First Report of Alphacoronavirus Circulating in Cavernicolous Bats from Portugal

Abstract

The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the presence of CoVs of four cavernicolous bats in six locations in the centre and south of Portugal. We collected faeces, anal, and buccal swab samples, as well as air samples from the locations using a Coriolis air sampler. Our results indicate that CoVs were more readily detected in faecal samples compared to anal and buccal swab samples. No CoVs were detected in the air samples. Phylogenetic analysis showed that the detected viruses belong to the Alphacoronavirus genus. This study represents the first report of Alphacoronaviruses circulating in bats in Portugal and highlights the importance of continuous surveillance for novel CoVs in bat populations globally. Ongoing surveillance for CoVs in bat populations is essential as they are a vital source of these viruses. It is crucial to understand the ecological relationships between animals, humans, and the environment to prevent and control the emergence and transmission of infectious diseases. Further ecological studies are needed to investigate the factors contributing to the emergence and transmission of zoonotic viruses.

Presence of Alphacoronavirus in Tree- and Crevice-Dwelling Bats from Portugal

“…From this screening only one sample showed to be positive for Alpha-CoV (1.15%; 95% confidence interval [CI]: 0.03–6.24), which is low compared to other studies that reported prevalence rates usually ranging from 3% to 17% [ 26 , 41 , 56 , 57 ]. Unexpectedly, our prior investigation into CoV excretion in Portugal revealed an occurrence of 8.87%, indicating a higher prevalence of CoVs in cave-dwelling bats than crevice- and tree-dwelling bats [ 49 ]. This could be because of different habitat characteristics, variations in bat species behaviour, proximity to potential virus reservoirs, and fluctuations in bat population density.…”

“…In contrast, the research involving cave-dwelling bats revealed that the clustering of bat CoVs was not primarily determined by the species of bat. Instead, it appeared that geographical location played a more significant role in influencing the evolution and dissemination of these viruses [ 49 ]. This suggests that environmental factors, such as habitat characteristics and local ecological dynamics, may exert a more significant influence on the genetic diversity and distribution of coronaviruses in cave-dwelling bat populations.…”

“…Human-induced alterations, such as deforestation, habitat fragmentation, and land conversion for agriculture and urban development, can exert profoundly adverse effects on the transmission of infectious diseases from wild animals to both livestock and humans [ 25 ] and favour the emergence of infectious diseases. The faecal–oral route has also been described in CoVs from other animals such as feline CoVs (FCoV), canine CoVs, and swine CoVs (SADS-CoV)—all of which are classified as Alpha-CoV, highlighting the potential for similar transmission mechanisms across diverse animal taxa [ 49 ] Both Alpha- and Beta-CoVs have high detection rates in bat stool samples, suggesting gastrointestinal replication and that these animals’ excretions are a major environmental source for the shedding of CoVs in spillover events [ 67 , 68 ]. A previous study also confirmed the gastrointestinal replication by not finding evidence of CoVs in the caves where bats and bat excretion was found [ 49 ].…”

“…The extracted RNA was tested for CoVs by employing a broad-spectrum pan-CoV nested RT-PCR assay, which focused on the conserved section of the RNA-dependent RNA polymerase (RdRp) and resulted in a final product measuring 440 bp [ 51 ]. The first and second rounds of the PCRs, as well as electrophoresis, were carried out as described in [ 49 , 52 ].…”

“…In Portugal, research into the presence of CoVs in bats remains limited, with only one study conducted [ 49 ]. This investigation targeted a diverse array of bat roosts such as caves and large buildings across the country, providing an understanding of the distribution and prevalence of CoVs among cave-dwelling bats in Portugal.…”