Twenty years of prospective molecular epidemiology in Senegal: changes in HIV diversity

Over a 20-year period we have observed the dynamics of HIV-1 subtypes and HIV-2 infection in a prospective cohort of registered female sex workers (FSW) in Dakar, Senegal. Prevalence and incidence rates for HIV-1 and HIV-2 are described from 290 seroprevalent and 193 seroincident subjects who were among the 3,910 women enrolled between 1985 and 2004. We report a significant decrease of HIV-2 prevalence in the cohort, parallel to the introduction and rise of HIV-1 infection. In 328 HIV-1-infected women, a 385-bp C2-V3 fragment of the envelope gene was sequenced and classified into the following subtypes or recombinant forms: 239 (72%) were subtype A [of which 180 (55%) were CRF02_AG and 53 (16%) were A3], 10 (3%) were B, 12 (4%) were C, 11 (4%) were D, 18 (6%) were G, 24 (7%) were CRF06_cpx, and 7 (2%) were CRF09_cpx. We found an increasing proportion of CRF02_AG over many years, but recently subsubtype A3 has over-taken CRF02_AG, with the largest proportion of new infections. The predominance of existing HIV-1 subtypes did not preclude the emergence and increase of other closely related subtypes or recombinant forms. This 20-year prospective serological and sequence analysis of HIV viruses reveals a complex and changing HIV epidemic in Senegal.     

福建省艾滋病分子流行病学的初步调查

艾滋病病毒 (ＨＩＶ)基因的高度变异性 ,使其在传播过程中产生出许多具有基因序列特性的亚型(ｓｕｂｔｙｐｅ) ,并在全球范围流行蔓延过程中形成一定的地区性分布特点。根据ＨＩＶ -ｌ基因组中变异性最大、同时也被研究最多的膜蛋白基因 (ｅｎｖ)核酸和氨基酸序列的同源性 ,目前已确定了由Ａ～Ｊ和Ｏ至少 11种ＨＩＶ - 1亚型。各亚型间基因核苷酸序列的差异较大 ,Ａ～Ｊ亚型间的差异一般在 2 2 %～ 35% ,而Ｏ亚型与Ａ～Ｊ各亚型间的差异则高达50 %以上[1～ 3] 。ＨＩＶ -ｌ基因的高度变异性是研制ＡＩＤＳ疫苗的一个较大障碍。分析和鉴定感…     

分子流行病学在低收入、高负担国家的作用

分子流行病学的出现已经有约20年的历史,其出现的标志是1991年第1个分子菌株分型技术的问世。之后,很多种用于分型的替代技术被开发出来,并被不同程度的应用,其中基于IS6110的RFLP指纹技术、spoligotyping和MIRU—VNTR分型技术已经成功地发展为非常有价值的工具,用于监测和了解疾病在宿主人群中的发病过程。     

Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

Background

Rhinoviruses (RV) are a well-established cause of respiratory illness. RV-C has been associated with more severe illness. We aimed to characterize and compare the clinical presentations and disease severity of different RV type circulating in South Africa.

Method

We performed two analyses of RV-positive specimens identified through surveillance in South Africa across all age groups. First, RV-positive specimens identified through severe acute respiratory illness (SARI) surveillance in four provinces was randomly selected from 2009 to 2010 for molecular characterization. Second, RV-positive specimens identified through SARI, influenza-like illness (ILI) and control surveillance at hospitals and outpatient clinics in during 2012–2013 were used to determine the association of RV type with severe disease. Selected specimens were sequenced, and phylogenetic analysis was performed.

Results

Among the 599 sequenced specimens from 2009 to 2010 and 2012 to 2013, RV-A (285, 48%) and RV-C (247, 41%) were more commonly identified than RV-B (67, 11%), with no seasonality and a high genetic diversity. A higher prevalence of RV infection was identified in cases with SARI [515/962 (26%); aRRR = 1·6; 95% CI 1·21; 2·2] and ILI [356/962 (28%); aRRR = 1·9; 95% CI 1·37; 2·6] compared with asymptomatic controls (91/962, 22%). There was no difference in disease severity between the different type when comparing SARI, ILI and controls.

Conclusion

All three type of RV were identified in South Africa, although RV-A and RV-C were more common than RV-B. RV was associated with symptomatic respiratory illness; however, there was no association between RV type and disease severity.     

Sampling designs for HIV molecular epidemiology with application to Honduras

Proper sampling is essential to characterize the molecular epidemiology of human immunodeficiency virus (HIV). HIV sampling frames are difficult to identify, so most studies use convenience samples. We discuss statistically valid and feasible sampling techniques that overcome some of the potential for bias due to convenience sampling and ensure better representation of the study population. We employ a sampling design called stratified cluster sampling. This first divides the population into geographical and/or social strata. Within each stratum, a population of clusters is chosen from groups, locations, or facilities where HIV-positive individuals might be found. Some clusters are randomly selected within strata and individuals are randomly selected within clusters. Variation and cost help determine the number of clusters and the number of individuals within clusters that are to be sampled. We illustrate the approach through a study designed to survey the heterogeneity of subtype B strains in Honduras.     

The molecular epidemiology of HIV type 1 of men in Mexico

Genotypic characteristics of human immunodeficiency virus type 1 (HIV-1) in Mexico were investigated in a multicenter study that involved centers in five geographic regions of the country. Study samples (n = 65) collected from male patients in 1998-1999 were sequenced within the C2-V5 region of the gp120 env gene. Phylogenetic analysis revealed that subtype B predominates in Mexico. The level of interpatient nucleotide diversity (mean value of 8.9%) was congruent with multiple introductions of the virus and the "aging" epidemic in Mexico. One-third of samples (30.8% of cases) showed polymorphism within the crown of the V3 loop demonstrating non-GPGR motifs. Two new motifs in the V3 loop crown - HPGG and GPEG - were observed. The evolution of the AIDS epidemic in Mexico should be closely monitored since non-B HIV-1 subtypes might be introduced. The nucleotide sequences were deposited in the GenBank under accession numbers AF200855-AF200869, AF200871-AF200892, and AF200894-AF200921.     

Present status of studies on epidemiology and molecular epidemiology of Mycobacterium kansasii, in special reference to its molecular epidemiology

There appears to be some genetic diversity among Mycobacterium kansasii (M. kansasii) isolates recovered throughout the world. Restriction analysis of heat shock protein 65-polymerase chain reaction-restriction analysis (hsp65PRA) showed that M. kansasii contains seven subspecies genetically distinct from M. kansasii isolates. M. kansasii genotype I is predominant in Japan and shows a very tight clonal structure. Different molecular typing methods including the 16S-23S rRNA spacer (ITS) region, RFLP, and PFGE analysis have been applied to isolates worldwide, and M. kansasii genotype I, as defined by hsp65PRA, appears to be highly clonal and the most common genotype associated with human disease. However, the identification of M. kansasii at the subtype level may possibly be more than just an interesting epidemiological tool; it may be relevant to determining the infectious pathway and clinical management of individual cases, as it allows the differentiation of potentially pathogenic subtypes from nonpathogenic subtypes. This review has been followed by the first review of the epidemiology of M. kansasii, and summarizes the evidence of molecular epidemiology and establishes the validity and importance of studies of M. kansasii. Further, the more precise definition of various M. kansasii isolates herein should provide a significant contribution to the understanding of key aspects of its biology, genotype, and molecular epidemiology.     

Transmission network structure and newly diagnosed HIV infections: a molecular epidemiology study

Background

Improved understanding of network structure—one of the driving forces of HIV transmission—could facilitate the design of interventions. We aimed to assess the structure of HIV transmission networks and their relationship to newly diagnosed cases in Hong Kong, where sexual transmission between men prevails.

HIV epidemiology and prevention interventions

Several presentations at the 2007 Conference on Retroviruses and Opportunistic Infections focused on the underlying factors driving the HIV epidemic in selected regions of the world and on selected populations. The conference also provided updated data on 1 of 2 successful adult male circumcision efficacy trials to prevent HIV acquisition, and a review of 1 of 2 unsuccessful efficacy trials of the microbicide cellulose sulfate. Presentations also focused on strategies to prevent HIV acquisition through pre-exposure prophylaxis, treatment of sexually transmitted diseases, and prevention of mother-to-child transmission through breastfeeding.     

HIV/AIDS epidemiology, pathogenesis, prevention, and treatment

The HIV-1 pandemic is a complex mix of diverse epidemics within and between countries and regions of the world, and is undoubtedly the defining public-health crisis of our time. Research has deepened our understanding of how the virus replicates, manipulates, and hides in an infected person. Although our understanding of pathogenesis and transmission dynamics has become more nuanced and prevention options have expanded, a cure or protective vaccine remains elusive. Antiretroviral treatment has transformed AIDS from an inevitably fatal condition to a chronic, manageable disease in some settings. This transformation has yet to be realised in those parts of the world that continue to bear a disproportionate burden of new HIV-1 infections and are most affected by increasing morbidity and mortality. This Seminar provides an update on epidemiology, pathogenesis, treatment, and prevention interventions pertinent to HIV-1.     

The influence of the expanding HIV genetic diversity on molecular diagnosis in the Philippines

Since the discovery in the Philippines of the first AIDS case in 1984, several subtypes of HIV-1 have been discovered. From the persons diagnosed in the early 1980s only subtype B was found and thereafter other subtypes, C, D, E, and F were also identified although HIV was not particularly prevalent at that time. In this paper, we determine whether the rapid expansion of genetic diversity will influence molecular diagnosis by polymerase chain reaction (PCR). First, we determine HIV-1 subtype on env (V3) and gag (p24) gene as a means of rapid genetic diversity. Secondly, we tried to analyse and identify homologous regions of gag (p24) gene of HIV genome for diagnostic purposes of designing primers. Out of 46 samples analysed, six subtypes were classified based on gag and env gene subtyping namely: 33 subtype B/B (71.2%), nine subtype A/E and one each subtype C/C, A/B and G/A (2.2% each). As a result, occurrence of non-subtype B and inter-subtype recombinant contributed to expanding genetic diversity. Based on inter- and intra-subtype gag alignment, oligonucleotides (>10 bases in length) could be easily selected as a universal primer to produce the PCR product composed of more than 100bp. This indicates that the PCR technology can be safely used with limited length of primers for the diagnosis of HIV infection in this country.     

The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002

CRF01_AE and subtype B have dominated the HIV-1 epidemic in Thailand since 1989. We reported a new circulating recombinant form of HIV-1, CRF15_01B, as well as other unique CRF01_AE/B recombinants among prevalent HIV infections in Thailand. We sought to study this challenging molecular picture through assessment of subtypes among recent HIV-1 seroconverters in northern Thai drug users. A total of 847 HIV-1 seronegative drug users (342 IDU and 505 non-IDU) were enrolled, from 1999 to 2002, in a prospective study; 39 HIV-1 incident cases were identified and characteristics were collected. The overall HIV-1 incidence rate was 2.54/100PY, but it was 10.0/100PY among male IDU. HIV was strongly associated with injection history; 38 of 39 seroconverters gave a history of IDU. A near full-length genome of HIV-1 was recovered by PCR amplification and sequenced from peripheral mononuclear cell extracted DNA of 38 seroconverters. Phylogenetic analysis revealed that 33 (86.8%) were CRF01_AE and 5 (13.2%) were CRF01_AE/B recombinants. These recombinants had different structure but shared some common breakpoints, indicating an ongoing recombination process. Recombinant infection increased with year of sampling (0 to 57.1%). The molecular epidemiology of HIV-1 among drug users in northern Thailand has thus entered a new era. CRF01_AE remains predominant while pure subtype B is becoming rare, and now a substantial component of the epidemic. These findings support the need for CRF01_AE and subtype B components in clade-matched vaccine strategies for Thai phase III trials. Ongoing molecular surveillance of circulating HIV-1 strains is imperative for the evaluation of HIV vaccine efficacy.     

The molecular epidemiology of HIV type 1 among Vietnamese Australian injecting drug users in Melbourne, Australia

The proportion of human immunodeficiency virus type 1 (HIV-1) among Vietnamese injecting drug users (IDUs) in Melbourne, Australia exceeds that of the background population. To investigate the molecular epidemiology of HIV-1 among this group, the C2-V4 region of the HIV-1 envelope was directly sequenced from 11 Vietnamese Australians and 19 non-Vietnamese Australian controls. A significant difference in the distribution of the HIV-1 subtypes was demonstrated, with greater than 50% of Vietnamese Australian IDU shown to be infected with CRF01_AE-the predominant subtype in Southeast Asia, rather than subtype B, which dominates the Australian epidemic and which was found in 89.5% of the non-Vietnamese controls. The genetic diversity of the CRF01_AE epidemic in Vietnamese Australian IDUs was substantially lower that that of the background subtype B, consistent with a more recent introduction of a limited number of viral strains from Vietnam. These results support public health policy targeting Australian IDUs of Vietnamese ethnicity as a distinct vulnerable population.     

结膜吸吮线虫病原学 流行病学及遗传多态性研究进展

目前,有3种吸吮线虫可感染人体导致吸吮线虫病：结膜吸吮线虫（Thelaziacallipaeda）、加利福尼亚吸吮线虫（T. californiensis）和大口吸吮线虫（T. gulosa）。结膜吸吮线虫主要分布在欧洲和亚洲地区,加利福尼亚吸吮线虫和大口吸吮线虫主要分布在北美地区。结膜吸吮线虫病主要流行于经济卫生条件较差的地区且当地有大量的家养或野生动物感染,虫种鉴定主要依赖口及生殖器官的特征,果蝇为其传播媒介,在亚洲是冈田绕眼果蝇（Phorticaokadai）,在欧洲传播媒介则为变色伏绕眼果蝇（P. variegate）。我国是世界上结膜吸吮线虫病例数最多的国家,其他亚洲国家如韩国、日本等也有大量病例报道;欧洲地区病例较少,但在多数国家感染该虫的野生及家养动物较普遍。基于cox1基因,在全球范围内共鉴定出21个单倍型,其中单倍型1（Haplotype1）仅在欧洲不同地区不同宿主之间循环,其他20个单倍型分布于东亚国家（中、韩、日）,又以我国的结膜吸吮线虫遗传多态性水平最高。遗传差异性分析表明,亚洲结膜吸吮线虫类群与欧洲类群存在长期地理隔离,且这两个类群在更新世中期已经开始分化。