I know less about measles, but the broader question of how to identify viruses by DNA sequencing is what I'm now doing professionally. You write: "Also we cann

I know less about measles, but the broader question of how to identify viruses by DNA sequencing is what I'm now doing professionally. You write: "Also we cannot sequence the DNA/RNA of the virus in order to establish it's identity, when we are testing a soup that has other DNA/RNA in it." That is generally not correct. When you sequence, what you get are subsequences ("reads") of around 200 base pairs. Generally a very large number of them. Then you try to figure out what genetic sequences could have led to you observing those reads, through a process called "assembly". The idea here is that if I have one read that looks like ABCDE and another like BCDEF, it's very likely that these were generated from an original sequence of ABCDEF. If your reads were drawn from a sample that has multiple things in it you will piece each one together separately, and as long as you took enough reads you'll be able to get the genetic sequence for each. I've been working on wastewater recently, which is a huge mixture of many different things, but we see some extremely common genetic sequences. When you look up these sequences with BLASTN they turn out to be ones people have previously identified as plant viruses from vegetables people commonly eat, such as tomatoes, peppers, and cucumbers. [1] You can download the data and play with it yourself if you want? Here's an approach that should let you replicate the identification of these sequences and is simple enough that you could code yourself: 1. Download one of the 180 FASTQ files the authors published 2. Extract the nucleotide sequences ("grep '^[ACTG]' fname.fastq") 3. Write a little program that emits all subsequences of length 40. Short enough not to get too many read errors, long enough that mismatches are unlikely. 4. Sort those subsequences. (Unix sort will do it, even though this will exceed the memory available on your machine unless you have a much better machine than I do.) 5. uniq -c 6. sort -nr 7. At this point the data should all fit in memory. Write a program where you make a map from the first 39 characters in a sequence to the last character, and from the last 39 characters to the first. Take the most frequent subsequence in the data and attempt to extend it using those two maps. You should end up with a sequence about 6k long. 8. Enter that sequence into https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_SPEC=GeoBlast&PAGE_TYPE=BlastSearch https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAS... It will probably identify it as Tomato brown rugose fruit virus. I don't know how I would explain this if viruses didn't exist? [1] https://journals.asm.org/doi/10.1128/AEM.01448-21 https://journals.asm.org/doi/10.1128/AEM.01448-21