Post-COVID immune dysregulation is an area of ongoing research, though often focused on issues around autoimmunity:
The SARS-CoV-2 virus may be causing confusion within the body's immune system. To learn more about this immune dysregulation, visit RTHM.
rthm.com
However, some studies already point to reactivation of various latent viruses in SARS-CoV-2 convalescents (eg DOI:
10.3389/fimmu.2022.949787), which could be considered a contribution to PASC.
The apparent ability of recent omicron lineage variants to down-regulate various aspects of innate immunity (eg DOI:
10.1101/2022.07.12.499603) may also perhaps play a role here.
Widely available RAT overwhelmingly focus on nucleocapsid antigen, structural proteins, which tend to be largely invariant: specificity hasn't changed much. However sensitivity has - populations have much higher levels of acquired immunity and lower viral loads, with commensurate reduced peak window sampling sizes.
Whole genome or next generation Sanger sequencing are exactly how new variants are discovered. Whilst these methods have predominately used amplicons from nasopharyngeal SARS-CoV-2 RT-PCR testing, test samples can just as easily, actually even more easily, be obtained via other routes. For example, wastewater sampling (sewerage treatment facilities, aircraft toilets) is increasingly flagging up crypto-variant (and potential zoonotic) development well ahead of clear signals in the primary healthcare system.