Avian Flu Diary: Preprint: SARS-CoV-2 Exposure in Norwegian rats (Rattus norvegicus) from New York City

#17,139

While many remain hopeful that that after three long years our COVID pandemic may be winding down, there are many unknowns surrounding the future trajectory and impact of the SARS-CoV-2 virus.

The virus is making significant inroads into China's largely immunologically naive population, new variants (e.g. XBB, BQ.1.1, BN.1, etc) still emerge with unnerving regularity, and we see continued evidence of this virus infecting, and evolving within, non-human hosts.

Nature: Divergent SARS-CoV-2 Variant Emerges in White-tailed Deer with Deer-to-Human Transmission (Revisited)

Preprint: Wildlife Exposure to SARS-CoV-2 Across a Human Use Gradient

CDC: Investigating Possible Mink-To-Human Transmission Of SARS-CoV-2 In The United States

Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus

The concern is that the virus might adapt to another species, follow a divergent evolutionary path, only to `spill back' into humans as a `new', and potentially more dangerous, threat.

And the reality is, we've already seen this happen.

In late 2020, Danish authorities announced the spillover of COVID into millions of susceptible farmed mink, and the discovery of several `mink specific' mutations in the virus (see Denmark Orders Culling Of All Mink Following Discovery Of Mutated Coronavirus), which subsequently jumped back into the human population.

Although this `mink variant' was quickly overtaken by the Alpha variant - and no longer circulates - over the summer of 2021 we learned from an SSI Study: Denmark's Cluster-5 mink Variant Had Increased Antibody Resistance.

This served as a `proof of concept' that - if allowed to spread in a non-human species - SARS-CoV-2 could evolve into something `new' and potentially more dangerous, and spillover into the human population with unpredictable results.

Until 18 months ago, mice were believed largely immune to the coronavirus, but in March of 2021 in PrePrint: The B1.351 and P.1 Variants Extend SARS-CoV-2 Host Range to Mice, we learned hat some SARS variants had overcome that barrier.

Six weeks ago, in Preprint: SARS-CoV-2 Infection in Domestic Rats After Transmission From Their Infected Owner, we saw further evidence of the susceptibility of rodents to COVID, with the author's writing:

We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.

While controversial, there is even some evidence to suggest that the Omicron variant may have evolved after the virus jumped to mice or other rodents (see Evidence for a mouse origin of the SARS-CoV-2 Omicron variant), and then spilled back into humans.

For more on this, see Maryn McKenna's Wired article Where Did Omicron Come From? Maybe Its First Host Was Mice.

How often SARS-CoV-2 infects animals in the wild is largely unknown, but the spillover of the virus into other species is increasingly viewed as a serious threat (see WHO/FAO/OIE Joint Statement On Monitoring SARS-CoV-2 In Wildlife & Preventing Formation of Reservoirs).

All of which brings us to a new preprint, posted Monday on the bioRxiv server, which documents the detection of SARS-CoV-2 in sewer rats in New York City, and the results of challenge studies using various COVID VOCs on laboratory rats.

These researchers found a relatively high percentage of rats tested had been exposed to the coronavirus, and found that both Delta and Omicron variants can also cause robust infections in Sprague Dawley® rats.

I've only posted the abstract and some excerpts from a much longer report, so follow the link to read it in its entirety. I'll have a brief postscript when you return.

SARS-CoV-2 exposure in Norwegian rats (Rattus norvegicus) from New York City

Yang Wang, Julianna Lenoch, Dennis Kohler, Thomas J. DeLiberto, Cynthia Tang, Tao Li, Yizhi Jane Tao, Minhui Guan, Susan Compton, Caroline Zeiss, Jun Hang, Xiu-Feng Wan

doi: https://doi.org/10.1101/2022.11.18.517156

PDF

Abstract

Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of SARS-CoV-2 from humans to rats and other wildlife. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021.

Results showed that 13 of 79 rats (16.5%) tested IgG or IgM positive, and partial genomes of SARS-CoV-2 were recovered from four rats that were qRT-PCR positive.

Using a virus challenge study, we also showed that Alpha, Delta, and Omicron variants can cause robust infections in wild-type Sprague Dawley (SD) rats, including high level replications in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity.

In summary, our results indicated that rats are susceptible to infection with Alpha, Delta, and Omicron variants, and rats in the NYC municipal sewer systems have been exposed to SARS-CoV-2. Our findings highlight the potential risk of secondary zoonotic transmission from urban rats and the need for further monitoring of SARS-CoV-2 in those populations.

(SNIP)

Discussion

Both serological and molecular data from this study suggested the rats from NYC were exposed to SARS-CoV-2. We found that of the tested rats, 16.5% were seropositive and 5.1% were qRT-PCR positive to SARS-CoV-2, which showed a higher exposure frequency than previous reports (11, 163 12).
Genomic analyses suggested that the viruses in the rats that we collected were associated with the B lineage virus. We speculate SARS-CoV-2 exposure could have occurred during the early stages of the pandemic when the B lineage virus was predominant in NYC.
SARS-CoV-2 in sewer rats in New York City,
This is supported by a recent study that reported that the Wuhan-Hu-1-like virus can infect SD rats (16), although an earlier study showed that the prototype Wuhan-Hu-1-like SARS-CoV-2 cannot infect SD rats (6). Such a discrepancy may be due to variation in additional mutations in the challenge Wuhan-Hu-1-like strains or genetic variations in the SD rats used in these studies.
Thus, further surveillance is needed to understand the virological prevalence in NYC rats, particularly for several emerging variants with high infectivity among rats, including those that circulated in NYC during the past two years of the COVID-19 pandemic.

(SNIP)

By using animal models, we further demonstrated that, in addition to Alpha and Beta variants reported earlier (6-9), Delta and Omicron variants can also cause robust infections in SD rats. The tested variants caused robust replication in both upper and lower respiratory tracts of rats, although they did not cause any body weight loss or other clinical signs.
cal prevalence in NYC rats, particularly for several emerging variants with high infectivity among rats, including those that circulated in NYC during the past two years of the COVID-19 pandemic.
Of the three testing variants, Delta replicated the most efficiently. The omicron variant showed a lower viral replication than both Alpha and Delta, although the difference did not reach a statistically significant level between Omicron and Alpha. This finding is in line with earlier reports that Omicron replicated less efficiently and caused less lung pathology in wildtype or human ACE2 transgenic mice or hamsters compared with other variants (19, 20).

(Continue . . . )

Just over a year ago we looked at a perspective article, published in China's CCDC Weekly by two well-known Chinese scientists - George F. Gao and Liang Wang - on the continual spread of SARS-CoV-2 from humans to other animal hosts, and the impacts that could have going forward (see Perspectives: COVID-19 Expands Its Territories from Humans to Animals).