Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador (preprint)

Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

Is WGS Appropriate for SARS-CoV-2 Epidemiological Studies in Low- and Middle-Income Countries? An Epidemiologic Study of D614G Mutation Using a Rapid Low-Cost Method in Quito-Ecuador (preprint)

As the world continues to endure the tribulation of the SARS-COV2 pandemic, increasingly it is apparent that a quick simple and inexpensive methodology is in order to meet the demand for more epidemiologically relevant information in particular with respect to a number of new and arising mutation variants which carry phenotypically important characteristics. These variants may convey new traits with regard to transmissibility, virulence and antigenicity thus affecting the course of the pandemic or the development of efficient vaccines and vaccination strategies. While whole genome sequencing (WGS) is a most powerful methodology and often the method of choice, the cost and availability make it impractical for widespread use in many low- to middle-income nations. In this study a simple Sanger sequencing based method along with in-house designed primers, is utilized to analyse a statistically significant number of samples for the SARS-CoV-2 D614G mutation thus rendering a rapid low cost yet more complete snapshot of the natural history of this mutation as presented in the city of Quito, Ecuador during the current pandemic. Our results demonstrate that for the most part, the D614G mutation has been present from the early onset of the pandemic in Quito and may partially account for the extremely rapid spread of this virus throughout Ecuador despite the precautionary measures taken by local authorities. With the emergence of new SNPs of importance a low cost alternative to WGS is a certain necessity in every epidemiologist’s toolbox.