Highlights d A SARS-CoV-2 variant with Spike G614 has replaced D614 as the dominant pandemic form d The consistent increase of G614 at regional levels may indicate a fitness advantage d G614 is associated with lower RT PCR Cts, suggestive of higher viral loads in patients d The G614 variant grows to higher titers as pseudotyped virions

This Version (2) corrects analysis that was based on the codon encoding Spike position 943; the apparent mutation at 943 was the result of a sequence error. The main conclusions of the paper regarding the mutation in Spike at 614 and recombination still hold. The key difference in version 2 is that we have removed the original figure 6, which was based on the 943 sequencing artifact, and instead moved a figure illustrating recombination that was independent of position 943 from the supplement into the main text. BK SummaryWe 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.

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We have completed a new set of total cross section measurements of 31 elements and isotopes spanning the periodic table from Aϭ1 to 238. We employed the same technique as in Finley et al. ͓Phys. Rev. C 47, 237 ͑1993͔͒ with refinements intended to allow measurements on separated isotopes and improved systematic error control. The goal of the new measurement was 1% statistical accuracy in 1% energy bins with systematic errors less than 1%. This was achieved for all but the thinnest samples. Stringent checks of systematic errors in this measurement resulted in a reassignment of systematic uncertainties to the neutron total cross sections reported in Finley et al. Microscopic optical model calculations were carried out to interpret the results of the experiment. Two specific types of optical models were employed. The Jeukenne-Lejeune-Mahaux model was used in the range of 5-160 MeV, and a model based on the empirical effective interaction of Kelly was used from 135 to 650 MeV. These models are shown to be useful for predicting both neutron total cross sections and proton reaction cross sections. They are particularly important for light nuclei, for which standard global phenomenological parametrizations of the optical potential are insufficiently accurate.

Humanity is currently facing the challenge of two devastating pandemics caused by two very different RNA viruses: HIV-1, which has been with us for decades, and SARS-CoV-2, which has swept the world in the course of a single year. The same evolutionary strategies that drive HIV-1 evolution are at play in SARS-CoV-2. Single nucleotide mutations, multi-base insertions and deletions, recombination, and variation in surface glycans all generate the variability that, guided by natural selection, enables both HIV-1's extraordinary diversity and SARS-CoV-2's slower pace of mutation accumulation. Even though SARS-CoV-2 diversity is more limited, recently emergent SARS-CoV-2 variants carry Spike mutations that have important phenotypic consequences in terms of both antibody resistance and enhanced infectivity. We review and compare how these mutational patterns manifest in these two distinct viruses to provide the variability that fuels their evolution by natural selection.