SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021

The severe acute respiratory coronavirus-2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. Evidence suggests that the virus is evolving to allow efficient spread through the human population, including vaccinated individuals. Here we report a study of viral variants from surveillance of the Delaware Valley, including the city of Philadelphia, and variants infecting vaccinated subjects. We sequenced and analyzed complete viral genomes from 2621 surveillance samples from March 2020 to September 2021 and compared them to genome sequences from 159 vaccine breakthroughs. In the early spring of 2020, all detected variants were of the B.1 and closely related lineages. A mixture of lineages followed, notably including B.1.243 followed by B.1.1.7 (alpha), with other lineages present at lower levels. Later isolations were dominated by B.1.617.2 (delta) and other delta lineages; delta was the exclusive variant present by the last time sampled. To investigate whether any variants appeared preferentially in vaccine breakthroughs, we devised a model based on Bayesian autoregressive moving average logistic multinomial regression to allow rigorous comparison. This revealed that B.1.617.2 (delta) showed three-fold enrichment in vaccine breakthrough cases (odds ratio of 3; 95% credible interval 0.89-11). Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of 1.25-3.18). This study thus provides a detailed picture of viral evolution in the Delaware Valley and a geographically matched analysis of vaccine breakthroughs; it also introduces a rigorous statistical approach to interrogating enrichment of viral variants.

Philadelphia and the Delaware Valley: A Geographically Distributed and Expanding Life Science Ecosystem

Philadelphia has been considered by many to be the birthplace of the modern US pharmaceutical industry with Merck & Co. Inc.’s research division Merck Research Labs [originally called MSDRL] based in West Point and GSK’s primary US labs [originally SKF] now based in Collegeville. The City of Philadelphia is also home to two of the oldest medical schools in the US: Perelman School of Medicine at the University of Pennsylvania founded in 1765 and the Sydney Kimmel Medical College [formerly Jefferson Medical College] founded in 1824. The conjunction of those two touchpoints along with the other big pharma players, e.g., Johnson & Johnson/Janssen and emerging biotech entities in the wider Delaware Valley region is significant. Also noteworthy is the presence of other research intensive universities such as Drexel University, Temple University, Jefferson University and research institutes such as the Wistar Institute, Fox Chase Cancer Center [associated with Temple University School of Medicine], Lankenau Institute, Monell Chemical Senses Center and the Coriell Institute in Southern New Jersey.

The millennia-long use history of triangular bifaces

Relatively small, triangular bifaces often considered to be projectile points have a demonstrable use history that includes the Middle Archaic, Late Archaic, Early Woodland, late Middle Woodland, Late Woodland, and Contact periods of regional archaeology. Radiocarbon dates and other data are used to document this extensive history using the Upper Delaware Valley of New Jersey, Pennsylvania, and New York as a case study. Observed trends are evaluated in a broader regional context. The degree to which triangles of different ages can be distinguished from one another is addressed and suggestions for future research are made.