7 documents found, page 1 of 1
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/50...
O'Toole, Áine; Hill, Verity; Pybus, Oliver G.; Watts, Alexander; Bogoch, Issac I.; Khan, Kamran; Messina, Jane P.; Tegally, HouriiyahLate in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account f...
Importation and early local transmission of COVID-19 in Brazil, 2020
Jesus, Jaqueline Goes de; Sacchi, Claudio; Candido, Darlan da Silva; Claro, Ingra Morales; Sales, Flávia Cristina Silva; Manuli, Erika ReginaWe conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil.
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and ...
Deng, Xianding; Achari, Asmeeta; Federman, Scot; Yu, Guixia; Somasekar, Sneha; Bártolo, Inês; Yagi, Shigeo; Mbala-Kingebeni, Placide; Kapetshi, JimmyMetagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high c...
Author Correction: Metagenomic sequencing with spiked primer enrichment for vir...
Deng, Xianding; Achari, Asmeeta; Federman, Scot; Yu, Guixia; Somasekar, Sneha; Bártolo, Inês; Yagi, Shigeo; Mbala-Kingebeni, Placide; Kapetshi, Jimmy
Tracing the impact of public health interventions on HIV-1 transmission in Port...
Vasylyeva, Tetyana I.; Plessis, Louis du; Pineda-Peña, Andrea C.; Kühnert, Denise; Lemey, Philippe; Vandamme, Anne-Mieke; Gomes, PerpétuaBackground Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies. Methods Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific ef...
Synonymous substitution rates predict HIV disease progression as a result of un...
Lemey, Philippe; Pond, Sergei L. Kosakovsky; Drummond, Alexei J.; Pybus, Oliver G.; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, Andrew
Synonymous substitution rates predict HIV disease progression as a result of un...
Lemey, Philippe; Kosakovsky Pond, Sergei L.; Drummond, Alexei J.; Pybus, Oliver G.; Shapiro, Beth; Barroso, Helena; Taveira, Nuno; Rambaut, AndrewUpon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune res