Molecular epidemiology of coronaviruses and astroviruses in rodent populations in Hong Kong

Abstract

This surveillance study conducted in Hong Kong from February 2021 to 2023 focused on the detection and prevalence of coronaviruses and astroviruses in rodents. These viruses have the zoonotic potential to cross species barriers and infect both animals and humans. Understanding the molecular epidemiology of these viruses in rodents is crucial because rodents often serve as reservoirs or intermediate hosts for zoonotic diseases.

A global COVID-19 pandemic was caused by coronaviruses with outbreaks of severe respiratory illnesses, caused by SARS-Co V-2. The susceptibility of rodents to some strains of SARS-Co V-2, as well as the detection of coronaviruses in rodents suggests that they may serve as potential reservoirs for viruses with zoonotic potential, posing a risk to human populations. This study aims to study the potential role of rodents as zoonotic pathogens carriers and to evaluate their implications for public health.

The surveillance study involved the collection of urban and peri-urban rodent swabs and tissue samples from 18 districts in Hong Kong, analyzing 890 rats using polymerase chain reaction amplification and Sanger sequencing, next-generation sequencing and serological surveys to detect the presence of coronaviruses and astroviruses. NGS is used to understand more about the viral diversity and obtain representative genomes for some of the AstV- or CoV-positive individuals.

The results revealed a 4. 7% positivity rate for coronaviruses and a 1. 75% positivity rate for astroviruses among the sampled rodents, raising concerns about their potential role in disease transmission since rodents are known to be natural reservoirs for a number of emerging infectious diseases.

The metagenomics sequencing showed diversity of the coronavirus-positive samples revealed a diverse rodent virome. Coronaviridae and Straboviridae were the mostly detected viral families. Other RNA viruses including Spinareoviridae and Picobimaviridae were also detected by metagenomics. Three complete coronavirus genomes were assembled, all closely related to Lucheng rat coronavirus. The study also showed coinfection in 6 rodent' rectal swab samples for both astroviruses and coronaviruses.

Enzyme-linked immunosorbent assay (ELISA) was conducted to analyse the exposure of rodents to SARS-CoV-2. Although viral RNA was not detected, the results showed that there was potential exposure to SARS-Co V-2. We tested 823 blood serum samples from rodents using ELISA. We identified 5 positives serum samples with both replicates, 2 borderline positives for both replicates. The presence of seropositive SARS-Co V-2 rodents indicated that there could be a risk of zoonotic transmission from rodents to humans and a past infection history in rodents through environmental exposure.

To conclude, these findings emphasized the importance of ongoing surveillance efforts and research related to astroviruses and coronaviruses in rodents, due to the zoonotic potential in humans. Understanding the presence and diversity of coronaviruses and astroviruses in rodent populations is important in highlighting their implications for public health. Continued surveillance efforts and further research are essential to mitigate the risk of zoonotic disease transmission and protect human populations from emerging viral threats. Public health authorities should consider integrating rodent surveillance for early detection and risk assessment into their broader disease surveillance systems to better control infectious diseases.