Analysis of HIV-1 pol sequences from Panama: identification of phylogenetic clusters within subtype B and detection of antiretroviral drug resistance mutations.

We report the first study to examine phylogenetic relationships and drug resistance mutations in HIV-1 pol sequences from Panama. For this study, we used plasma RNA samples from 135 HIV-1-infected subjects from Panama, of which 82 (61%) had AIDS and 53 (39%) were asymptomatic drug-naïve individuals. Phylogenetic analyses revealed that 133 (98%) subjects were infected with subtype B viruses and 2 AIDS patients harboured recombinant viruses, CRF02_AG/A3 and CRF12_BF/B, respectively. Using a Bayesian phylogeny inference method, 5 strongly supported clusters of > or =5 sequences, designated B-PA1 to B-PA5, were identified within subtype B, together comprising 87 (65.4%) subtype B viruses. Cluster B-PA1 (n=42) was significantly associated with East Panama and clusters B-PA2 (n=15) and B-PA4 (n=10) were associated with West Panama. A Bayesian coalescent analysis indicated that the most recent common ancestors of the four largest clusters were dated in the 1980s and that of the fifth in the early 1990s. The analysis of antiretroviral drug resistance-associated mutations revealed that 8 (9.7%) AIDS patients, all of them antiretroviral drug-experienced, harboured mutations conferring high or intermediate resistance levels to antiretroviral drugs. No drug resistance mutations were detected among the asymptomatic drug-naïve individuals. In conclusion, the phylogenetic analysis of HIV-1 pol sequences from Panama reveals that a majority of subtype B viruses, which are predominant in Panama, branch within well supported intrasubtype phylogenetic clusters, most of them originating in the 1980s, and some with geographical associations, which may reflect either multiple HIV-1 subtype B introductions or the existence of local transmission networks originating in the early epidemic in Panama.

High divergence within the major HIV type 1 subtype B epidemic in Panama.

The first molecular epidemiology study of human immunodeficiency virus type 1 (HIV-1) in Panama has been performed with plasma samples from 66 AIDS patients infected by different transmission routes and obtained from distinct locations. All samples were amplified by RT-PCR and sequenced in gag (p17) and env (C2-C4) genes. Phylogenetic analyses revealed that 64 (97%) of the samples belong to subtype B. We also identified the presence of two CRF, one CRF12_BF and one CRF02_AG. The most notable feature of the subtype B epidemic in Panama was the large genetic distance among isolates with a mean of 15.2% but reaching up to 31.3 % in env, indicating an epidemic with a long period of evolution.

Determination of human cytomegalovirus genetic diversity in different patient populations in Costa Rica.

Seroprevalence of HCMV in Costa Rica is greater than 95% in adults; primary infections occur early in life and is the most frequent congenital infection in newborns. The objectives of this study were to determine the genetic variability and genotypes of HCMV gB gene in Costa Rica. Samples were collected from alcoholics, pregnant women, blood donors, AIDS patients, hematology-oncology (HO) children and HCMV isolates from neonates with cytomegalic inclusion disease. A semi-nested PCR system was used to obtain a product of 293-296 bp of the gB gene to be analyzed by Single Stranded Conformational Polymorphism (SSCP) and sequencing to determine the genetic polymorphic pattern and genotypes, respectively. AIDS patients showed the highest polymorphic diversity with 14 different patterns while fifty-six percent of HO children samples showed the same polymorphic pattern, suggesting in this group a possible nosocomial infection. In neonates three genotypes (gB1, gB2 and gB3), were determined while AIDS patients and blood donors only showed one (gB2). Of all samples analyzed only genotypes gB1, 2 and 3 were determined, genotype gB2 was the most frequent (73%) and mixed infections were not detected. The results of the study indicate that SSCP could be an important tool to detect HCMV intra-hospital infections and suggests a need to include additional study populations to better determine the genotype diversity and prevalence.

Determination of human cytomegalovirus genetic diversity in different patient populations in Costa Rica

La seroprevalencia de citomegalovirus es mayor del 95 por cento en la población adulta de Costa Rica; la infección primaria ocurre muy temprano en la vida y es la infección congénita más frecuente en recién nacidos. El objetivo de este trabajo fue determinar la variabilidad genética y los genotipos del gene gB del citomegalovirus humano. Se recolectaron muestras de sangre de mujeres embarazadas, alcohólicos, pacientes con SIDA, niños con trastornos hemato-oncológicos, donadores de sangre y se incluyeron aislamientos de citomegalovirus de neonatos con enfermedad congénita. Se utilizó un sistema de PCR semi-anidado para obtener una banda de 293-296 pares de bases, la cual fue analizada por la técnica de Polimorfismo conformacional de banda simple (PCBS) y secuenciada para determinar los patrones genéticos polimórficos y los genotipos, respectivamente. La mayor diversidad polimórfica se encontró en los pacientes con SIDA con 14 patrones diferentes mientras que en los niños con trastornos hemato-oncológicos se demostró el mismo patrón en el 56 por cento de los casos, sugiriendo una posible infección nosocomial en este grupo. En los neonatos se encontraron tres genotipos (gB1, gB2, gB3) mientras que en los pacientes con SIDA y en los donadores de sangre solo se demostró el gB2. En las muestras analizadas se determinaron los genotipos gB1, gB2 y gB3 y el gB2 se determinó en el 73 por cento de los casos, no se detectaron infecciones mixtas. Los resultados de este trabajo indican que la técnica del PCBS puede ser una herramienta importante para detectar el citomegalovirus humano en infecciones intrahospitalarias y se sugiere la importancia de incluir poblaciones de estudio adicionales para determinar mejor la diversidad genética y su prevalencia.