Andrew Nelson

Sep 5, 2024 | nature.com | Sonia Irigoyen |Andrew Nelson |Naga Rajitha Kavuri

AbstractLong intergenic non-coding RNAs (lincRNAs) are emerging as regulators of protein-coding genes (PCGs) in many plant and animal developmental processes and stress responses. In this study, we characterize the genome-wide lincRNAs in potatoes responsive to a vascular bacterial disease presumably caused by Candidatus Liberibacter solanacearum (CLso). Approximately 4397 lincRNAs were detected in healthy and infected potato plants at various stages of zebra chip (ZC) disease progression.

Jun 25, 2024 | nature.com | Andrea Cattaneo |Serkan Girgin |Theresa McMenomy |Andrew Nelson

AbstractUrban centers are pivotal in shaping societies, yet a systematic global analysis of how countries are organized around multiple urban centers is lacking. We enhance understanding by delineating city–regions worldwide, classifying over 30,000 urban centers into four tiers—town, small, intermediate and large city—based on population size and mapping their catchment areas based on travel time, differentiating between primary and secondary city–regions.

Apr 2, 2024 | mdpi.com | Meghan S. Vermillion |Andrew Nelson |Nathan Saari |Mathieu Bray

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Feb 26, 2024 | cell.com | Chenyu Wang |Kimberly D Derderian |Elizabeth Hamada |Xujia Zhou |Andrew Nelson |Henry Kyoung | +3 more

Feb 21, 2024 | nature.com | Matthew Hall |David Buck |Andrew Nelson |Rui Dos Santos |Jeff Barrett |Daniel Ayoubkhani | +17 more

Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1–5, give rise to highly divergent lineages6–8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as ‘persistent infections’ as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1–0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11–14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution. Using viral sequence data, individuals with persistent SARS-CoV-2 infections were identified, and had higher odds of self-reporting long COVID, in a large community surveillance study.