Integrating real-world data from Brazil and Pakistan into the OMOP common data model and standardized health analytics framework to characterize COVID-19 in the Global South.

OBJECTIVES: The aim of this work is to demonstrate the use of a standardized health informatics framework to generate reliable and reproducible real-world evidence from Latin America and South Asia towards characterizing coronavirus disease 2019 (COVID-19) in the Global South. MATERIALS AND METHODS: Patient-level COVID-19 records collected in a patient self-reported notification system, hospital in-patient and out-patient records, and community diagnostic labs were harmonized to the Observational Medical Outcomes Partnership common data model and analyzed using a federated network analytics framework. Clinical characteristics of individuals tested for, diagnosed with or tested positive for, hospitalized with, admitted to intensive care unit with, or dying with COVID-19 were estimated. RESULTS: Two COVID-19 databases covering 8.3 million people from Pakistan and 2.6 million people from Bahia, Brazil were analyzed. 109 504 (Pakistan) and 921 (Brazil) medical concepts were harmonized to Observational Medical Outcomes Partnership common data model. In total, 341 505 (4.1%) people in the Pakistan dataset and 1 312 832 (49.2%) people in the Brazilian dataset were tested for COVID-19 between January 1, 2020 and April 20, 2022, with a median [IQR] age of 36 [25, 76] and 38 (27, 50); 40.3% and 56.5% were female in Pakistan and Brazil, respectively. 1.2% percent individuals in the Pakistan dataset had Afghan ethnicity. In Brazil, 52.3% had mixed ethnicity. In agreement with international findings, COVID-19 outcomes were more severe in men, elderly, and those with underlying health conditions. CONCLUSIONS: COVID-19 data from 2 large countries in the Global South were harmonized and analyzed using a standardized health informatics framework developed by an international community of health informaticians. This proof-of-concept study demonstrates a potential open science framework for global knowledge mobilization and clinical translation for timely response to healthcare needs in pandemics and beyond.

Morphological, molecular characterization and taxonomic status of Triplophysa marmorata and Triplophysa kashmirensis (Cypriniformes: Nemacheilidae) from Kashmir valley, India

AbstractIn India the distribution of genus Triplophysa has been reported only in the upper drainage of the Indus River in Jammu and Kashmir and Lahul and Spiti area of Himachal Pradesh. There is no study on the taxonomic characterization of this genus from Kashmir Himalaya. Therefore the present study was aimed to characterize two important fish species Triplophysa marmorata and T. kashmirensis from Kashmir valley, by using morphometric and molecular tools. It is difficult to discriminate these two species due to the poor quality of original descriptions, and the lack of good reviews. Keeping this in view, a morphometric and molecular study was conducted. Morphometric data were analyzed by using univariate analysis of variance (ANOvA) and multivariate analyses (Principal component analysis) and mtDNA marker Cytochrome oxidase 1 was used for molecular support. Altogether, 22 morphometric characters were used and 15 characters were found significantly variable (P < 0.05). First two components of principal component analysis (PCA) i.e. PC1 and PC2 grouped these two species into separate clusters. The Cytochrome oxidase 1 analysis showed that the mean intraspecific nucleotide divergence (K2P) was 0.001 and interspecific nucleotide divergence was 0.007. Despite having low K2P divergence, these two species got separated into two distinct clades in both Neighbour joining (NJ) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree building methods. But the pattern of clade formation showed that these species were recently radiated from each other and may have the same ancestor. Furthermore, these two species were found closer to Nemacheilidae than to Balitoridae family in the phylogenetic analysis. The molecular divergence between these species was also supported by variance in morphometric data. This work may build the base for the revision of taxonomic identity of these two important fishes of genus Triplophysa. The present investigation formulated that, based on morphological and mtDNA COI sequences analysis, these two taxonomic Triplophysa species should be considered as valid. The results may further assist to enhance the knowledge of the ichthyologists in understanding the ichthyofauna of Kashmir valley and will help them in planning strategies for conservation and management of these less studied small indigenous species along their natural range of distribution. Rev. Biol. Trop. 64 (2): 473-482. Epub 2016 June 01.

ResumenEn la India, la distribución del género Triplophysa se ha reportado solo en la parte superior del río Indus en Jammu, Kashmir, Lahul y Spiti en el área de Himachal Pradesh. No existen publicaciones acerca de la caracterización taxonómica de este género en Kashmir Himalaya. Por lo tanto, en este estudio se caracterizaron dos especies del valle de Kashmir: Triplophysa marmorata y T. kashmirensi, mediante el uso de herramientas morfométricas y moleculares. Es difícil diferenciar entre estas dos species debido a las vagas descripciones originales y a la falta de buenas revisiones. Debido a esto se realizó un estudio morfométrico y molecular. Los datos morfométricos se analizaron mediante un ANOvA y un análisis de componentes principales y el marcador del gen de la citocromo oxidasa 1 se usó para apoyo molecular. En general, se usaron 22 caracteres morfométricos y 15 fueron significativos (P < 0.05). Los dos primeros componentes del análisis de components principales (PCA), PC1 y PC2, agruparon estas dos especies en clusters separados. El análisis con citocromo oxidasa 1 mostró que el promedio de divergencia del nucleótido intraespecífico (K2P) fue de 0.001 y la divergencia del nucleótido intraespecífico fue de 0.007. A pesar de la baja divergencia de K2P, estas dos species se separan en dos clados diferentes tanto por el método NJ como por el método UPGMA. Sin embargo, el patrón de formación del clado mostró que estas species radiaron recientemente una de la otra y que podrían tener un ancestro en común. Además, en el análisis filogenético estas dos especies se encontraron más cerca de la familia Nemacheilidae que de Balitoridae. La divergencia molecular entre estas dos especies también fue respaldada por la varianza en los datos morfométricos. Este estudio puede establecer la base para una revisión taxonómica de estos dos importantes peces del género Triplophysa. Esta investigación postuló que, basada en análisis morfológicos y de secuencia de ADNm COI, estas dos especies taxonómicas de Triplophysa deben considerarse válidas. Los resultados pueden contribuir a mejorar el conocimiento de los ictiólogos en la comprensión de la ictiofauna del valle de Kashmir y les ayudará a planear estrategias de conservación y manejo de estas dos pequeñas especies indígenas y poco estudiadas en su rango de distribución natural.

Morphometric variation and molecular characterization of snow trout species from Kashmir valley, India.

There is a significant taxonomic ambiguity among snow trout species due to their morphometric similarities. In view of this, a morphometric and molecular study was conducted on five different species of genus Schizothorax that have been reported from Kashmir valley. Morphometric data analyzed using multivariate statistics (Principal component analysis and cluster analysis) indicated the significant grouping of species to individual clusters. Mitochondrial DNA cytochrome oxidase I (COI) gene analysis revealed 0.2%-4.5% genetic divergence among the five species. This study confirms that utility of cytochrome oxidase I in species delineation along with morphometric data. Phylogenetic tree obtained using Neighbor-Joining method revealed that all the five species represented distinct species group. The Schizothorax genus formed two distinct clades; one containing S. niger, S. curvifrons and S. plagiostomus, while other clade containing S. esocinus and S. labiatus. This phlogeny trend was also supported by cluster analysis of morphometric characters. The phylogenetic analysis with other published COI sequences revealed distinct nature of these five species. The study may aid in the taxonomic identification of snow trout species in India. This may further increase the knowledge of the ichthyologists in planning conservation and management strategies for these important fish species along with their natural habitat.

Morphological, molecular characterization and taxonomic status of Triplophysa marmorata and Triplophysa kashmirensis (Cypriniformes: Nemacheilidae) from Kashmir valley, India.

In India the distribution of genus Triplophysa has been reported only in the upper drainage of the Indus River in Jammu and Kashmir and Lahul and Spiti area of Himachal Pradesh. There is no study on the taxonomic characterization of this genus from Kashmir Himalaya. Therefore the present study was aimed to characterize two important fish species Triplophysa marmorata and T. kashmirensis from Kashmir valley, by using morphometric and molecular tools. It is difficult to discriminate these two species due to the poor quality of original descriptions, and the lack of good reviews. Keeping this in view, a morphometric and molecular study was conducted. Morphometric data were analyzed by using univariate analysis of variance (ANOVA) and multivariate analyses (Principal component analysis) and mtDNA marker Cytochrome oxidase 1 was used for molecular support. Altogether, 22 morphometric characters were used and 15 characters were found significantly variable (P < 0.05). First two components of principal component analysis (PCA) i.e. PC1 and PC2 grouped these two species into separate clusters. The Cytochrome oxidase 1 analysis showed that the mean intraspecific nucleotide divergence (K2P) was 0.001 and interspecific nucleotide divergence was 0.007. Despite having low K2P divergence, these two species got separated into two distinct clades in both Neighbour joining (NJ) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree building methods. But the pattern of clade formation showed that these species were recently radiated from each other and may have the same ancestor. Furthermore, these two species were found closer to Nemacheilidae than to Balitoridae family in the phylogenetic analysis. The molecular divergence between these species was also supported by variance in morphometric data. This work may build the base for the revision of taxonomic identity of these two important fishes of genus Triplophysa. The present investigation formulated that, based on morphological and mtDNA COI sequences analysis, these two taxonomic Triplophysa species should be considered as valid. The results may further assist to enhance the knowledge of the ichthyologists in understanding the ichthyofauna of Kashmir Valley and will help them in planning strategies for conservation and management of these less studied small indigenous species along their natural range of distribution.