The Post-Acute Phase of SARS-CoV-2 Infection in Two Macaque Species Is Associated with Signs of Ongoing Virus Replication and Pathology in Pulmonary and Extrapulmonary Tissues

Abstract

The post-acute phase of SARS-CoV-2 infection was investigated in rhesus (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis). During the acute phase of infection, SARS-CoV-2 was shed via the nose and throat, and viral RNA was occasionally detected in feces. This phase coincided with a transient change in systemic immune activation. Even after the alleged resolution of the infection, computed tomography (CT) and positron emission tomography (PET)-CT revealed pulmonary lesions and activated tracheobronchial lymph nodes in all animals. Post-mortem histological examination of the lung tissue revealed mostly marginal or resolving minimal lesions that were indicative of SARS-CoV-2 infection. Evidence for SARS-CoV-2-induced histopathology was also found in extrapulmonary tissue samples, such as conjunctiva, cervical, and mesenteric lymph nodes. However, 5–6 weeks after SARS-CoV-2 exposure, upon necropsy, viral RNA was still detectable in a wide range of tissue samples in 50% of the macaques and included amongst others the heart, the respiratory tract and surrounding lymph nodes, salivary gland, and conjunctiva. Subgenomic messenger RNA was detected in the lungs and tracheobronchial lymph nodes, indicative of ongoing virus replication during the post-acute phase. These results could be relevant for understanding the long-term consequences of COVID-19 in humans.

Subgenomic and negative sense RNAs are not markers of active replication of SARS-CoV-2 in nasopharyngeal swabs

“…Several studies have proposed using subgenomic RNA or negative sense SARS-CoV-2 RNA as a marker of active replication of the virus within an individual [7,11,13,14,24] . However, we recently reported that we were able to detect subgenomic RNA and negative sense RNA in samples up to 17 days post infection, and that subgenomic RNAs are relatively stable and likely persist in samples protected by the double membrane structures created during the replication of the virus in the cytoplasm of SARS-CoV-2 infected cells [23] .…”

“…Given that there is ongoing interest in subgenomic RNAs as a potential marker of active replication and a dichotomy of conclusions being drawn within the scientific community as to the utility of subgenomic RNA as a marker of infectivity [7,9,11,13,14,23,24] , we decided to further examine the presence of subgenomic RNAs in a larger number of routine diagnostic SARS-CoV-2 positive nasopharyngeal swab samples. These swabs were collected subsequent to our last study during the second SARS-CoV-2 epidemic wave in Victoria, Australia in mid-to late 2020 [23,26] .…”

A Comparative Study of Chest CT With Lung Ultrasound After SARS-CoV-2 Infection in the Assessment of Pulmonary Lesions in Rhesus Monkeys (Macaca Mulatta)

“…All macaques received 0.25 mL in each nostril and 4.5 mL intratracheally. Total dose was 1 × 10 5 TCID 50 (9). There were 25/28 animals that were sub-genomic PCR positive for at least 1 day in the throat sample.…”

“…To obtain more insights in the longitudinal progress of the disease process, experiments in controlled settings in an appropriate animal model are necessary. Non-human primates (NHPs), and more specifically rhesus monkeys, are such a model due to their close evolutionary relationship to humans, and because they show the mild-to-moderate symptoms seen in most human cases (7)(8)(9).…”

“…Medical imaging, traditionally via chest X-rays (CXR) or computed tomography (CT) has already been widely used in both clinical and veterinary practice. Moreover, CT as an imaging modality to assess the longitudinal process of SARS-CoV-2 infection is already used in rhesus monkeys (9). SARS-CoV-2 infected rhesus monkeys often show pleural line irregularities and bilateral ground glass opacifications in the periphery of the lungs.…”