Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility (preprint)

The SARS-CoV-2 variant carrying the Spike protein mutation G614 was first detected in late January 2020 and within a few months became the dominant form globally. In the months that followed, many studies, both in vitro and in animal models, showed that variants carrying this mutation were more infectious and more readily transmitted than the ancestral Wuhan form. Here we investigate why a recently published study by van Dorp et al. failed to detect such higher transmissibility of the G614 variant using homoplasy-based methods. We show that both low diversity and recombination confound the methods utilized by van Dorp et al. and significantly decrease their sensitivity. Furthermore, though they claim no evidence of recombination in their dataset, we and several other studies identify a subset of the sequences as recombinants, possibly enough to affect their statistic adversely.

Information retrieval in an infodemic: the case of COVID-19 publications (preprint)

In the context of searching for COVID-19 related scientific literature, we present an information retrieval methodology for effectively finding relevant publications for different information needs. We discuss different components of our architecture consisting of traditional information retrieval models, as well as modern neural natural language processing algorithms. We present recipes to better adapt these components to the case of an infodemic, where, from one hand, the number of publications has an exponential growth and, from the other hand, the topics of interest evolve as the pandemic progresses. The methodology was evaluated in the TREC-COVID challenge, achieving competitive results with top ranking teams participating in the competition. In retrospect to this challenge, we provide additional insights with further useful impacts.

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2 (preprint)

We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.