The Post-Acute Phase of SARS-CoV-2 Infection in Two Macaque Species Is Associated with Signs of Ongoing Virus Replication..., 2021,

[Hutan]

https://www.mdpi.com/1999-4915/13/8/1673

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

Primarily a Dutch study
Biomedical Primate Research Centre (BPRC), Department of Virology, 2288 GJ Rijswijk, The Netherlands

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.

 

[Hutan]

With respect and thanks to the animals that died in this study; it's never nice to read about primate research that ends in the animals being killed. Also thanks to the people who took care of the animals - it must be difficult work.

This seems to be a well-conducted study aiming to infect some macaques with CoV-2 and follow the infection, checking for viral dissemination in body tissues after 6 weeks. While persisting virus had been found in people who have suffered severe Covid-19 infections, less was known about viral persistence in people who have asymptomatic or mild disease. These macaques had mild infections.

In patients who died of COVID-19, viral RNA was found widely disseminated throughout tissues and organs, and a wide variety of pathologies was found in postmortem tissue. The majority of human infections however are asymptomatic or cause mild disease. This is also the case in NHP. Little is known about the long-term consequences of asymptomatic or mild infection in humans. Here, we took a unique approach and focused our research on the first weeks of the post-acute phase, after a mild to moderate SARS-CoV-2 disease course in two macaque species. We followed SARS-CoV-2 replication in rhesus and cynomolgus macaques and monitored the animals for signs of COVID-19-like disease symptoms. The macaques were infected in parallel with the same virus stock and the same dose and underwent a fully identical treatment. The course of infection was followed for up to six weeks using the same analyses, including the monitoring of virus-induced metabolic and anatomic findings with CT and PET-CT, and continuous telemetric recording of body temperature and physical activity of the animals. The animals were sacrificed to investigate histopathological tissue changes related to SARS-CoV-2, as well as to examine viral dissemination in organs.

 

[Hutan]

The macaques had sensors inserted into their abdomen cavity to measure activity. There were two species of macaques - rhesus (shown in warm colours) and cynomolgus (shown in cool colours). Each animal is represented by one colour.



The activity of the cynomolgus macaques didn't change throughout the study, whereas the activity of the rhesus macaques increased 3 weeks after infection. There was a pattern of reduced activity after the third week.
Edit - unfortunately, we don't know what their usual activity levels (under the study conditions) was.

 

[Hutan]

Macroscopically, the lungs of the rhesus and cynomolgus macaques appeared mostly unremarkable. One rhesus macaque (R15096) had few small foci with hyperemia at the dorsal aspects of the caudal left and right lung lobes, and in three cynomolgus macaques, the lungs had similar foci of hyperemia, confined also to the caudal pulmonary lobes. The gross examination of extrapulmonary organs revealed mildly to moderately enlarged cervical and mesenteric lymph nodes. The rest of the organs were macroscopically unremarkable.

Have a look at the places the virus is turning up - it's really variable from animal to animal. No virus at all was found in 4 out of the 8 animals. Virus was found in a calf vein, in lymph nodes, in the heart and in the throat, the spleen, among other places.

SARS-CoV-2 replication was evidenced by using sgmRNA PCR analysis on all tissue samples that tested positive in previous viral RNA tests. As sgmRNA is synthesized during virus replication, this assay is recognized as an alternative to virus isolation from tissue samples. In Table 2 and Figure 7, the sgmRNA-positive tissues are shown. Despite the virus being no longer detectable in nasal and tracheal swabs from the 4 animals for more than 26 days (R14002), 30 days (J16017), or even 34 days (J16012 and Ji408005), sgmRNA was detectable in the respiratory tract tissues of all four macaques, convincingly indicating that SARS-CoV-2 continued to replicate in these animals after the alleged resolution of infection that was concluded from the negative nasal and tracheal swab samples.

They looked for subgenomic messenger RNA (sgmRNA). They say that this is indicative of viral replication.

 

[Hutan]

However, the conjunctiva of cynomolgus macaque J16017 showed multifocal and perivascular foci of moderate lymphocytic infiltrates in the substantia propria (Figure 8C panel 2). Indeed, this finding was supported by PET-CT images (Figure 8C): an increased FDG-uptake was measured in the left eye compared to the right eye of J16017 which is indicative of ongoing SARS-CoV-2-induced pathogenesis. PCR analysis confirmed the presence of viral RNA in the eye of this animal (Figure 7), clearly demonstrating ocular SARS-CoV-2 infection in J16017. In addition, the cervical lymph node of the same animal exhibited marked lymphoid hyperplasia (follicular type) (Figure 8B panel 1). Similar to the conjunctiva, this histological finding was accompanied by the detection of SARS-CoV-2 RNA in this lymph node.

The finding of virus in the eye of an animal reminds me of the finding of Ebola virus persisting in the eye tissue of survivors.


Some other quotes from the Discussion that I found interesting:

During the entire study, including the acute infection phase, only mild clinical symptoms were noticed.

activity of each animal was performed continuously by using telemetry. This is an important asset as in both macaque species a small, but notable elevation in body temperature was recorded in the first two weeks, the period of active virus replication. Differences in animal activity indicated that SARS-CoV-2 infection also influenced the well-being of the animals without causing obvious clinical symptoms.

It became evident that after the assumed resolution of infection, as witnessed by negative testing for viral RNA in nasal and tracheal swabs, clear signs of pneumonia were still present in the lungs, with both sustained and newly formed lesions. Besides, an increased 18F-FDG uptake was detectable in the lungs and tracheobronchial lymph nodes of all animals. This indicates that despite mild disease symptoms in the acute phase of infection, and resolved viremia, SARS-CoV-2-induced pathogenesis continued. In addition, the detection of subgenomic messenger RNA in the respiratory tract and lung lymph nodes of 50% of animals implies that replication of SARS-CoV-2 continued unnoticed, and one can only hypothesize that this can cause disease symptoms in the macaques at a later stage. This finding in a recognized NHP model for COVID-19 research is of particular interest because of the growing concern for long-COVID in humans [60]. More than a year after the start of the pandemic, it is evident that humans can suffer from COVID-19-related symptoms, weeks to months after seemingly resolving the infection [5,6,7].

Our data indicate widespread tissue dissemination of SARS-CoV-2 in individual monkeys and provide evidence for continuing virus replication in lungs and surrounding lymph nodes after alleged convalescence of infection. This finding is intriguing as it has been hypothesized that persistent infection contributes to long COVID-19 in humans [60]. One wonders whether the current worldwide COVID-19 vaccination program will not only eliminate the acute disease but will have a positive effect on minimizing the long-COVID-related pathologies as well.

Sadly, the comment in this 2021 paper about the vaccination program (potentially eliminating both the acute disease and minimising long-Covid) has not been borne out in reality. I wonder if the people who did this study are continuing their work.

Establishing whether viral persistence is causing ME/CFS-like Long Covid in humans is surely not an impossible task?

 

[rvallee]

Establishing whether viral persistence is causing ME/CFS-like Long Covid in humans is surely not an impossible task?

It never was. The impossible is to get people to actually want to do it and respect the outcome. Human failure, never technical.

Almost seems like we're organisms, not some collection of organs that only interface with each other through some imagine "axis" always involving the brain for some obsessive reason.

 

[SNT Gatchaman]

The finding of virus in the eye of an animal reminds me of the finding of Ebola virus persisting in the eye tissue of survivors.

See thread: Ebola virus disrupts the inner blood-retinal barrier by induction of vascular endothelial growth factor in pericytes

Here, we found that Ebola virus-like particles stimulate retinal pericytes to secrete vascular endothelial growth factor (VEGF) to cause iBRB breakdown. VEGF causes [inner blood-retinal-barrier] breakdown by disrupting the tight junction protein claudin-1.