], 4.63; P < 0.001) and 29.25 (SD, 3.99; P < 0.001) when collected concomitantly and the next morning, respectively, compared to NPS (22.07 [SD, 4.63]). CT values obtained with spit (23.51 [SD, 4.57]; P = 0.11) and sputum (25.82 [SD, 9.21]; P = 0.28) specimens were close to those of NPS. All alternative specimen collection methods were as sensitive as NPS, but spit collection appeared more promising, with a low CT value and ease of collection. Our findings warrant further investigation. IMPORTANCE Control of the COVID-19 pandemic relies heavily on a test-trace-isolate strategy. The most commonly used specimen for diagnosis of SARS-CoV-2 infection is a nasopharyngeal swab. However, this method is quite uncomfortable for the patient, requires specific equipment (nose swabs and containers), and requires close proximity to health care workers, putting them at risk of infection. Developing alternative sampling strategies could decrease the burden for health care workers, help overcome potential shortages of equipment, and improve acceptability of testing by reducing patient discomfort. publishedVersion

Background: A robust estimate of the number of people with chronic hepatitis C virus (HCV) infection is essential for an appropriate public health response and for monitoring progress toward the WHO goal of eliminating viral hepatitis. Existing HCV prevalence studies in the European Union (EU)/European Economic Area (EEA) countries are heterogeneous and often of poor quality due to non-probability based sampling methods, small sample sizes and lack of standardization, leading to poor national representativeness. This project aimed to develop and pilot standardized protocols for undertaking nationally representative HCV prevalence surveys in the general adult population.Methods: From 2016 to 2019 a team from the Robert Koch-Institute contracted by the European Centre for Disease Prevention and Control synthesized evidence on existing HCV prevalence surveys and survey methodology and drafted a protocol. The methodological elements of the protocol were piloted and evaluated in Bulgaria, Finland and Italy, and lessons learnt from the pilots were integrated in the final protocol. An international multidisciplinary expert group was consulted regularly.Results: The protocol includes three alternative study approaches: a stand-alone survey; a “nested” survey within an existing health survey; and a retrospective testing survey approach. A decision algorithm advising which approach to use was developed. The protocol was piloted and finalized covering minimum and gold standards for all steps to be implemented from sampling, data protection and ethical issues, recruitment, specimen collection and laboratory testing options, staff training, data management and analysis and budget considerations. Through piloting, the survey approaches were effectively implemented to produce HCV prevalence estimates and the pilots highlighted the strengths and limitations of each approach and key lessons learnt were used to improve the protocol.Conclusions: An evidence-based protocol for undertaking HCV prevalence serosurveys in the general population reflecting the different needs, resources and epidemiological situations has been developed, effectively implemented and refined through piloting. This technical guidance supports EU/EEA countries in their efforts to estimate their national hepatitis C burden as part of monitoring progress toward the elimination targets.

Hepatitis B virus (HBV) infection remains a global health threat. The World Health Organization (WHO) established a goal to eliminate HBV infection as a public health threat by 2030, and defined targets for key interventions to achieve that goal. We evaluated HBV burden and relevant national recommendations for progress towards WHO targets in circumpolar countries. Viral hepatitis experts of circumpolar countries were surveyed regarding their country’s burden of HBV, achievement of WHO targets and national public health authority recommendations for HBV prevention and control. Eight of nine circumpolar countries responded. All countries continue to see new HBV infections. Data about HBV prevalence and progress in reaching WHO 2030 elimination targets are lacking. No country was able to report data for all seven WHO target measures. All countries have recommendations targeting the prevention of mother-to-child transmission. Only the USA and Greenland recommend universal birth dose vaccination. Four countries have recommendations to screen persons at high risk for HBV. Existing recommendations largely address prevention; however, recommendations for universal birth dose vaccination have not been widely introduced. Opportunities remain for the development of trackable targets and national elimination planning to screen and treat for HBV to reduce incidence and mortality.

Migrants are disproportionately affected by HIV in many European countries, including Finland. We aimed to compare the HIV-related knowledge, attitudes and practices (KAP) of young asylum seekers to those of the general young adult population. Two cross-sectional surveys were conducted among 20- to 25-year-old young adults: The TIE study among asylum seekers (n=47) and the World AIDS Day 2014 study among the general population (n=485). Important gaps in HIV KAP were identified especially among the young asylum seekers. For the general young adult population, previous HIV testing was associated with female gender, better HIV knowledge and increased sexual activity. Health education concerning HIV needs to be further enforced among young adults in Finland. Due to poorer HIV knowledge, young asylum seekers might be especially vulnerable to HIV. The asylum process is a window of opportunity for health education and HIV testing.

Background: Migrants are considered a key population at risk for sexually transmitted and blood-borne diseases in Europe. Prevalence data to support the design of infectious diseases screening protocols are scarce. We aimed to estimate the prevalence of hepatitis B and C, human immunodefiency virus (HIV) infection and syphilis in specific migrant groups in Finland and to assess risk factors for missed diagnosis. Methods: A random sample of 3000 Kurdish, Russian, or Somali origin migrants in Finland was invited to a migrant population-based health interview and examination survey during 2010-2012. Participants in the health examination were offered screening for hepatitis B and C, HIV and syphilis. Notification prevalence in the National Infectious Diseases Register (NIDR) was compared between participants and non-participants to assess non-participation. Missed diagnosis was defined as test-positive case in the survey without previous notification in NIDR. Inverse probability weighting was used to correct for non-participation. Results: Altogether 1000 migrants were screened for infectious diseases. No difference in the notification prevalence among participants and non-participants was observed. Seroprevalence of hepatitis B surface antigen (HBsAg) was 2.3%, hepatitis C antibodies 1.7%, and Treponema pallidum antibodies 1.3%. No cases of HIV were identified. Of all test-positive cases, 61% (34/56) had no previous notification in NIDR. 48% of HBsAg, 62.5% of anti-HCV and 84.6% of anti-Trpa positive cases had been missed. Among the Somali population (n = 261), prevalence of missed hepatitis B diagnosis was 3.0%. Of the 324 Russian migrants, 3.0% had not been previously diagnosed with hepatitis C and 2.4% had a missed syphilis diagnosis. In multivariable regression model missed diagnosis was associated with migrant origin, living alone, poor self-perceived health, daily smoking, and previous diagnosis of another blood-borne infection. Conclusions: More than half of chronic hepatitis and syphilis diagnoses had been missed among migrants in Finland. Undiagnosed hepatitis B among Somali migrants implies post-migration transmission that could be prevented by enhanced screening and vaccinations. Rate of missed diagnoses among Russian migrants supports implementation of targeted hepatitis and syphilis screening upon arrival and also in later health care contacts. Coverage and up-take of current screening among migrants should be evaluated.

Objectives: The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. Methods: This was a multicentre, cross-sectional study within the European SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score >= 10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65 samples were selected for 454 integrase sequencing. Results: For the population sequencing analysis, 278 samples were retrieved and successfully analysed. No signature resistance mutations to any of the InSTIs were detected. Eleven (4%) subjects had mutations at resistance-associated positions with an HIVdb score >= 10. Of the 56 samples successfully analysed with 454 sequencing, no InSTI signature mutations were detected, whereas integrase substitutions with an HIVdb score >= 10 were found in 8 (14.3%) individuals. Conclusions: No signature InSTI-resistant variants were circulating in Europe before the introduction of InSTIs. However, polymorphisms contributing to InSTI resistance were not rare. As InSTI use becomes more widespread, continuous surveillance of primary InSTI resistance is warranted. These data will be key to modelling the kinetics of InSTI resistance transmission in Europe in the coming years.

EU/EEA HIV Surveillance Network: Daniela Schmid, André Sasse, Dominique Van Beckhoven, Tonka Varleva, Tatjana Nemeth Blazic, Linos Hadjihannas, Maria Koliou, Marek Maly, Susan Cowan, Kristi Rüütel, Kirsi Liitsola, Mika Salminen, Françoise Cazein, Josiane Pillonel, Florence Lot, Barbara Gunsenheimer-Bartmeyer, Stavros Patrinos, Dimitra Paraskeva, Maria Dudas, Haraldur Briem, Gudrun Sigmundsdottir, Derval Igoe, Kate O'Donnell, Darina O'Flanagan, Barbara Suligoi, Šarlote Konova, Sabine Erne, Irma Caplinskiene, Aurélie Fischer, Jackie Maistre Melillo, Tanya Melillo, Eline Op de Coul, Hans Blystad, Magdalena Rosinska, Isabel Aldir, Helena Cortes Martins, Mariana Mardarescu, Peter Truska, Irena Klavs, Asunción Díaz, Maria Axelsson, Valerie Delpech Helena Cortes Martins: Departamento de Doenças Infeciosas do Instituto Nacional de Saúde Doutor Ricardo Jorge. Background: The HIV burden is increasing in older adults in the European Union (EU) and European Economic Area (EEA). We investigated factors associated with HIV diagnosis in older adults in the 31 EU/EEA countries during a 12 year period. Methods: In this analysis of surveillance data, we compared data from older people (aged ≥50 years) with those from younger people (aged 15–49 years). We extracted new HIV diagnoses reported to the European Surveillance System between Jan 1, 2004, and Dec 31, 2015, and stratified them by age, sex, migration status, transmission route, and CD4 cell count. We defined late diagnosis as CD4 count of less than 350 cells per μL at diagnosis and diagnosis with advanced HIV disease as less than 200 cells per μL. We compared the two age groups with the χ² test for difference, and used linear regression analysis to assess temporal trends. Findings: During the study period 54 102 new HIV diagnoses were reported in older adults. The average notification rate of new diagnoses was 2·6 per 100 000 population across the whole 12 year period, which significantly increased over time (annual average change [AAC] 2·1%, 95% CI 1·1–3·1; p=0·0009). Notification rates for new HIV diagnoses in older adults increased significantly in 16 countries in 2004–15, clustering in central and eastern EU/EEA countries. In 2015, compared with younger adults, older individuals were more likely to originate from the reporting country, to have acquired HIV via heterosexual contact, and to present late (p

HIV-1 set-point viral load—the approximately stable value of viraemia in the first years of chronic infection—is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%–43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical “Brownian motion” model and another model (“Ornstein–Uhlenbeck”) that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%–43%) is consistent with other studies based on regression of viral load in donor–recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation., Author summary The severity of the outcome of infection by a pathogen depends on many distinct factors. These include the environment and the genetic sequences of both the host and the pathogen, among others. The fraction of variability in disease outcome explained by pathogen genetic factors is termed “heritability”, because these factors are “inherited” by the new host upon infection. Quantifying heritability is key to understanding the development of the disease and the evolution of the virus. Here, we determined heritability of set-point viral load (SPVL) in HIV-1. SPVL is the stable value of viraemia in asymptomatic infection and it is a strong predictor of disease severity. While heritability of SPVL has been estimated using comparisons of viral genome sequences, this has resulted in widely variable estimates of heritability. Using a large dataset of patients living in Europe, standardised viral loads measures, and new methods, we obtain a more definitive estimate of HIV-1 SPVL heritability in Europe at about 30%. Thus, a significant amount of the variation in disease outcome is explained by the genetics of the virus.

Next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of rapid between- and within-host evolution may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions.De novoassembly avoids this bias by effectively aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the toolshiverto preprocess reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We useshiverto reconstruct the consensus sequence and minority variant information from paired-end short-read data produced with the Illumina platform, for 65 existing publicly available samples and 50 new samples. We show the systematic superiority of mapping toshiver’s constructed reference over mapping the same reads to the standard reference HXB2: an average of 29 bases per sample are called differently, of which 98.5% are supported by higher coverage. We also provide a practical guide to working with imperfect contigs.

Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions. Funding Agencies|Swedish Research CouncilSwedish Research Council [350-2012-6628, 623-2011-1100, 623-2013-8905]; ABBOTT molecular diagnostics (Celera Diagnostics); AIDS foundation in Denmark; Danish Research CouncilDet Frie Forskningsrad (DFF) [271-06-0619]; Beckett foundation, Denmark; Jens Christensen og hustru Korna Christensen foundation, Denmark

To determine the prevalence of parvovirus 4 infection and its clinical and sociodemographic correlations in Finland, we used virus-like particle-based serodiagnostic procedures (immunoglobulin [Ig] G, IgM, and IgG avidity) and PCR. We found 2 persons with parvovirus 4 primary infection who had mild or asymptomatic clinical features among hepatitis C virus-infected injection drug users.

Detailed phylogenetic analyses were performed to characterize an HIV-1 outbreak among injection drug users (IDUs) in Stockholm, Sweden, in 2006. This study investigated the source and dynamics of HIV-1 spread during the outbreak as well as associated demographic and clinical factors. Seventy Swedish IDUs diagnosed during 2004 to 2007 were studied. Demographic, clinical, and laboratory data were collected, and the V3 region of the HIV-1 envelope gene was sequenced to allow detailed phylogenetic analyses. The results showed that the Stockholm outbreak was caused by a CRF01_AE variant imported from Helsinki, Finland, around 2003, which was quiescent until the outbreak started in 2006. Local Swedish subtype B variants continued to spread at a lower rate. The number of new CRF01_AE cases over a rooted phylogenetic tree accurately reflected the transmission dynamics and showed a temporary increase, by a factor of 12, in HIV incidence during the outbreak. Virus levels were similar in CRF01_AE and subtype B infections, arguing against differences in contagiousness. Similarly, there were no major differences in other baseline characteristics. Instead, the outbreak in Stockholm (and Helsinki) was best explained by an introduction of HIV into a standing network of previously uninfected IDUs. The combination of phylogenetics and epidemiological data creates a powerful tool for investigating outbreaks of HIV and other infectious diseases that could improve surveillance and prevention.

Aims: The aim of this study was to assess the acceptability of human immunodeficiency virus (HIV) testing among migrants in Finland and the factors contributing to non-acceptance. Methods: The Finnish Migrant Health and Wellbeing Study ‘Maamu’ was the first national population-based Health Interview and Examination Survey (HIS/HES) among migrants in Finland. A total of 386 Kurdish, Russian and Somali immigrants in Helsinki participated in the study. Results: Despite the participants’ different sociodemographic backgrounds, a high rate of test acceptability (92%, 95% CI 90–95) was achieved. HIV test acceptance was associated with pretest counselling, ability to understand spoken Finnish or Swedish and employment status. No participants tested positive for HIV. Conclusions: The results imply that a universal HIV testing strategy is well accepted in a low-HIV prevalence immigrant population and can be included in a general health examination in immigrant population-based surveys.

HIV-1 infection has been rare in Estonia. In 2000, an explosive epidemic among injecting drug users was detected in the Eastern border region, resulting in 3603 newly reported cases by the end of 2003. The molecular epidemiology of the outbreak was studied to establish whether the Estonian epidemic is linked to the epidemics in Eastern Europe. Over 200 newly infected individuals were prospectively sampled from June 2000 to March 2002 in a geographically representative way, with known dates of diagnosis and information of probable route of transmission. Viral regions coding for two viral gene regions were directly sequenced from plasma viral RNA and phylogenetically analyzed. In addition, a larger region coding for the entire env gene was sequenced from one sample and studied for indications of possible recombinant structure. The Estonian HIV outbreak was found to be caused by simultaneous introduction of two strains: a minor subtype A strain very similar to the Eastern European subtype A strain (approximately 8% of cases), and a second major strain (77%) found to be most closely related to the CRF06-cpx strain, previously described only from African countries. The variability in the two clusters was very low, suggesting point source introductions. Ten percent of cases seemed to be newly generated recombinants of the A and CRF06-cpx strains. Analysis of viral diversification over time revealed a rate of change within the V3 region of 0.83%/year for the CRF06-cpx strain, consistent with findings from other subtypes. Due to the relatively frequently found novel recombinant forms, the Estonian HIV-1 epidemic may allow studies of coinfection and intersubtype recombination in detail.

In the former Soviet Union (SU) increasing numbers of HIV-1 infections among injecting drug users (IDU) have been reported, especially in the Ukraine. The main subtype transmitted among the IDUs seems to be subtype A, but limited numbers of subtype B cases have also been reported. In Kaliningrad, Russia, an AB recombinant strain was earlier shown to be responsible for the local outbreak. Here we describe the genetic relationship of HIV-1 strains circulating among IDUs in the former SU. For subtype A and the AB recombinant strains nearly full-length genomes were sequenced, and for one subtype B strain the entire envelope gene was cloned. The relationship between the AB recombinant strain and the subtype A and subtype B strains and the mosaic structure of the recombinant was studied by phylogenetic analysis. Ukrainian A and B strains were shown to be the probable parental viruses of the Kaliningrad AB recombinant strain. In the envelope gene the recombination breakpoint could also be precisely mapped to a region of similarity of only 14 base pairs. This suggests that only short stretches of absolute sequence identity may be needed for efficient RNA recombination between HIV-1 subtypes.

The molecular epidemiology of HIV-1 genetic subtypes was studied in a cross-sectional sample collected from HIV-infected individuals living in Finland between 1988 and 1994 and compared with independently collected epidemiological data. Subtypes were determined by sequencing and phylogenetic analysis of the gag NCp7 and the env coding regions of PBMC provirus. Finnish viruses belonging to 7 subtypes were found. Two thirds (n = 70) of the sequences could be classified as subtype B, while others belonged to subtypes A, C, D, F and G and the circulating recombinant form AE(CM240) (n = 25). There were significant differences in gender distribution and mode-of-transmission between B-type infections and infections with the other subtypes. Most subtype B strains in Finland were associated with homosexual transmission and about half of these were acquired in Finland, while most individuals harbouring non-B infections indicated heterosexual transmission and direct or indirect contact with Africa or Southeast Asia. The heterogeneity of genetic subtypes in the country was in good agreement with the epidemiological data suggesting that a significant proportion of infections were imported. HIV-1 subtype determination may prove to be a valuable tool for providing objective epidemiological data.

293 THE RAPID VIRAL TURNOVER and high mutation rate of HIV1 result in remarkable genetic variation among strains obtained from different parts of the world. This has led to the development of evolutionary lineages (genetic subtypes) that can be identified by phylogenetic analysis of gene sequences.2,3 Eight genetic subtypes, named A through H in group M (major) and a group of other strains, group O (outlier), have previously been determined by phylogenetic analysis, mainly of gag and env genes. The genetic subtype classification is based on consistent clustering of the sequences in different parts of the genome, and approximate equidistance to strains belonging to other subtypes. Two additional subtypes, I and J, have been proposed, on the basis of analysis of gene subfragments. Sequences from these strains were shown to group as independent, monophyletic lineages in phylogenetic comparisons to representative reference strains of previously described subtypes A through H.2,3 However, the definition of a genetic subtype is dependent on consistent clustering of sequences independent of the genome fragment analyzed (provided that enough informative variation is present in the region). This means that the classification results must be similar regardless of the genome region examined. Since HIV-1 strains of different subtypes have been shown to recombine, a classification based on a single subgenomic fragment does not necessarily indicate the genetic subtype of the complete genome. When a putative new genetic subtype is found the complete genome should be analyzed to verify that all regions of the virus cluster independently. In this study we have cloned and sequenced the first virtually complete proviruses of two independently obtained, epidemiologically unlinked primary isolates of HIV-1 subtype J. They form an independent cluster, approximately equidistant to the other subtypes over all of the genome, verifying their classification as a new subtype. Blood samples SE9173 and SE9280 for virus isolation were collected in Sweden from two previously identified HIV-1-infected individuals carrying the putative new subtype J viruses.8 Both individuals were immigrants from the Democratic Republic of Congo (formerly Zaire). A thorough epidemiological investigation, including contact tracing, did not reveal any direct or indirect contact between the two individuals. The initial identification of subtype J was based on direct sequencing and phylogenetic analysis of the gag p17 and env V3 regions amplified from uncultured patient lymphocytes. Samples SE9173 and SE9280 were obtained from the same individuals as the previously described samples SE7022 and SE7887, respectively. A seminested extended polymerase chain reaction (PCR) was used to amplify the virtually complete provirus from peripheral blood mononuclear cell (PBMC) cocultures essentially as has been previously described. Briefly, primers MSF12, binding to the tRNA-binding site located in the U5-gag leader junction of the 59 long terminal repeat (LTR), and MSR5, binding to the mRNA-polyadenylation signal site located in the R-U5 junction of the 3 9 LTR10 (Fig. 1), were used for first-round amplification. For second-round amplification one-tenth of the reaction was reamplified using primers MSF14 and MSR5. Second-round amplicons were cloned with a TA-cloning kit (pCR2.1 cloning kit; Invitrogen, San Diego, CA). Clones were sequenced on both strands by primer walking, using an ABI 377 automated sequencer and dye-terminator chemistry (Perkin-Elmer Applied Biosystems Division, Foster City, CA). The sequences have been submitted to GenBank with accession numbers AF082394 and AF082395. The lengths of the clones from strains SE9173 and SE9280 were 8953 and 8943 bp, respectively. The genome structure was similar to all other subtypes of HIV-1, with the gag, pol, and env structural genes, and reading frames for vif, vpr, vpu, and nef single exon regulatory/accessory genes (Table 1). The tat and rev exons 1 and 2 were also discernible at their usual positions. All reading frames appeared open and of complete length. The newly obtained SE9173 and SE9280 sequences were 94.2 and 97.6% similar to the SE7022 and SE7887 sequences in the V3 region, respectively.

The objectives were to investigate the molecular epidemiology and genetic structure of the virus strain(s) causing an outbreak of HIV-1 infection in the Kaliningrad province of the Russian Federation and to investigate the relationship of this outbreak to some other emerging HIV-1 epidemics in the countries of the former Soviet Union. A molecular epidemiological investigation was conducted in the city of Kaliningrad amongst individuals recently diagnosed as HIV-1-positive. Samples were also collected from neighbouring Lithuania and from the Ukraine. Incident and population data was collected from official health statistics in Kaliningrad. A standardized questionnaire was administered to newly diagnosed individuals to assess risk factors for HIV-1 infection. For genotyping two regions of the virus (env C2-V3 and gag NCp7) were directly sequenced. The number of newly diagnosed individuals testing seropositive for HIV-1 infection in Kaliningrad rose from less than one per month to more than 100 per month during the period of July--October 1996. A total of 1335 new infections were identified between 1 July 1996 and 30 June 1997. The main reported risk factor for HIV-1 infection (80%) was injecting drug use in particular with a locally produced opiate. Sequence analysis of patient viruses in Kaliningrad (n = 50) showed that the epidemic was caused by a highly homogenous HIV-1 strain recombinant between the genetic subtypes A and B. Comparison with subtype A strains prevalent amongst injecting drug users (IDU) in the Ukraine showed that one of these strains was the direct subtype A parent of the epidemic A/B recombinant strain in Kaliningrad. The HIV-1 epidemic in Kaliningrad probably started from a single source with rapid spread of the virus through the IDU population. The origin of the epidemic strain is a recombination event occurring between the subtype A strain virus prevalent among IDU in some southern CIS countries and a subtype B strain of unknown origin. (authors)

An outbreak of HIV was detected amongst Finnish injecting-drug users (IDUs) in 1998. The outbreak was caused by CRF01-AE virus [1]. A comprehensive care programme including infectious diseases, addiction medicine, low threshold methadone program, needle exchange, accommodation and other social services started in December 2000. Funding was provided by municipalities. We have described earlier how the outbreak became geographically and socially restricted [2]. The data of newly diagnosed HIV infections in the hospital district of Helsinki and Uusimaa (Helsinki region) amongst IDUs and HIV-1 subtypes were obtained from the Finnish national HIV registry. The Helsinki University Central Hospital (HUCH) registry was used to obtain the number of IDUs in HIV care, on antiretroviral therapy (ART), and plasma HIV-1 RNA (VL) amongst IDUs. The HUCH registry also includes IDUs diagnosed with HIV infection in other Finnish regions, but currently living in Helsinki region. The highest number (n=65) of newly diagnosed HIV infections among IDUs in Helsinki region was observed in 1999 (Figure 1). Between 1998 and 2011, 249 IDUs were diagnosed with HIV infection. From 1998 to 2004 the subtype was CRF01-AE in 187 (92%) cases, other subtypes in 5 (2%) cases and not subtyped in 11 (5%) cases. From 2005 to 2011 the subtype was CRF01-AE in 25 (54%) cases, other subtypes in 15 (33%) cases and not subtyped in 6 (13%) cases. In 2011 there were 4 IDUs diagnosed with HIV, one of them with CRF01-AE. In the Helsinki region out of 183 HIV-infected IDUs in 2005, 100 (55%) had VL

The seroepidemiology of hepatitis A virus (HAV) for the period 1990–2007 and the molecular epidemiology for the period 1994–2007 in Finland were studied. The incidence of hepatitis A has been very low since 1990, at 0.3–3.6/100,000 inhabitants, excluding two outbreaks in 1994–1995 and 2002–2003, both of which were connected to intravenous drug use. Serum samples (3,217) collected in the period 1997–1998 were tested for hepatitis A antibodies to assess the percentage of seropositive Finns. More than 50% of Finns aged over 55 were seropositive for hepatitis A, while less than 5% of those aged under 40 were seropositive. In addition, patient samples (52,012) from the period 1990 to 2007 were assessed for antibodies against HAV. In these samples the proportion of acute HAV infections stayed at around 2% per year (excluding outbreaks), whereas the overall seropositivity for hepatitis A increased from some 30% to 45%, which was most likely due to increased vaccinations. For molecular epidemiology, samples from 1994 to 2007 were analyzed by RT-PCR and sequencing. The results showed that most of the strains (82%) of HAV were of genotype IA but with an increasing number of genotypes IB and IIIA appearing during the last years of the study. All the cases seemed to be travel related and there was no endemic strain circulating in Finland. The low seroprevalence, especially in younger age groups, makes the population vulnerable to infection, which can be compensated for by increasing the number of vaccinations. J. Med. Virol. 82:934–941, 2010. © 2010 Wiley-Liss, Inc.

A rapidly advancing epidemic of HIV-1 infection has been documented among injecting drug users (IDUs) in Russia. The Northwestern Federal District was the first of the seven Russian Federal Districts involved in a drug-related HIV epidemic through an outbreak in Kaliningrad in 1996. The Northwestern Federal District has a high HIV prevalence rate having reached 252 per 100,000 by the end of 2003, exceeding the Russian average (180) by 1.4 times. The epidemic peaked in 2001. Since then the annual number of new cases has decreased, probably reflecting saturation among at least some IDU populations. However, at the same time, the heterosexual spread of HIV has become more prominent. To study the genetic epidemiology of HIV-1, samples were collected from 150 individuals covering a wide geographical area and different transmission groups in the Northwestern Federal District. Phylogenetic analysis revealed that an Eastern European subtype A HIV-1 strain similar to those reported earlier among IDUs in other regions of Russia accounted for 80% of HIV-1 infections and was the predominant subtype in six out of seven administrative territories studied both among IDUs and heterosexually infected persons. As an exception to the dominant role of the Eastern European subtype A strain, the CRF03-AB strain was found to be dominant in the city of Cherepovets located in the north central European Russian territory of Vologda Oblast. This is the first report of the CRF03-AB strain causing an outbreak outside the Kaliningrad region.

An explosive outbreak of HIV-1 caused by the recombinant subtype AE (CRF01-AE) was detected in 1998 among Finnish injecting drug users (IDUs). These IDUs were compared with IDUs from the Amsterdam Cohort Study (ACS) infected with subtype B, to detect possible differences between 2 western IDU cohorts infected with different subtypes. Markers for progression (viral load and CD4+lymphocyte count) were compared between 93 IDUs with CRF01-AE and 63 IDUs with subtype B. Only persons with a seroconversion interval =2 y were included. During 48 months of follow-up, both cohorts were similar in CD4+ cell decline, but the Finnish IDUs had 0.34-0.94 log10 copies/ml higher viral loads. The Amsterdam IDUs had a low viral load (1000 copies/ml) significantly more often than the Finnish IDUs. The difference could not be explained by the use of antiretrovirals. The higher viral load may have contributed to the rapid spread of the recombinant virus in the Finnish outbreak.

BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383 519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16 280 897/34 921 639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4 235 299/34 921 639) of infections, followed by subtype A (10·3%; 3 587 003/34 921 639), CRF02_AG (7·7%; 2 705 110/34 921 639), CRF01_AE (5·3%; 1 840 982/34 921 639), subtype G (4·6%; 1 591 276/34 921 639), and subtype D (2·7%; 926 255/34 921 639). Subtypes F, H, J, and K combined accounted for 0·9% (311 332/34 921 639) of infections. Other CRFs accounted for 3·7% (1 309 082/34 921 639), bringing the proportion of all CRFs to 16·7% (5 844 113/34 921 639). URFs constituted 6·1% (2 134 405/34 921 639), resulting in recombinants accounting for 22·8% (7 978 517/34 921 639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None. ispartof: LANCET INFECTIOUS DISEASES vol:19 issue:2 pages:143-155 ispartof: location:United States status: published