A new lineage nomenclature to aid genomic surveillance of dengue virus.

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

DNA Barcoding Analysis of Trinidad Haemagogus Mosquitoes Reveals Evidence for Putative New Species.

Background: Haemagogus janthinomys is a primary sylvan vector of yellow fever virus and the emerging Mayaro virus. However, despite its medical importance, there is a dearth of data on the molecular taxonomy of this mosquito species. Methods: In this study, DNA barcoding analysis was performed on 64 adult female mosquitoes from Trinidad morphologically identified as Hg. janthinomys. The mitochondrial cytochrome c oxidase I (COI) gene and ribosomal DNA internal transcribed spacer 2 (ITS2) region of the mosquitoes were PCR amplified and sequenced, and molecular phylogenies inferred. Results: The BLASTN analysis showed that only 20% (n = 13/66) of COI sequences had high similarity (>99% identity) to Hg. janthinomys and the remaining sequences had low similarity (<90% identity) to reference GenBank sequences. Phylogenetic analysis of COI sequences revealed the presence of four strongly supported groups, with one distinct clade that did not align with any reference sequences. Corresponding ITS2 sequences for samples in this distinct COI group clustered into three clades. Conclusions: These molecular findings suggest the existence of a putative new Haemagogus mosquito species and underscore the need for further, more in-depth investigations into the taxonomy and classification of the Haemagogus genus.

Chikungunya: a decade of burden in the Americas.

In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 countries or territories in the Americas. Here, we outline the current status and epidemiological aspects of chikungunya in the Americas and discuss prospects for future research and public health strategies to combat CHIKV in the region.

Human papillomavirus genotypes and their prevalence in a cohort of women in Trinidad / Genotipos del papilomavirus humano y su prevalencia en una cohorte de mujeres en Trinidad

OBJECTIVE: Human papillomavirus (HPV) genotypes and their relative prevalences were determined in a cohort of 310 sexually active women in Trinidad, West Indies. METHODS: Cervical samples were collected with Ayre's spatulas and endocervical brushes. Samples were used for the conventional Papanicolaou test and for determining HPV genotypes by amplification of a section of the viral L1 gene, followed by DNA sequencing and probe hybridization. RESULTS: HPV infections were identified in 126 of 310 (40.6 percent) women. Of them, 83 (65.8 percent) were infected with high-risk HPV, 16 (12.7 percent) with low-risk HPV, and 27 (21.4 percent) with HPV types of unknown risk. HPV 52 (12.7 percent) was the most frequently occurring high-risk type, followed by HPV 66 (10.3 percent), HPV 16 (9.5 percent), and HPV 18 (8.6 percent). High-risk types HPV 16 and HPV 66 were each found in 3 (20.0 percent) and HPV 18 was found in 1 (6.6 percent) of the 15 women with abnormal cytology. CONCLUSIONS: Cervical HPV prevalence and heterogeneity of HPV genotypes are high in this Trinidad cohort. The relative importance of HPV genotypes in the development of cervical lesions needs further investigation in Trinidad in order to better understand the epidemiology of HPV infections as well as to determine the role of HPV testing in the screening, prevention, and control of cervical cancer. This pilot study provided important information on the prevalence of HPV genotypes, which will be used in future nationwide studies.

OBJETIVO: Se determinaron los genotipos del papilomavirus humano (PVH) y su prevalencia relativa en una cohorte de 310 mujeres sexualmente activas de Trinidad, en la zona de las Indias Occidentales. MÉTODOS: Se tomaron muestras del cuello uterino con espátula de Ayre y cepillo endocervical. Las muestras se usaron para llevar a cabo la prueba convencional de Papanicolaou y para determinar los genotipos de PVH mediante la amplificación de una sección del gen vírico L1, seguida de secuenciación del ADN e hibridación con sonda. RESULTADOS: Se encontró una infección por PVH en 126 de las 310 mujeres (40,6 por ciento). De ellas, 83 (65,8 por ciento) estaban infectadas con PVH de alto riesgo, 16 (12,7 por ciento) con PVH de bajo riesgo, y 27 (21,4 por ciento) con tipos de PVH de riesgo desconocido. De los PVH de alto riesgo, el más frecuente fue el PVH 52 (12,7 por ciento), seguido por el PVH 66 (10,3 por ciento), el PVH 16 (9,5 por ciento) y el PVH 18 (8,6 por ciento). Entre las 15 mujeres con citología anormal se encontraron los PVH de alto riesgo 16 y 66 en 3 (20,0 por ciento) mujeres cada uno, y el PVH 18 en 1 (6,6 por ciento). CONCLUSIONES: Tanto la prevalencia de PVH en el cuello uterino como la heterogeneidad de los genotipos de PVH son elevadas en esta cohorte de Trinidad. La importancia relativa de los genotipos de PVH en la aparición de las lesiones cervicales requiere de mayor investigación en Trinidad para conocer más a fondo las características epidemiológicas de las infecciones por PVH, así como para determinar el papel del estudio de los PVH en la detección sistemática, la prevención y el control del cáncer del cuello uterino. Este estudio piloto suministró información importante sobre la prevalencia de los genotipos de PVH, que se usará en futuros estudios que se lleven a cabo en todo el país.

Pfcrt and pfmdr1 alleles associated with chloroquine resistance in Plasmodium falciparum from Guyana, South America

Using DNA extracted from 112 parasitised blood blots, we screened for the population marker of chloroquine resistance (CQR) pfcrt K76T in Plasmodium falciparum infections from Guyana. Pfmdr1 mutations S1034C, N1042D, and D1246Y also associated with CQR were surveyed as well in 15 isolates for which the in vitro responses to CQ were known. Results indicate that the pfcrt K76T is ubiquitous in this environment, and confirmatory sequencing of codons 72 and 76 revealed two novel allelic sequences SVMIT and RVMNT in addition to the previously identified CVMNT and SVMNT haplotypes. The frequency of the pfcrt K76T despite its presence in both CQR and CQS (chloroquine sensitive) infections measured in vivo and in vitro, suggests that it is a useful population marker in this low-transmission setting of sweeping CQR.