Rotavirus mutations that affect transcriptase activity (and a lesson on why you should carefully read an entire paper if you are going to rely on it)

Today I was looking at an article on the structure of the rotavirus. It has a roughly spherical structure like this:

Angel J, Franco MA, Greenberg HB. Rotavirus vaccines: recent developments and future considerations. Nat Rev Microbiol 2007;5(7):531; online at https://pubmed.ncbi.nlm.nih.gov/17571094/

Rotavirus is most known for causing gastroenteritis in young children, but it can affect areas other than the gastrointestinal tract. A 2011 article from Japan reported the death of 2.5 year old girl who had rotavirus-caused gastroenteritis and also had rotavirus particles in her heart, brain, and liver. Her brain tissue showed evidence of the presence of the rotavirus VP6 protein. See Nakano ITaniguchi K, Ishibashi-Ueda H, Maeno Y, Yamamoto N, Yui A, Komoto S, Wakata Y, Matsubara T, Ozaki N. 2011. Sudden Death from Systemic Rotavirus Infection and Detection of Nonstructural Rotavirus Proteins . J Clin Microbiol 49; online at https://doi.org/10.1128/jcm.01303-11

VP6 forms part of the protein shell of rotavirus, as you can see in the interior of the rotavirus shell in the illustration above.

Researchers reported in a 2002 article that they created 13 different VP6 mutations to see what effects those mutations would have on the ability of VP6 to assemble correctly with the rotavirus VP2 protein, as well as on the ability of VP6 to restore the RNA transcriptase (RNA-dependent RNA polymerase) activity of the rotavirus VP1 protein. See Charpilienne A, Lepault J, Rey F, Cohen J. Identification of rotavirus VP6 residues located at the interface with VP2 that are essential for capsid assembly and transcriptase activity. Journal of Virology. 2002 Aug;76(15):7822-7831. DOI: 10.1128/jvi.76.15.7822-7831.2002; online at https://europepmc.org/article/PMC/136406.

In the discussion section, the authors stated, "An oversimplified summary of our data could indeed be stated as follows: VP6 single mutants assemble with VP2 but double mutants do not." They immediately afterwards note that one of their VP6 double mutants, one labeled "QAAL," does actually assemble like a VP6 single mutant:

"However, comparison of the QLAA, QALA, and QAAL mutants suggests that the last of these [i.e., QAAL] has the highest affinity for VP2, given that it was the only one of the three to give rise to a single band in CsCl density gradients (Table 1). This double mutant behaved effectively like the QLNL single mutant." https://journals.asm.org/doi/10.1128/jvi.76.15.7822-7831.2002). 

But they neglected to name another VP6 double mutant that behaves like the QAAL mutant. Earlier in the paper, before the discussion section, they wrote: 

"Three VP6 single mutants (ELLL, QLNL, and QLLN), two VP6 double mutants (QANL and QAAL), and the D29A control mutant were able to assemble into particulate structures that could easily be visualized as a single band in CsCl density gradients at the same density as that of native VLP....Mutants in the first class, QLNL, QANL, QAAL, and the D29A control mutant, allowed a complete recovery of transcriptase activity when added in at least stoichiometric amounts....Most of the single (ELLL, QLNL, and QLLN) and two of the double (QAAL and QANL) mutants that have slightly more hydrophilic* residues than does the wild type at positions L65, L70, and/or L71 assembled well with VP2." https://journals.asm.org/doi/10.1128/jvi.76.15.7822-7831.2002

* "The VP6 and VP2 layers interact through predominantly hydrophobic surfaces." https://journals.asm.org/doi/10.1128/jvi.76.15.7822-7831.2002

Their own results clearly show that the VP6 double mutant labeled "QANL" assembled with VP2, but they omitted saying so in the discussion section of their article. This seems like a small error...after all, they looked at 13 VP6 mutants. However, the purpose of the paper is to correctly identify VP6 variations that affect rotavirus assembly and transcriptase activity.

I have learned that reading the short abstract or even the longer discussion part of a paper is not enough. There are important errors that even the authors miss and which you can only catch by looking at the data results.