Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants (preprint)

Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralising public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidences to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.

Dramatic decline of observed atmospheric CO2 and CH4 during the COVID-19 lockdown over the Yangtze River Delta of China

The temporal variation of greenhouse gas concentrations in China during the COVID-19 lockdown in China is analyzed in this work using high resolution measurements of near surface △CO2, △CH4 and △CO concentrations above the background conditions at Lin'an (LAN), a regional background station in the Yangtze River Delta region. During the pre-lockdown observational period (IOP-1), both △CO2 and △CH4 exhibited a significant increasing trend relative to the 2011-2019 climatological mean. The reduction of △CO2, △CH4 and △CO during the lockdown observational period (IOP-2) (which also coincided with the Chinese New Year Holiday) reached up to 15.0 ppm, 14.2 ppb and 146.8 ppb, respectively, and a reduction of △CO2/△CO probably due to a dramatic reduction from industrial emissions. △CO2, △CH4 and △CO were observed to keep declining during the post-lockdown easing phase (IOP-3), which is the synthetic result of lower than normal CO2 emissions from rural regions around LAN coupled with strong uptake of the terrestrial ecosystem. Interestingly, the trend reversed to gradual increase for all species during the later easing phase (IOP-4), with △CO2/△CO constantly increasing from IOP-2 to IOP-3 and finally IOP-4, consistent with recovery in industrial emissions associated with the staged resumption of economic activity. On average, △CO2 declined sharply throughout the time of day during IOP-2 but increased gradually throughout the day during IOP-4. The findings showcase the significant role of emission reduction in accounting for the dramatic changes in measured atmospheric △CO2 and △CH4 associated with the COVID-19 lockdown and recovery.