I'm not a virologist, but know a little bit about genetics.
Firstly, let me define a few terms.
RaTG13 is the name of the known coronavirus found on a bat species thought to be the original host of SARS-CoV2 (not sure how certain it is though).
Genome assembly is a way to determine the DNA sequence of something. It basically uses computational methods to assemble sequences of short stretches of DNA fragments and eventually get the sequence of the entire organism.
Amplicons are either the sources or products of natural or artificial gene amplification and duplication. Amplicons can be artificially generated through many lab gene amplification methods... Hehehe... I can almost smell the blood of many conspiracy theorists is boiling at this moment
Well, amplicons also form naturally through gene duplication in several types of cancer, where certain sections of the chromosome is amplified and moved to somewhere else, which leads to cancer.
In the context of viruses, you generate amplicons whenever you want to detect or study a DNA sample. For instance, a patient comes to you and asks you to test him for COVID-19. You take his sputum and pop it into a polymerase chain reaction (PCR) machine. Most of the currently available test kits for COVID-19 use PCR to amplify viral DNA so that we can identify the viral particles. The process of PCR extensively amplifies the viral DNA and generates a whole series of amplicons, which we can use to compare with a library of viral amplicons on file to identify the virus. If his sample contains a positive match, he has COVID-19. In that sense, we use PCR to intentionally generate a whole bunch of amplicons, like how we use magnifying glass to magnify certain parts of a painting to help us judge whether the painting belongs to a famous painter.
OK, in the tweet, Alina Chan is wondering if Shing Hei Zhan will try to analyze the sequence of the known bat coronavirus again. I don't know what amplicons reads of 2018 are. It must be another the sequence of another coronavirus that someone analyzed back in 2018. And she wants to compare the original bat coronavirus with the 2018 coronavirus, I guess.