scholarly journals A High HIV-1 Strain Variability in London, UK, Revealed by Full-Genome Analysis: Results from the ICONIC Project

2017 ◽  
Author(s):  
Gonzalo Yebra ◽  
Dan Frampton ◽  
Tiziano Gallo Cassarino ◽  
Jade Raffle ◽  
Jonathan Hubb ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Wellcome Trust Sanger Institute ◽  
Illumina Miseq ◽  
Sub Saharan Africa ◽  
Full Genome ◽  
Genome Sequences ◽  
Full Dataset ◽  
Sub Saharan ◽  
The Uk ◽  
Ngs Data

AbstractBackground & MethodsThe ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. fromgagtonef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospital and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.ResultsThe pipeline generated sequences of at least 1Kb of length (median=7.4Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n=149, 40.8%) and C (n=77, 21.1%) and the circulating recombinant form CRF02_AG (n=32, 8.8%). We found 14 different CRFs (n=66, 18.1%) and multiple URFs (n=32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RTpolregion, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similarpolsequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset.ConclusionsThe initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.

scholarly journals The BabySaver: Design of a New Device for Neonatal Resuscitation at Birth with Intact Placental Circulation

Children ◽  
2021 ◽  
Vol 8 (6) ◽  
pp. 526
Author(s):  
James Ditai ◽  
Aisling Barry ◽  
Kathy Burgoine ◽  
Anthony K. Mbonye ◽  
Julius N. Wandabwa ◽  
...  
Keyword(s):  
Low Cost ◽  
Neonatal Resuscitation ◽  
Sub Saharan Africa ◽  
Skilled Birth Attendants ◽  
New Device ◽  
Birth Attendants ◽  
Premature Babies ◽  
Sub Saharan ◽  
The Uk ◽  
The University

The initial bedside care of premature babies with an intact cord has been shown to reduce mortality; there is evidence that resuscitation of term babies with an intact cord may also improve outcomes. This process has been facilitated by the development of bedside resuscitation surfaces. These new devices are unaffordable, however, in most of sub-Saharan Africa, where 42% of the world’s 2.4 million annual newborn deaths occur. This paper describes the rationale and design of BabySaver, an innovative low-cost mobile resuscitation unit, which was developed iteratively over five years in a collaboration between the Sanyu Africa Research Institute (SAfRI) in Uganda and the University of Liverpool in the UK. The final BabySaver design comprises two compartments; a tray to provide a firm resuscitation surface, and a base to store resuscitation equipment. The design was formed while considering contextual factors, using the views of individual women from the community served by the local hospitals, medical staff, and skilled birth attendants in both Uganda and the UK.

scholarly journals SAT0640-HPR RHEUMATOLOGY CARE OF MIGRANTS FROM SUB-SAHARAN AFRICA; A QUALITATIVE PILOT STUDY OF PATIENTS’ PERSPECTIVES

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1279.1-1279
Author(s):  
Z. Rutter-Locher ◽  
J. Galloway ◽  
H. Lempp
Keyword(s):  
Rheumatoid Arthritis ◽  
Health Care ◽  
Health Care Providers ◽  
Unmet Need ◽  
Primary Care Providers ◽  
Sub Saharan Africa ◽  
Care Providers ◽  
Specialist Care ◽  
Sub Saharan ◽  
The Uk

Background:Rheumatological diseases are common in Sub-Saharan Africa [1] but specialist healthcare is limited and there are less than 150 rheumatologists currently serving 1 billion people in Sub-Saharan Africa [2]. Rheumatologists practising in the UK NHS are likely to be exposed to migrant patients. There is therefore, an unmet need for health care providers to understand the differences in rheumatology healthcare provision between Sub-Saharan Africa and the UK and the barriers which migrants face in their transition of rheumatology care.Objectives:To gain an understanding of the experiences of patients with rheumatological conditions, about their past healthcare in Sub-Saharan Africa and their transition of care to the UK.Methods:A qualitative study using semi-structured interviews was conducted. Participants were recruited from two rheumatology outpatient clinics in London. Thematic analysis was applied to identify key themes.Results:Seven participants were recruited. Five had rheumatoid arthritis, one had ankylosing spondylitis and one had undifferentiated inflammatory arthritis. Participants described the significant impact their rheumatological conditions had on their physical and emotional wellbeing, including their social and financial implications. Compared to the UK, rheumatology healthcare in Sub-Saharan Africa was characterised by higher costs, limited access to specialists, lack of investigations and treatments, the use of traditional medicines and poor communication by clinicians. Barriers to transition of rheumatology care to the UK were: poor understanding of rheumatological conditions by the public and primary care providers, lack of understanding of NHS entitlements by migrants, fear of data sharing with immigration services and delayed referral to specialist care. Patient, doctor and public education were identified by participants as important ways to improve access to healthcare.Conclusion:This study has described, for the first time, patients’ perspectives of rheumatology health care in Sub-Saharan Africa and the transition of their care to the UK. These initial findings allow healthcare providers in the UK to tailor management for this migrant population and suggests that migrants need more information about their NHS entitlements and specific explanations on what non-clinical data will be shared with immigration services. To increase access to appropriate care, a concerted effort by clinicians and public health authorities is necessary to raise awareness and provide better education to patients and migrant populations about rheumatological conditions.References:[1]G. Mody, “Rheumatology in Africa-challenges and opportunities,” Arthritis Res. Ther., vol. 19, no. 1, p. 49, 2017.[2]M. A. M. Elagib et al., “Sudan and Sweden Active Rheumatoid Arthritis in Central Africa: A Comparative Study Between,” J. Rheumatol. J. Rheumatol. January, vol. 43, no. 10, pp. 1777–1786, 2016.Acknowledgments:We are grateful to the patients involved in this study for their time and involvement.Disclosure of Interests:None declared

scholarly journals Continuing high levels of HIV diagnoses in men who have sex with men in the United Kingdom

2008 ◽  
Vol 13 (14) ◽  
pp. 3-4
Author(s):  
B Rice ◽  
A Nardone ◽  
N Gill ◽  
V Delpech
Keyword(s):  
United Kingdom ◽  
Confidence Intervals ◽  
Sub Saharan Africa ◽  
Newly Diagnosed ◽  
The United Kingdom ◽  
Reporting Delays ◽  
Sub Saharan ◽  
Sex With Men ◽  
The Uk ◽  
Almost All

The latest HIV data for 2007 has recently been published for the United Kingdom (UK). During the year, an estimated 6,840 (95% confidence intervals 6,600-7,050) persons (adjusted for reporting delays) were newly diagnosed with HIV in the UK. This represents a 12% decline from a peak of new HIV diagnoses reported in 2005 (7,800). Almost all this decline in new HIV diagnoses was in HIV-infected heterosexuals from sub-Saharan Africa who were probably infected in their country of origin.

scholarly journals HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences

2017 ◽  
Vol 33 (11) ◽  
pp. 1083-1098 ◽  
Author(s):  
Oliver Ratmann ◽  
Chris Wymant ◽  
Caroline Colijn ◽  
Siva Danaviah ◽  
Max Essex ◽  
...  
Keyword(s):  
Sub Saharan Africa ◽  
Full Genome ◽  
Next Generation ◽  
Sub Saharan ◽  
Hiv 1

Malaria

2019 ◽  
Author(s):  
Angelina Jayakumar ◽  
Zahir Osman Eltahir Babiker
Keyword(s):  
Southeast Asia ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Parasitic Infection ◽  
Sub Saharan Africa ◽  
Anopheline Mosquito ◽  
Sub Saharan ◽  
The Uk ◽  
Almost All ◽  
Human Infections

Malaria is a tropical parasitic infection of the red blood cells caused by the protozoal species Plasmodium falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi. It is transmitted through the bite of the female Anopheles mosquito. The average incubation period is twelve to fourteen days. Congenital and blood-borne transmissions can also occur. P. falciparum and P. vivax account for most human infections but almost all deaths are caused by P. falciparum, with children under five years of age bearing the brunt of morbidity and mortality in endemic countries. P. falciparum is dominant in sub-Saharan Africa whereas P. vivax predominates in Southeast Asia and the Western Pacific. P. ovalae and P. malaria are less common and are mainly found in sub-Saharan Africa. P. knowlesi primarily causes malaria in macaques and is geographically restricted to southeast Asia. While taking a blood meal, the female anopheline mosquito injects motile sporozoites into the bloodstream. Within half an hour, the sporozoites invade the hepatocytes and start dividing to form tissue schizonts. In P. vivax and P. ovale, some of the sporozoites that reach the liver develop into hypnozoites and stay dormant within the hepatocytes for months to years after the original infection. The schizonts eventually rupture releasing daughter merozoites into the bloodstream. The merozoites develop within the red blood cells into ring forms, trophozoites, and eventually mature schizont. This part of the life cycle takes twenty-four hours for P. knowlesi; forty-eight hours for P. falciparum, P. vivax, P. ovale; and seventy-two hours for P. malariae. In P. vivax and P. ovale, some of the sporozoites that reach the liver develop into hypnozoites and stay dormant within the hepatocytes for months to years after the original infection. The hallmark of malaria pathogenesis is parasite sequestration in major organs leading to cytoadherence, endothelial injury, coagulopathy, vascular leakage, pro-inflammatory cytokine production, and tissue inflammation. Malaria is the most frequently imported tropical disease in the UK with an annual case load of around 2000. P. falciparum is the predominant imported species, and failure to take chemoprophylaxis is the commonest risk factor.

scholarly journals Homozygosity for TYK2 P1104A underlies tuberculosis in about 1% of patients in a cohort of European ancestry

2019 ◽  
Vol 116 (21) ◽  
pp. 10430-10434 ◽  
Author(s):  
Gaspard Kerner ◽  
Noe Ramirez-Alejo ◽  
Yoann Seeleuthner ◽  
Rui Yang ◽  
Masato Ogishi ◽  
...  
Keyword(s):  
Odds Ratio ◽  
Genetic Basis ◽  
Sub Saharan Africa ◽  
European Ancestry ◽  
Uk Biobank ◽  
The United Kingdom ◽  
The Common ◽  
Sub Saharan ◽  
The Uk ◽  
High Level

The human genetic basis of tuberculosis (TB) has long remained elusive. We recently reported a high level of enrichment in homozygosity for the common TYK2 P1104A variant in a heterogeneous cohort of patients with TB from non-European countries in which TB is endemic. This variant is homozygous in ∼1/600 Europeans and ∼1/5,000 people from other countries outside East Asia and sub-Saharan Africa. We report a study of this variant in the UK Biobank cohort. The frequency of P1104A homozygotes was much higher in patients with TB (6/620, 1%) than in controls (228/114,473, 0.2%), with an odds ratio (OR) adjusted for ancestry of 5.0 [95% confidence interval (CI): 1.96–10.31, P = 2 × 10−3]. Conversely, we did not observe enrichment for P1104A heterozygosity, or for TYK2 I684S or V362F homozygosity or heterozygosity. Moreover, it is unlikely that more than 10% of controls were infected with Mycobacterium tuberculosis, as 97% were of European genetic ancestry, born between 1939 and 1970, and resided in the United Kingdom. Had all of them been infected, the OR for developing TB upon infection would be higher. These findings suggest that homozygosity for TYK2 P1104A may account for ∼1% of TB cases in Europeans.

Impact of the HIV epidemic in sub-Saharan Africa on the pattern of HIV in the UK

AIDS ◽  
2003 ◽  
Vol 17 (11) ◽  
pp. 1683-1690 ◽  
Author(s):  
Katy Sinka ◽  
Janet Mortimer ◽  
Barry Evans ◽  
Dilys Morgan
Keyword(s):  
Sub Saharan Africa ◽  
Hiv Epidemic ◽  
Sub Saharan ◽  
The Uk

Postharvest losses and waste in developed and less developed countries: opportunities to improve resource use

2010 ◽  
Vol 149 (S1) ◽  
pp. 37-45 ◽  
Author(s):  
R. J. HODGES ◽  
J. C. BUZBY ◽  
B. BENNETT
Keyword(s):  
Financial Incentives ◽  
Poverty Reduction ◽  
Developed Countries ◽  
Sub Saharan Africa ◽  
Less Developed Countries ◽  
The Usa ◽  
Private And Public ◽  
Food Losses ◽  
Sub Saharan ◽  
The Uk

SUMMARYThis review compares and contrasts postharvest food losses (PHLs) and waste in developed countries (especially the USA and the UK) with those in less developed countries (LDCs), especially the case of cereals in sub-Saharan Africa. Reducing food losses offers an important way of increasing food availability without requiring additional production resources, and in LDCs it can contribute to rural development and poverty reduction by improving agribusiness livelihoods. The critical factors governing PHLs and food waste are mostly after the farm gate in developed countries but before the farm gate in LDCs. In the foreseeable future (e.g. up to 2030), the main drivers for reducing PHLs differ: in the developed world, they include consumer education campaigns, carefully targeted taxation and private and public sector partnerships sharing the responsibility for loss reduction. The LDCs’ drivers include more widespread education of farmers in the causes of PHLs; better infrastructure to connect smallholders to markets; more effective value chains that provide sufficient financial incentives at the producer level; opportunities to adopt collective marketing and better technologies supported by access to microcredit; and the public and private sectors sharing the investment costs and risks in market-orientated interventions.

Experience of HIV Disease in a London District General Hospital

1995 ◽  
Vol 6 (1) ◽  
pp. 47-49
Author(s):  
R J Coker ◽  
N Desmond ◽  
M Poznansky ◽  
C Smith ◽  
M S Shafi ◽  
...  
Keyword(s):  
General Hospital ◽  
District General Hospital ◽  
Sub Saharan Africa ◽  
Epidemiological Surveillance ◽  
Hiv Disease ◽  
Middlesex Hospital ◽  
Hiv Test ◽  
Sub Saharan ◽  
The Uk ◽  
Hiv 1

The aim of this paper is to describe and discuss the experience of HIV disease in Central Middlesex Hospital, London up to June 1993. A retrospective study of the total number of HIV-positive patients cared for was performed. In addition, prospectively collected data as part of local epidemiological surveillance from January 1987 to June 1993 on all HIV test requests was analysed. Between January 1987 and June 1993 3695 individuals were tested for HIV-1 antibody at Central Middlesex Hospital. Of these, 101 HIV-1 seropositive individuals were identified and have attended this District General Hospital. Seven HIV-1 seropositive individuals were identified from before December 1986. Sixty (56%) had acquired their infection heterosexually. Thirty-eight (35%) originated from the UK and 47 (44%) from sub-Saharan Africa; the remaining 23 (21%) originated from the rest of Europe, South America and the Caribbean. Thirty-four (31%) of the patient group developed AIDS during follow-up at the hospital and in 26 individuals AIDs developed within 2 months of their first positive HIV result. The mean survival of 20 patients after AIDS-defining diagnoses was 7 months 18 days. This unselected group of HIV-1 seropositive patients present late in the course of their HIV disease and survival following AIDS is poor.

Making prevention public: The co-production of gender and technology in HIV prevention research

2012 ◽  
Vol 42 (6) ◽  
pp. 922-944 ◽  
Author(s):  
Catherine M. Montgomery
Keyword(s):  
Hiv Prevention ◽  
New Technologies ◽  
Sub Saharan Africa ◽  
Therapeutic Success ◽  
Vaginal Microbicides ◽  
Gender And Technology ◽  
Sub Saharan ◽  
The Uk ◽  
Design And Testing

This paper brings together the study of transnational flows in global health and the gendering of technological artefacts. It does so through a case study of vaginal microbicides for HIV prevention, which have commonly been advocated for as a tool for women’s empowerment in parts of the world where HIV is most prevalent, namely sub-Saharan Africa. Drawing on fieldwork in the UK and Zambia, I argue that there is nothing inherently gendered about this ‘woman-controlled’ technology. Combining the notions of scripting and ‘making things public’, I demonstrate the political nature of transnational technology design and testing in the field of sexual health. Rather than framing this in terms of ethical debates, as is frequently the case in studies about the ‘global South’, I ground the analysis in the scripting and de-scripting of technologies and users. By focusing on how things are made public in HIV prevention, I draw attention to the normative, transformative and political potentials of new technologies, such as microbicides, and discuss the implications for their therapeutic success.

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