Figure 5.

A comparison of transition patterns in major clades

(A) Major HIV-1 clades and CRF sampling frequencies in two 6-year windows: 2000–2005 and 2015–2020. The circle area reflects the relative number of sequences available from a given region within each map.

(B) Frequency of sampling of the SARS-CoV-2 G clade (carrying D614G) and its descendants (shown in blue) versus the frequency of sampling of the ancestral form of the virus that carried D614 (shown in orange) in two time-windows, roughly the first 10 weeks of the pandemic (through March 1, 2020), and the last 3 months of 2020.

(C) The top two graphs show the frequency of sampling of different variant forms in the United Kingdom between November 1, 2020 and May 10, 2021. In the fall, the G clade (light gray), and the GV clade (the G clade with an additional A222V mutation (darker gray) were co-circulating, with a gradual relative increase in the GV clade relative to G clade over the summer and fall. B.1.1.7 (orange) was first sampled in September, and rapidly increased in prevalence in the UK, comparable to the global transitions we found when the G clade became globally dominant (Korber et al., 2020b). In the spring of 2021, B.1.627.2, initially sampled in India, had begun to rise significantly in frequency in the UK. In this evolutionary pattern, one form gave way successively to another: G to GV to B.1.1.7. Currently B.1.617.2 has begun to be increasing sampled; over the next few months we will learn if B.1.617.2 continues in this upward trajectory in the UK and elsewhere. The same data are plotted two ways: weekly average tallies of each form, to give a sense of sampling, and weekly average frequencies. Below, the same data is plotted for North America. The G clade is dominant in the fall. G clade forms which carried additional mutations near the furin cleavage site (magenta and purple) became increasingly frequently sampled, but then gave way to variants with more complex forms of Spike, which often still carried a positive charge near the furin cleavage site. When the B.1.1.7 variant began to be sampled in early December, there are already distinct forms with an established presence and relative fitness advantages co-circulating, and VOI/VOCs first sampled from California, Brazil, and New York all had a significant presence. Still, B.1.1.7 has been increasingly sampled throughout North America, although P.1 and B.1.526 are also continuing to maintain or increase in frequency in some regions states in the USA. As of early May, 2021, B.1.617.2 is still rare but present and increasing in frequency in North America.