Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a respiratory RNA virus that first appeared in 2019 and has been linked to various clinical phenotypes ranging from asymptomatic to more severe disease. Coronavirus disease 2019 (COVID-19) causes a moderate flu-like illness in most young and healthy people, with symptoms such as restricted respiratory tract congestion, fever, myalgia, headache, and anosmia. COVID-19 can cause severe respiratory distress, multi-organ problems, and death in older adults, especially men and those with comorbidities.

Study: SARS-CoV-2 infection results in lasting and systemic perturbations post recovery. Image Credit: Kateryna Kon/Shutterstock

The development of neutralizing antibodies to the Spike (S) attachment protein clears the viral infection in most people. In general, the manifestation of the humoral response is linked to the remission of SARS-CoV-2 symptoms. However, a growing body of research suggests that SARS-CoV-2 infection causes long-term consequences in a subgroup of people, including shortness of breath, recurrent fevers, exhaustion, sadness, anxiety, and a state of chronic memory and concentration impairment known as "brain fog." The etiology of these deficits, generally known as "long COVID" or post-acute sequelae of COVID-19 (PASC), is unknown at this time.

A group of researchers used the golden hamster as a model system to better understand the long-term impacts of SARS-CoV-2 infection. The hamster model has been shown to closely phenocopy COVID-19 biology without the need for SARS-CoV-2 adaption and a propensity for severe lung morphology and tropism similar to those seen in human patients.

A preprint version of the study is available on the bioRxiv* server while the article undergoes peer review.

The study

The findings showed that both respiratory RNA viruses studied (SARS-CoV-2 and IAV) could reproduce in the golden hamster's lungs but at differing clearance rates, which is consistent with previous research. IAV challenge resulted in peak titers of 10^7 plaque-forming units per gram of lung tissue (pfu/g) on day three, followed by a dramatic fall in infectious material and full loss of infectivity by day seven. Peak virus titers for SARS-CoV-2 were likewise reported three days post-infection (dpi), although these levels were maintained until day five before falling.

Despite the differences in controlling overall virus levels, no infectious virus could be isolated in either model system on day seven. However, trace levels of RNA for the nucleoprotein (NP) of influenza and the sub-genomic mRNA of the nucleocapsid (N) from SARS-CoV-2 were detectable via quantitative reverse-transcription-based PCR (qRT-PCR). Based on these findings, the authors compared the acute host response to these two respiratory infections on day three.

The authors matched the RNA-seq results to published studies from lungs of COVID-19 deceased persons who still had high viral loads at the time of death to confirm the clinical validity of the SARS-CoV-2 acute hamster data. The scientists discovered that both groups' transcriptional profiles were dominated by a substantial elevation of the IFN-I response as well as TNF-α signaling via NFκB, which agrees with the published data.

The authors used gene set enrichment analysis (GSEA) to identify curated ontology gene sets from the aforementioned tissues to examine the acute response systematically. Following SARS-CoV-2 or IAV infection, a substantial acute activation of the IFN-I response in all three organs. This was also shown in equivalent human tissues. IFN-I signatures were also accompanied by overexpression of IFN-I-associated pathways, including NFκB- and IL6-associated target genes, in the lungs of hamsters and COVID-19 cadavers.

Positive regulation of complement activation in the kidney and negative regulation of calcium channel development in the heart were two other enriched pathways induced when directly comparing SARS-CoV-2 to IAV infection. However, both enrichments were small in comparison to the IFN-I signatures. These findings back up previous research and support the use of the golden hamster as a model for SARS-CoV-2 pathogenesis in humans.

Given the very long duration of the proinflammatory response to SARS-CoV-2 in the olfactory bulb, the researchers looked into the genes that drive this transcriptional pathway. The unusual persistence of this transcriptional signature in response to SARS-CoV-2 was highlighted by comparing genes implicated in the IFN-I response generated by either IAV or SARS-CoV-2 at 3 and 31 dpi. This study found a long-term increase in canonical interferon-stimulated genes (ISGs) such as Isg15, Mx2, and Irf7, independently confirmed by qRT-PCR.

The authors used immunostaining for MX1 on sections taken from the olfactory bulbs of hamsters that had been mock-treated or infected with SARS-CoV-2 or IAV at 3 and 31dpi to corroborate their findings. These findings confirmed the transcriptome findings at the protein level, demonstrating increased MX1 in response to SARS-CoV-2 at both 3 and 31dpi, with immunolabeling staying at the olfactory bulbs' periphery. SARS-CoV-2 infection was also observed to cause protracted chemokine induction, as indicated by Cxcl10 and Ccl5, among other chemokines. Compared to the IFN-I signature, the chemokine response appears to be more sustained or perhaps amplified at 31dpi.

Implications

The data from the peripheral organs and central nervous system point to transcriptional and histologic markers caused by SARS-CoV-2 infection, which could lead to various sensorimotor, affective, and cognitive deficits that last long after the initial infection. The authors believe these findings clarify a biological basis for much of the heterogeneous symptomology that characterizes protracted COVID-19 because of their systemic reach.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.