An updated examination of the perception of barriers for pharmacogenomics implementation and the usefulness of drug/gene pairs in Latin America and the Caribbean

Pharmacogenomics (PGx) is considered an emergent field in developing countries. Research on PGx in the Latin American and the Caribbean (LAC) region remains scarce, with limited information in some populations. Thus, extrapolations are complicated, especially in mixed populations. In this paper, we reviewed and analyzed pharmacogenomic knowledge among the LAC scientific and clinical community and examined barriers to clinical application. We performed a search for publications and clinical trials in the field worldwide and evaluated the contribution of LAC. Next, we conducted a regional structured survey that evaluated a list of 14 potential barriers to the clinical implementation of biomarkers based on their importance. In addition, a paired list of 54 genes/drugs was analyzed to determine an association between biomarkers and response to genomic medicine. This survey was compared to a previous survey performed in 2014 to assess progress in the region. The search results indicated that Latin American and Caribbean countries have contributed 3.44% of the total publications and 2.45% of the PGx-related clinical trials worldwide thus far. A total of 106 professionals from 17 countries answered the survey. Six major groups of barriers were identified. Despite the region's continuous efforts in the last decade, the primary barrier to PGx implementation in LAC remains the same, the "need for guidelines, processes, and protocols for the clinical application of pharmacogenetics/pharmacogenomics". Cost-effectiveness issues are considered critical factors in the region. Items related to the reluctance of clinicians are currently less relevant. Based on the survey results, the highest ranked (96%-99%) gene/drug pairs perceived as important were CYP2D6/tamoxifen, CYP3A5/tacrolimus, CYP2D6/opioids, DPYD/fluoropyrimidines, TMPT/thiopurines, CYP2D6/tricyclic antidepressants, CYP2C19/tricyclic antidepressants, NUDT15/thiopurines, CYP2B6/efavirenz, and CYP2C19/clopidogrel. In conclusion, although the global contribution of LAC countries remains low in the PGx field, a relevant improvement has been observed in the region. The perception of the usefulness of PGx tests in biomedical community has drastically changed, raising awareness among physicians, which suggests a promising future in the clinical applications of PGx in LAC.

Pruebas moleculares para el diagnóstico de COVID-19: La respuesta de Sudamérica

Actualmente a nivel mundial se utiliza la reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR) como una técnica de alta precisión en la detección y amplificación de secciones específicas de la estructura génica. En tal sentido es considerado como prueba diagnóstica molecular en la detección del SARS-CoV-2. Se realizó una revisión de la literatura en artículos publicados en los últimos 5 años (2015 – 2020). Se consultaron las bases de datos: PUBMED (Medline), PUBMED CENTRAL, y SCIELO. Se recuperaron artículos en español, portugués, e inglés, mediante los términos de búsqueda SARS-CoV-2, RT-PCR, y COVID-19. Las RT-PCR que utilicen especímenes de hisopado nasal y faríngeos son considerados como gold standard en casos sospechosos de COVID-19. Mediante lo revisado a nivel de Sudamérica, la RT-PCR resultó ser la prueba de elección durante el período menor a 7 días de infección, resaltando la producción in house en escala por Uruguay y la Prueba de amplificación isotérmica mediada por bucle (RT-LAMP) adaptado en Perú, como una alternativa diagnóstica rápida con principios similares a la RT-PCR, solo que para establecimientos de salud con menor equipamiento, e infraestructura y personal entrenado. La disponibilidad de pruebas diagnósticas moleculares también es crucial para el aislamiento de casos positivos y el seguimiento de la cadena epidemiológica de transmisión.

HLA-G 3'UTR haplotype frequencies in highland and lowland South Native American populations

Human Leukocyte Antigen (HLA)-G participates in several biological processes, including reproduction, vascular remodeling, immune tolerance, and hypoxia response. HLA-G is a potential candidate gene for high altitude adaptation since its expression is modulated in both micro and macro environment under hypoxia and constant cellular stress. Besides the promoter region, the HLA-G 3'untranslated region (UTR) influences HLA-G expression patterns through several post-transcriptional mechanisms. Currently, the 3'UTR genetic diversity in terms of altitude adaptation of Native American populations is still unexplored, particularly at high altitude ecoregions. Here, we evaluated 288 Native Americans from 9 communities located in the Andes [highland (HL); ≥2,500 m (range = 2,838-4,433 m)] and 8 populations located in lowland (LL) regions [<2,500 m (range = 80-431 m); Amazonian tropical forest, Brazilian central plateau, and Chaco] of South America. In total, nine polymorphic sites and ten haplotypes were observed. The most frequent haplotypes (UTR-1, UTR-2, and UTR-3) accounted for ∼ 77% of haplotypes found in LL, while in the HL, the same haplotypes reach ∼ 93%. Also, a remarkable high frequency of putative ancestral UTR-5 haplotype was observed in LL (21.5%), while in HL UTR-2 reaches up to 47%. Further, UTR-2 frequency positively correlates with altitude-related variables, while a negative correlation for UTR-5 was observed. From an evolutionary perspective, we observed a tendency towards balancing selection in HL and LL populations thus suggesting that haplotypes of ancient and more derived alleles may have been co-opted for relatively recent adaptations such as those experienced by modern humans in the highland and lowland of South America. We also discuss how long-term balancing selection can be a reservoir of genetic variants that can be positively selected. Finally, our study provides some pieces of evidence that HLA-G 3'UTR haplotypes may have contributed to high altitude adaptation in the Andes.

Clinical characteristics of older patients with COVID-19: a systematic review of case reports

In the context of the current COVID-19 pandemic, higher morbidity and mortality have been reported in older adults. This age group presents physiological changes and its own clinical conditions such as frailty, dementia, among others.

OBJECTIVE

To describe the characteristics of COVID-19 patients, both over and under 80 years old, by conducting a systematic review of the literature describing case reports, and to summarize and critically assess these characteristics.

METHODS

Systematic review. The study was registered on the Registry of Health Research Projects (PRISA) of the Peruvian National Institute of Health (code EI00000631). Five electronic databases (Scopus, PubMed, PubMed Central, LILACS, and SCIELO) were systematically searched during the period between December 31, 2019 and April 16, 2020. The search focused on case reports, case studies, and case series of older people with COVID-19 infection aged over or under 80 years. When selecting the cases, priority was given to clinical and epidemiological profile, laboratory and imaging patterns, and comprehensive geriatric evaluation.

RESULTS

1,149 articles were identified; after applying the filters, a total of 15 publications of case reports and complete records of 27 older adults were obtained. The most frequent age group was between 60 to 69 years old. There is little literature regarding case reports of older adults aged over 80 years. The most frequent parameters were hypertension, fever, cough, respiratory distress, ground-glass opacification in chest radiography and tomography. Furthermore, decrease in PaO2/FiO2 ratio and lymphocytes, and increase in C-reactive protein and Interleukin 6 were observed.

CONCLUSIONS

This systematic review found little available information of patients under 80 years old, and far less for those over 80 years old, and an absence of comprehensive geriatric assessment.

Exploración de la actividad antibacteriana de Metformina frente a Escherichia coli, Staphylococcus aureus y Pseudomonas aeruginosa

El objetivo del estudio es determinar la actividad antibacteriana de Metformina frente a Escherichia coli, Staphylococcus aureus y Pseudomonas aeruginosa. Se evaluó la actividad antibacteriana mediante la técnica de Kirby Bauer. Se utilizó cepas de Escherichia coli (ATCC 25922), Staphylococcus aureus (ATCC 25923) y Pseudomonas aeruginosa (ATCC 27853), las cuales se expusieron a Metformina en concentraciones de 250 mg y 500 mg, Ciprofloxacino (CIP) 5 µg, Imipenem (IPM) 10 µg, y Cefoxitin (FOX) 30 µg. Frente a Escherichia coli, Staphylococcus aureus y Pseudomonas aeruginosa se presentó un halo de inhibición de 6 mm. para Metformina 250 mg, 6 mm. para Metformina 500 mg, y un halo de inhibición >25 mm. con el uso de Ciprofloxacino 5 µg, Cefoxitin 30 µg, e Imipenem 10 µg respectivamente. En conclusion, In vitro Metformina a dosis de 250 y 500 mg, no presentó efecto antibacteriano frente a Escherichia coli, Staphylococcus aureus y Pseudomonas aeruginosa.

The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations

This study focuses on the genetic history of the Quechua‐Lamistas, inhabitants of the Lamas Province in the San Martin Department, Peru, who speak their own distinct variety of the Quechua family of languages. It has been suggested that different pre‐Columbian ethnic groups from the Peruvian Amazonia, like the Motilones or “shaven heads”, assimilated the Quechua language and then formed the current native population of Lamas. However, many Quechua‐Lamistas claim to be direct descendants of the Chankas, a famous pre‐Columbian indigenous group that escaped from Inca rule in the Andes. To investigate the Quechua‐Lamistas and Chankas’ ancestries, we compared uniparental genetic profiles (17 STRs of Q‐M3 Y‐chromosome and mtDNA complete control region haplotypes) among autochthonous Amazonian and Andean populations from Peru, Bolivia and Ecuador. The phylogeographic and population genetic analyses indicate a fairly heterogeneous ancestry for the Quechua‐Lamistas, while they are closely related to their neighbours who speak Amazonian languages, presenting no direct relationships with populations from the region where the ancient Chankas lived. On the other hand, the genetic profiles of self‐identified Chanka descendants living in Andahuaylas (located in the Apurimac Department, Peru, in the Central Andes) were closely related to those living in Huancavelica and the assumed Chanka Confederation area before the Inca expansion.

Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes

The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.

The genetic history of indigenous populations of the Peruvian and Bolivian Altiplano: the legacy of the Uros

The Altiplano region of the South American Andes is marked by an inhospitable climate to which the autochthonous human populations adapted and then developed great ancient civilizations, such as the Tiwanaku culture and the Inca Empire. Since pre-Columbian times, different rulers established themselves around the Titicaca and Poopo Lakes. By the time of the arrival of Spaniards, Aymara and Quechua languages were predominant on the Altiplano under the rule of the Incas, although the occurrence of other spoken languages, such as Puquina and Uruquilla, suggests the existence of different ethnic groups in this region. In this study, we focused on the pre-Columbian history of the autochthonous Altiplano populations, particularly the Uros ethnic group, which claims to directly descend from the first settlers of the Andes, and some linguists suggest they might otherwise be related to Arawak speaking groups from the Amazon. Using phylogeographic, population structure and spatial genetic analyses of Y-chromosome and mtDNA data, we inferred the genetic relationships among Uros populations (Los Uros from Peru, Uru-Chipaya and Uru-Poopo from Bolivia), and compared their haplotype profiles with eight Aymara, nine Quechua and two Arawak (Machiguenga and Yanesha) speaking populations from Peru and Bolivia. Our results indicated that Uros populations stand out among the Altiplano populations, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Finally, our results support the distinctive ancestry for the Uros populations of Peru and Bolivia, which are likely derived from ancient Andean lineages that were partially replaced during more recent farming expansion events and the establishment of complex civilizations in the Andes.