SARS-CoV-2 mutations associated with COVID-19 related hospitalizations

From the Quantitative Genetic Epidemiology Group, Jerome Lab, and Geraghty Lab. A collaboration between the Clinical Research, Public Health Sciences, and Vaccine and Infectious Disease Divisions.

The SARS-CoV-2 spike protein is necessary for viral entry into host cells and for this reason was selected as a vaccine target in the SARS-CoV-2 vaccines currently available. However, viral proteins that drive transmissibility can be different than those that determine disease severity. Through a multi-division collaboration, Drs. Lue Ping Zhao, Pavitra Roychoudhury, Keith Jerome, and Dan Geraghty took a broad, sequence-based approach to reveal which SARS-CoV-2 proteins may drive COVID-19 related hospitalization. These findings were published recently in Scientific Reports.

An astounding three to four human virus species are discovered each year, but only half can transmit from person-to-person and luckily a miniscule number of these transmissible viruses cause pandemic outcomes of world-wide spread (Woolhouse 2012). While understanding the transmissibility of SARS-CoV-2 is of paramount importance for restricting or slowing virus spread, the study of disease drivers is equally relevant for the treatment of those infected. To reveal which proteins made by SARS-CoV-2 cause severe disease and hospitalization, the authors combined the utility of viral genome sequencing with documented hospitalization status. Specifically, two clinical studies were conducted between April 2020 and March 2021 to collect SARS-CoV-2 sequence data from individuals who tested positive for the virus. The hospitalization status was also obtained for these individuals as an indicator of disease severity and categorized as either inpatient (requiring hospitalization) or outpatient (not requiring hospitalization). From the sequence data, 53 single nucleotide polymorphisms (SNPs), generally known as mutations, were identified in the following viral genes: non-structural protein 2, endoRNASE, S-spike-protein, nucleocapsid, and open reading frames (ORFs) 3a and 8. Intriguingly, mutations found in the nucleocapsid (4 SNPs), endoRNASE (2 SNPs), and ORF3a (1 SNP) positively correlated with patient hospitalization. However, as noted by Dr. Zhao, “mutations in the Spike protein do not exhibit similar associations, even though the Spike protein is well known for its role in disease transmission.” These novel findings prompt a closer investigation of how these mutations within SARS-CoV-2 nucleocapsid, endoRNASE, and ORF3a proteins may increase COVID-19 disease severity.

The researchers further analyzed one SNP located in the endoRNASE gene and three SNPs in the nucleocapsid gene that were temporally synchronized in the collected SARS-CoV-2 genome sampling (figure). The SARS-CoV-2 reference haplotype was “tggg” where “t” at site 19839 was in the endoRNASE gene and three sites: “g” at site 28881, “g” at site 28882, and “g” at site 28883, were in the nucleocapsid gene. With “tggg” as the reference haplotype, three variant haplotypes were present at high frequencies within the sequence data: “caac”, “taac”, and “cggg”. Low frequency haplotypes were grouped together under “rares”. Compared to the other varient haplotypes, the “caac” haplotype had the greatest frequency expansion within the sampled viral genomes and positively correlated with inpatient hospitalization status. These results suggest that specific mutations within the endoRNASE and nucleocapsid proteins may coordinate a joint mechanism to alter COVID-19 disease severity.

The “caac” haplotype was present at higher frequencies for hospitalized (11-23%) versus outpatient (0-7%) subjects and this haplotype was most abundant in May and June 2020.
The “caac” haplotype was present at higher frequencies for hospitalized (11-23%) versus outpatient (0-7%) subjects and this haplotype was most abundant in May and June 2020.

These studies employed cross-division expertise to address current challenges of how to identify potential drivers of COVID-19 related hospitalizations. Dr. Jerome commented on this collaboration, “One of the few silver linings to the pandemic has been the opportunity to collaborate with scientists like Lue Ping Zhao and Dan Geraghty, who usually don’t spend much time on viral disease. They bring a unique perspective and different approaches to the problem of COVID-19, which enriches the field and hopefully leads to new insights.” The collaborative nature of this group of scientists and the importance of the research findings insight a call-to-action. Dr. Geraghty expanded on this, “The study emphasizes the need and evident utility of monitoring SARS-CoV-2 genome sequences in coordination with a measurement of disease outcome. Such real-time monitoring would direct appropriate public health action in real-time as new variants emerge. Such monitoring must include the whole SARS-CoV-2 genome since it can't be anticipated which variant positions are relevant to disease pathology.”

The research spotlighted in this article was funded by the National Institutes of Health.

UW/Fred Hutch Cancer Consortium members Lue Ping Zhao, Peter Gilbert, Keith Jerome, and Dan Geraghty contributed to this work.

Zhao LP, Roychoudhury P, Gilbert P, Schiffer J, Lybrand TP, Payne TH, Randhawa A, Thiebaud S, Mills M, Greninger A, Pyo CW, Wang R, Li R, Thomas A, Norris B, Nelson WC, Jerome KR, Geraghty DE. 2022. Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. Sci Rep. 12(1):1206.