The paper analyzes genomic and phenotypic data from Zika virus lineages to assess fitness differences during the 2015-2016 epidemic, finding moderate fitness changes but no significant virulence or transmission enhancement.

bioRxiv · Feb 1, 2022Evolutionary Biology

Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

R. Klitting, L. E. Kafetzopoulou, W. Thiery, G. Dudas, S. Gryseels, A. Kotamarthi, B. Vrancken, K. Gangavarapu, M. Momoh, J. Demby Sandy, A. Goba, F. Alhasan, D. S. Grant, R. F. Garry, A. R. Smither, , S. Dellicour

The paper predicts that Lassa virus endemic areas will expand beyond West Africa due to environmental changes, increasing the population at risk from 100 million to 700 million by 2070.

bioRxiv · Sep 22, 2021Microbiology

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, , P. Lemey

This study uses phylogeographic and phylodynamic methods to test hypotheses about West Nile virus dispersal and genetic diversity, finding temperature influences on spread and no strong evidence for migratory bird flyway restriction.

bioRxiv · Sep 19, 2020 · PreprintEvolutionary Biology

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.

P. Lemey, S. Hong, V. Hill, G. Baele, C. Poletto, V. Colizza, A. O'Toole, J. T. McCrone, K. G. Andersen, M. Worobey, M. I. Nelson, A. Rambaut, M. A. Suchard

This paper integrates travel history data into Bayesian phylogeographic analysis of SARS-CoV-2 to improve virus spread reconstructions and address sampling bias.

bioRxiv · Jun 22, 2020 · PreprintEvolutionary Biology

Reporter assays for Ebola virus nucleoprotein oligomerization, virion-like particle budding, and minigenome activity reveal the importance of nucleoprotein amino acid position 111

A. E. Lin, W. E. Diehl, Y. Cai, C. L. Finch, C. Akusobi, R. N. Kirchdoerfer, L. Bollinger, S. F. Schaffner, E. A. Brown, E. O. Saphire, K. G. Andersen, J. H. Kuhn, J. Luban, P. C. Sabeti

The paper develops reporter assays to study Ebola virus nucleoprotein (NP) function and finds that amino acid position 111 affects oligomerization, virion budding, and transcription/replication.

bioRxiv · Dec 10, 2019Microbiology

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

N. D. Grubaugh, K. Gangavarapu, J. Quick, N. L. Matteson, J. Goes De Jesus, B. J. Main, A. L. Tan, L. M. Paul, D. E. Brackney, S. Grewal, N. Gurfield, K. K. Van Rompay, S. Isern, S. F. Michael, L. L. Coffey, , K. G. Andersen

The paper evaluates PrimalSeq for measuring intrahost virus diversity, showing how factors like sequencing coverage and primer mismatches affect accuracy.

bioRxiv · Aug 5, 2018Evolutionary Biology

Common Piezo1 allele in African populations causes xerocytosis and attenuates Plasmodium infection

S. Ma, S. Cahalan, R. Lohia, G. LaMonte, W. Zeng, S. Murthy, E. Paytas, N. D. Grubaugh, R. Gamini, L. Berry, V. Lukacs, T. Whitwam, M. Loud, A. I. Su, K. G. Andersen, , A. Patapoutian

The paper identifies a common Piezo1 variant in African populations that causes xerocytosis and reduces Plasmodium infection.

bioRxiv · Jul 6, 2017Physiology