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Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015.

ABSTRACT: The global diversity of HIV forms a major challenge to the development of an HIV vaccine, as well as diagnostic, drug resistance, and viral load assays, which are essential to reaching the UNAIDS 90:90:90 targets. We sought to determine country level HIV-1 diversity globally between 1990 and 2015. We assembled a global HIV-1 molecular epidemiology database through a systematic literature search and a global survey. We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published from 1 January 1990 to 31 December 2015. We collected additional unpublished data through a global survey of experts. Prevalence studies with original HIV-1 subtyping data collected between 1990 and 2015 were included. This resulted in a database with 383,519 subtyped HIV-1 samples from 116 countries over four time periods (1990 to 1999, 2000 to 2004, 2005 to 2009, and 2010 to 2015). We analyzed country-specific numbers of distinct HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in each time period. We also analyzed country-specific proportions of infections due to HIV-1 recombinants, CRFs, and URFs and calculated the Shannon diversity index for each country. Finally, we analyzed global temporal trends in each of these measures of HIV-1 diversity. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries such as Chad, Democratic Republic of the Congo, Angola, and Republic of the Congo have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe (Spain and France) and North America (United States) (up to 39 distinct HIV-1 variants in Spain). The proportion of HIV-1 infections due to recombinants was highest in Southeast Asia (>95% of infections in Viet Nam, Cambodia, and Thailand), China, and West and Central Africa, mainly due to high proportions of CRF01_AE and CRF02_AG. Other CRFs played major roles (>75% of HIV-1 infections) in Estonia (CRF06_cpx), Iran (CRF35_AD), and Algeria (CRF06_cpx). The highest proportions of URFs (>30%) were found in Myanmar, Republic of the Congo, and Argentina. Global temporal analysis showed consistent increases over time in country level numbers of distinct HIV-1 variants and proportions of CRFs and URFs, leading to increases in country level HIV-1 diversity. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to prevention and treatment efforts. HIV-1 molecular epidemiological surveillance needs to be continued and improved.IMPORTANCE This is the first study to analyze global country level HIV-1 diversity from 1990 to 2015. We found extremely wide variation in complexity of country level HIV diversity around the world. Central African countries have the most diverse HIV epidemics. The number of distinct HIV-1 subtypes and recombinants was greatest in Western Europe and North America. The proportion of HIV-1 infections due to recombinants was highest in South-East Asia, China, and West and Central Africa. The highest proportions of URFs were found in Myanmar, Republic of the Congo, and Argentina. Our study provides epidemiological evidence that the HIV pandemic is diversifying at country level and highlights the increasing challenge to HIV vaccine development and diagnostic, drug resistance, and viral load assays.

SUBMITTER: Hemelaar J

PROVIDER: S-EPMC7944450 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Epilepsy is a major neurological disorder that affects approximately 65 million people worldwide. Globally, the burden of epilepsy is not evenly distributed, with more than 80% of sufferers residing in low- and middle-income countries. This study estimates the burden of epilepsy in mainland China from 1990 to 2015 and explores the variations of burden by age and gender.We conducted a systematic review of the peer-reviewed literature from 1990 to 2015 using Chinese and English academic databases (CNKI, WanFang, VIP and PubMed) to identify population-based prospective studies on the prevalence of epilepsy in mainland Chinese. Multilevel mixed-effects logistic regression was used to estimate the prevalence of lifetime epilepsy (LTE), and restricted cubic regression splines were applied to model the functional forms of the non-linear effects of age and LTE prevalence. Random-effect meta-analysis was used to obtain the pooled prevalence of 1-year active epilepsy (AE), 2-year AE and 5-year AE separately. To estimate the number of people with LTE and AE in the years 1990, 2000, and 2015, LTE and AE prevalence were multiplied by the total population of mainland China of the corresponding year.Analyses were conducted using 39 prevalence studies that met the inclusion criteria and comprised 77 separate data points (37 on LTE, 16 on 1-year AE, 12 on 2-year AE and 12 on 5-year AE). In 1990, the prevalence of LTE ranged from 1.31‰ (95% CI?=?0.85-2.00) in the 0-4 age group to 2.42‰ (95% confidence interval CI?=?1.60-3.65) in the 30-34 age group. By 2015, the LTE prevalence had increased to 4.57‰ (95% CI?=?2.52-8.27) in the 0-4 group and 8.43‰ (95% CI?=?4.71-15.04) in the 30-34 group. Over the 25-year period, the overall prevalence of LTE had steadily increased by 259%, from 1.99‰ (95% CI?=?1.31-3.02) in 1990 to 7.15‰ (95% CI?=?3.98-12.82) in 2015. The rates of increase were similar across the whole age spectrum, fluctuating around 250%. Between 1990 and 2015, the total number of people with LTE in mainland China increased by 328%, from 2.30 million (95% CI?=?1.51-3.49) in 1990 to 9.84 million (95% CI?=?5.48-17.64) in 2015. The pooled 1-year, 2-year, and 5-year AE prevalence were 3.79‰ (95% CI?=?3.31-4.34), 4.08‰ (95% CI?=?3.41-4.89) and 4.19‰ (95% CI?=?3.42-5.15).The burden of LTE in China has increased substantially between 1990 and 2015, with the prevalence of LTE having more than doubled and the number of people with LTE more than tripled. The large amount of AE cases in China calls for optimal management and treatment. More high-quality epidemiological studies on LTE and AE prevalence are still needed.

Project description:IntroductionPathogen molecular epidemiology determines the origin of specific outbreaks locality of foot-and-mouth disease virus serotype South African Territories-2 sequence-based analysis of highly variable Viral Protein 1 (VP1), which helps to identify the evolution of this virus through time and space. The objective of this study was to compare the differences between SAT-2 VP1 sequences of FMDV circulated in Ethiopia from 1990 to 2015 at the genetic level.MethodsThe nucleotide and amino acid sequences were analyzed using Basic Local Alignment Search Tools (BLAST), Multiple sequence alignment and sequence editing and Phylogenetic tree reconstruction. The nucleotide and amino acid sequences alignment, distance matrix, and phylogenetic tree constructions were done using the MEGA 6.0 software package.Result and discussionIn this analysis, we found 76% nucleotide identities and amino acid similarities among the sequences. The overall group mean distance at nucleotide level was 19% with a mean intra-population diversity of 2%. The lowest sequence variation was observed among sequences obtained from the years 2007/09/10, 2014/15, and 1990/91 which was less than 5% among them. This analysis revealed that in the last 25 years, four different topotypes of the FMDV SAT-2 were circulating in Ethiopia. The Arg-Gly-Asp (RGD) amino acid (AA) motif at AA position 144-146 within the G-H loop of the VP1 protein of FMDV is conserved, but up- and downstream hyper-variable AA sequences are identified. In this study, it was observed that four topotypes (IV, XIV, XIII, and VII) were circulating in Ethiopia for 25 years. Further, compared with sequences from neighboring countries (Sudan, Kenya) confirmed the presence of these topotypes.ConclusionPertinent to this genetic diversity control strategies in Ethiopia should be based on having regular antigenic and genetic vaccine matching tests with the circulating strain within a defined period, space, transboundary nature of the disease and applying biosecurity measures.

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Country Level Diversity of the HIV-1 Pandemic between 1990 and 2015.

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