Emergence and antibody evasion of BQ and BA.2.75 SARS-CoV-2 sublineages in the face of maturing antibody breadth at the population level (preprint)

The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and related sub-lineages. Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants at two levels: (i) we tracked over 400,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using antibody pools. (ii) we mapped the antibody response at the individual level using blood from strigently curated vaccine and convalescent cohorts. In pooled antibody samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases we observed increased antibody breadth to variants that were yet to be in circulation. Resolution of viral neutralisation at the cohort level supported equivalent coverage across prior and emerging variants with emerging isolates BQ.1.1, XBB.1 and BR.2.1 the most evasive. Further, these emerging variants were resistant to Evusheld, whilst neutralization resistance to Sotrovimab was restricted to BQ.1.1 and further supported by lack of Spike glycoprotein binding to this variant. An outgrowth advantage through better utilization of TMPRSS2 was observed across BQ lineages and not those derived from BA.2.75. We conclude at this current point in time that variants derived from BQ lineages can evade antibodies at levels equivalent to their most evasive BA.2.75 counterparts but sustain an entry phenotype that would promote an additional outgrowth advantage.

Modelling vaccination capacity at mass vaccination hubs and general practice clinics (preprint)

COVID-19 population vaccination programs are underway globally. In Australia, the federal government has entered into three agreements for the supply of vaccines, with roll-out beginning for the highest priority groups in February 2021. Expansion of the vaccination program throughout February and March failed to meet government targets and this has been attributed to international supply issues. However, Australia has local capacity to manufacture one million doses of the AstraZeneca vaccine weekly and once fully operational this will greatly increase the national vaccination capacity. Under current plans, these vaccine doses will be distributed primarily through a network of general practices, to be joined in later phases by community pharmacies. It remains unclear whether these small distribution venues have the logistical capacity to administer vaccines at the rate they will become available. To inform this discussion, we applied stochastic queue network models to estimate the capacity of vaccination sites based on assumptions about appointment schedules, service times and available staff numbers. We specified distinct queueing models for two delivery modes: (i) mass vaccination hubs located in hospitals or sports arenas and (ii) smaller clinics situated in general practices or community pharmacies. Based on our assumed service times, the potential daily throughput for an eight hour clinic at a mass vaccination hub ranged from around 500 vaccinations for a relatively small hub to 1,400 vaccinations a day for a relatively large hub. For GP vaccination clinics, the estimated daily throughput ranged from about 100 vaccinations a day for a relatively small practice to almost 300 a day for a relatively large practice. Stress tests showed that for both delivery modes, sites with higher staff numbers were more robust to system pressures, such as increased arrivals or staff absences, and mass vaccination sites were more robust that GP clinics. Our analysis is accompanied by an interactive web-based queue simulation applet, which allows users to explore queue performance under their own assumptions regarding appointments, service times and staff availability. Different vaccine delivery modes offer distinct benefits and may be particularly appealing to specific population segments. A combination of expanded mass vaccination hubs and expanded GP vaccination is likely to achieve mass vaccination faster than either mode alone.