P.1 may be 1.7–2.4 more transmissible, and previous (non-P.1) infection may provide 54–79% protection
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages.
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
We find that delaying second vaccine doses reduces COVID-19 infections in the short term by increasing the proportion of immune individuals. In the longer term, however, both the infection burden and the relative potential for viral adaptation are highly dependent on the robustness of natural or vaccinal immune responses. Notably, we find that even if immunity conferred by a single vaccine dose is poor, starting with a one-dose policy early on to increase the number of individuals immunized and then switching to the manufacturer-recommended two-dose regime as vaccine capacity increases can mitigate potential negative longer-term epidemiological and evolutionary outcomes.
Socioeconomic status determines COVID-19 incidence and related mortality in Santiago, Chile
Here, we provide an in-depth characterization of disease incidence and mortality, and their dependence on demographic and socioeconomic strata in Santiago, a highly segregated city and the capital of Chile. Our analyses show a strong association between socioeconomic status and both COVID-19 outcomes and public health capacity. People living in municipalities with low socioeconomic status did not reduce their mobility during lockdowns as much as those in more affluent municipalities.
mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection
We examined whether sera from recovered and naïve donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization.
The emerging plasticity of SARS-CoV-2
Because only a few SARS-CoV-2 mutations were in circulation during most of 2020, it is likely that the three major variants are the result of selective pressures and adaptation of the virus during prolonged individual infections and subsequent transmission. All the case reports of individuals with extensive intrahost SARS-CoV-2 evolution indicated that they had been treated with suboptimal neutralizing antibodies (that is, the CP treatment did not neutralize the entire virus population). Whether or not antibody therapy played a role, it is likely that the same variants or variants containing new mutations will continue to emerge in different geographic locations as the result of intrahost selection and subsequent transmission. Indeed, other variants have been reported with multiple mutations in S1, including the lineages B.1.526 (detected in New York) and B.1.429 (which originated in California) containing a substitution in the RBD that is distinct from other variants; and B.1.525 and A.23.1 that are thought to have originated in Nigeria and Uganda, respectively (see the figure).