Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

Abstract

The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that currently tracks over 40 million combinations of PANGO lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials, and the general public. We describe the interpretable and opinionated visualizations in the variant and location focussed reports available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data, and the server infrastructure that enables widespread data dissemination via a high performance API that can be accessed using an R package. We present a case study that illustrates how outbreak.info can be used for genomic surveillance and as a hypothesis generation tool to understand the ongoing pandemic at varying geographic and temporal scales. With an emphasis on scalability, interactivity, interpretability, and reusability, outbreak.info provides a template to enable genomic surveillance at a global and localized scale.

Covid-19: is omicron less lethal than delta?

“…Quantitative polymerase chain reaction test results were mined for spike gene target failure, with specimens failing to amplify the S gene classified as BA.1 compatible. Although less reliable than whole genome sequencing, this technique can distinguish delta from BA.1 by detecting the deletion at positions 69 and 70 of the spike gene characteristic of BA.1 (present in almost 95% of BA.1 lineage sequences v 0.2% of delta) 5. Death certification records definitively identified over 350 covid-19 related deaths in the cohort.…”

“…Although less reliable than whole genome sequencing, this technique can distinguish delta from BA.1 by detecting the deletion at positions 69 and 70 of the spike gene characteristic of BA.1 (present in almost 95% of BA.1 lineage sequences v 0.2% of delta). 5 Death certification records definitively identified over 350 covid-19 related deaths in the cohort. Ultimately, the risk of covid-19 related death was found to be 66% lower in people infected with omicron than in those with delta, similar to the 69% lower risk reported by Nyberg and colleagues.…”

Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City

“…We detected the S:D614G substitution in all our samples. This mutation was first described in January 2020 and originated the B.1 lineage ( Hughes et al., 2022 ). In May 2020, its prevalence started to rise, and by June 2020 was reported in approximately 74% of all SARS-CoV-2 published sequences ( Yurkovetskiy et al., 2020 ).…”

Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay

“…The CoV-GLUE and outbreak.info (Lineage|Mutation) trackers were used to identify markers (SNPs and indels) in SARS-CoV-2 lineages ( Hughes et al, 2022 ; Singer et al, 2020 ).…”