Surveillance of SARS-like CoV in bats from Yucatán, Mexico

doi:10.21203/rs.3.rs-4638860/v1

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Surveillance of SARS-like CoV in bats from Yucatán, Mexico

https://doi.org/10.21203/rs.3.rs-4638860/v1

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SARS-like coronaviruses (SL-CoV) have been identified in bats globally and are of significant public health interest due to their potential to cause new epidemics and pandemics. However, their presence in the Americas remains largely unexplored. This study aimed to conduct surveillance for SL-CoV in bats from the Yucatán Peninsula, Mexico. Bat sampling was conducted between August 2022 and July 2023 in two municipalities (Tekax and Panabá) of Yucatán, Mexico. Rectal and oral swabs as well as whole blood samples were collected from each bat. RNA was extracted from all samples. SL-CoV RNA detection was performed using one-step RT-qPCR targeting the E gene of the viruses. One hundred forty-four bats from six species were included. All biological samples met the RNA concentration and viability criteria for analysis. Our study did not detect SL-CoV in bats from Yucatán, suggesting a low risk of SL-CoV emergence in southeastern Mexico. Continuous surveillance of SL-CoV in bat populations is recommended due to the dynamic of zoonotic disease risks and the potential for changes in virus circulation patterns.

SARS-like coronaviruses

bats

Yucatan

viruses

The family Coronaviridae, within the subfamily Orthocoronavirinae, includes the genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (Walker et al. 2020). Zoonotic coronaviruses (CoV) causing respiratory diseases are found within Alphacoronavirus and Betacoronavirus (Balboni et al. 2012; Cui et al. 2018). Evidence indicates a zoonotic origin (from bats and rodents) for two Alphacoronaviruses (HCoV-229E and HCoV-NL63) and five Betacoronaviruses (HCoV-OC43, HCoV-HKU1, MERS, SARS-CoV1, and SARS-CoV2) (Ruiz-Aravena et al. 2021). Notably, SARS-CoV1 and SARS-CoV2 originated from bats and caused significant epidemics and pandemics in the 21st century (V’kovski et al. 2020).

Genetically similar Betacoronaviruses (up to 96%) to SARS-CoV1 and SARS-CoV2 have been reported in bats (Ruiz-Aravena et al. 2021). These viruses, known as "SARS-like Coronaviruses (SL-CoV)" (Li et al. 2005), are of great public health interest due to their zoonotic potential and the possibility of causing new epidemics and pandemics (Menachery et al. 2015). SL-CoVs have been detected in bats from Asia, Europe, and Africa (Balboni et al. 2012), while their presence in the Americas remains largely unknown (Hernández-Aguilar et al. 2021). This is crucial as some regions in the Americas are considered high-risk areas for the emergence of zoonotic agents (Morse et al. 2021), particularly from bats (Brierley et al. 2016). Therefore, surveillance and monitoring of SL-CoV in high-risk regions of the Americas, such as southeastern Mexico, are essential. Priority should be given to areas with high bat density and diversity and significant natural area disturbance, like the Yucatán Peninsula (Haro et al. 2021). Our objective was to evaluate the presence of SL-CoV in bats from Yucatán, Mexico.

This study was approved by the Bioethics Committee of the Biological and Agricultural Sciences Campus at the Autonomous University of Yucatán (reference: CB-CCBA-D-2022-004). The Ministry of Environment and Natural Resources (SEMARNAT) of Mexico (references: SPARN/DGVS/06447/22 and SPARN/DGVS/09663/23) authorized captured and sampling.

Bat sampling was conducted between August 2022 and July 2023 in two municipalities of Yucatán (Tekax and Panabá), Mexico. The bats were captured using mist nets (6m x 2.4m; Redes Ramírez, Mexico). Bat species were identified using a field guide for bats of México (Medellin et al. 2008), and data on trophic guild, sex, and age (juvenile or adult) were recorded for every bat (Torres-Castro et al. 2019).

Rectal and oral swabs as well as whole blood from the brachial vein were collected. These biological samples were chosen for their minimally invasive nature and efficiency in detecting viral RNA of SL-CoV in bats (Anthony et al. 2013; V’kovski et al. 2020). All samples were placed in DMEM medium and transported to the Zoonoses and other Vector-borne Diseases Laboratory at the Regional Research Center ‘Dr — Hideyo Noguchi’ for storage at -80ºC until processing.

Total RNA extraction from each sample was performed using RNA get (Biotecnologías Moleculares, Mexico) following the manufacturer's instructions. RNA concentration and quality were determined by spectrophotometry using a Nanodrop 2000® (Thermo Scientific, USA), with optimal values of 50–100 ng/µL for concentration and 1.8-2 for integrity in the 260 nm/280 nm ratio. Additionally, the viability of the RNA extraction was assessed by RT-PCR of the constitutive GAPDH gene using the RevertAid HMinus First Strand Synthesis Kit® (Thermo Scientific, USA). Once the quality criteria of the extract were confirmed, RNA from each bat’s feces, saliva, and blood was pooled for subsequent analysis.

SL-CoV RNA detection was performed by amplifying a fragment of the virus's envelope protein E gene (Corman et al. 2020) using one-step RT-qPCR with the PrimeTime One-Step RT-qPCR Master Mix (Integrated DNA Technologies, USA) following the manufacturer's instructions. Nucleotide BLAST and Primer-BLAST confirmed the ability to amplify SL-CoV RNA with this primer pair and probe set (analysis not shown). The RT-qPCR protocol was conducted on a CFX-96 Touch (Bio-Rad, Hercules, California, USA). A positive control was employed using a human SARS-CoV2 isolate provided by the Virology Laboratory at the Dr. Hideyo Noguchi Regional Research Center.

A total of 144 bats from six species (Peropteryx macrotis, Glossophaga mutica, Sturnira parvidens, Artibeus jamaicensis, Dermanura phaeotis, and Molossus nigricans) were included in the study. The general characteristics of the evaluated population are described in Table 1. All samples met the RNA concentration and viability criteria for analysis. None of the samples tested positive for the presence of SL-CoV RNA.

Table 1

Main characteristics of sampled bat
Characteristics	n (%)
Species
Peropteryx macrotis	8 (5.6)
Glossophaga mutica	61 (42.4)
Artibeus jamaicensis	50 (34.7)
Dermanura phaeotis	6 (4.2)
Sturnira parvidens	16 (11.1)
Molossus nigricans	3 (2)
Trophic guild
Frugivore	72 (50)
Insectivore	11 (7.6)
Nectarivore	61 (42.4)
Sex
Female	68 (47.2)
Male	76 (52.8)
Age
Juvenile	115 (79.9)
Adult	29 (20.1)
Legend: number of specimens (n).

This is the first study focused on the surveillance of SL-CoV in bats of Yucatán State, Mexico. The absence of SL-CoV RNA in the sampled bats is consistent with previous findings in Mexico (Colunga-Salas and Hernández-Canchola 2021; Hernández-Aguilar et al. 2024). Despite the identification of several Betacoronaviruses in this country, no study has detected SL-CoV (Table 2), suggesting a low risk of SL-CoV emergence in Mexico. This could be related to the bat genera present in the Americas. SL-CoVs have been identified in Asia, Europe, and Africa, primarily in the genera Rhinolophus, Hipposideros, and Chaerophon (Balboni et al. 2012), which are not found in the Americas.

Table 2

SL-CoV in bats from Mexico
Region	Species	Year of sampling	Sample type	N	SL-CoV Positive	Reference
Jalisco	Artibeus jamaicensis, Artibeus phaeotis, Balantiopteryx plicata, Desmodus rotundus, Glossophaga soricina, Lasiurus cinereus, Mormoops megalophylla, Pteronotus davyi, Pteronotus parnellii, Pteronotus personatus, Sturnira lilium and Sturnira ludovici	2007–2010	Intestine	75	0¹	Goes et al. 2013
Morelos	Pteronotus parnellii, Artibeus spp. Artibeus phaeotis and Macrotus waterhousii	2016	Rectal swap	39	0²	Barrón-Rodriguez et al. 2022
Campeche, Chiapas and Mexico city.	Artibeus lituratus, Artibeus phaeotis, Artibeus jamaicensis, Artibeus watsoni, Glossophaga soricina, Glossophaga commissarisi, Carollia sowelli, Carollia perspicillata, Sturnira Ludovici, Sturnira lilium, Leptonycteris nivalis, Leptonycteris yerbabuenae, Centurio senex, Platyrrhinus helleri, Uroderma bilobatum, Desmodus rotundus, Micronycteris schmidtorum, Micronycteris microtis, Mimon cozumelae, Phyllostomus discolour, Choeroniscus godmani, Trachops cirrhosis, Tonatia saurophila, Chrotopterus auratus, Lonchorhina aurita, Phylloderma stenops, Mormoops megalohyla, teronotus davyi, Pteronotus parnellii, Nyctinomops macrotis, Nyctinomops laticaudatus, Tadarida brasiliensis, Myotis velifer, Myotis occultus, Myotis keaysi, Myotis nigricans, Eptesicus fuscus, Corynorhinus mexicanus, Lasiurus intermedius, Bauerus dubiaquercus, Rhynchonycteris naso and Saccopteryx bilineata.	2013	Blood	606	0³	Anthony et al. 2013
Oaxaca	Artibeus jamaicensis, Artibeus lituratus, Artibeus toltecus, Carolia perspicillata, Desmodus rotundus and Glossophaga mutica	2019–2022	Liver tissue	20	0	Hernández-Aguilar et al. 2024
Yucatan	Artibeus jamaicensis, Dermanura phaeotis, Glossophaga mutica, Molossus nigricans, Peropteryx macrotis and Sturnira parvidens	2023	Rectal and oral swab, and blood.	144	0	Present study
Legend: Severe acute respiratory virus like coronaviruses (SL-CoV)
[1] Identified one Betacoronavirus strain (non-SL-CoV).
[2] Identified in a pool of rectal samples (n = 13) a Betacoronavirus strain (non-SL-CoV).
[3] Identified nine Alphacoronavirus and four individuals with Betacoronavirus strains (non-SL-CoV).

In Mexico, most Alphacoronaviruses and Betacoronaviruses have been reported in bats of the genera Artibeus, Carollia, Eptesicus, Lonchorhina, Myotis, and Pteronotus (Anthony et al. 2013; Barrón-Rodriguez et al. 2022; Goes et al. 2013), which, according to phylogenetic analyses, are not related to SL-CoVs (Colunga-Salas and Hernández-Canchola 2021). Moreover, the overall prevalence of CoVs in bats is higher in Asia, Europe, Africa, and Oceania (around 13%) compared to the Americas (approximately 6.5%) (Warmuth et al. 2023). This indicates that despite the high diversity of bat species and the high risk of emerging zoonotic pathogens, the probability of zoonotic CoVs emergence from bats in the Americas might be low.

The combined effects of human impact, climate, and mammalian species richness influence CoVs prevalence in bats (Warmuth et al. 2023). In the Yucatán Peninsula, recent decades have seen significant natural area disturbances due to agriculture, population growth, tourism, and other factors (Haro et al. 2021). These disturbances lead to closer interactions between humans and animals, increasing the risk of emerging and re-emerging zoonotic disease outbreaks in humans (Bonilla-Aldana et al. 2021; Canche-Pool et al. 2022; Li et al. 2019). Although there is currently no evidence of SL-CoV circulation in bats in Mexico, this situation could change. Therefore, continuous surveillance of SL-CoV in wildlife species, including bats, is advisable.

In conclusion, our study did not detect the presence of SL-CoV in bats from Yucatán, suggesting that the risk of these viruses emerging in Mexico is low. Nevertheless, ongoing surveillance of these viruses in bats is recommended as a precautionary measure.

Conflict of interests:

The authors declare that they have no competing interests. Neither the authors nor their institutions have at any time received payment or services from a third party for any aspect of the submitted work (data monitoring board, study design, manuscript preparation, statistical analysis, or other aspects).

Funding:

This work was supported by the Andalusian General Secretariat for Research, Development, and Innovation in Health (PI-0287-2019), the Spanish Ministry of Health (RD12/0017/0012), co-financed by the European Regional Development Fund (ERDF). AYG was supported by CONAHCYT Grant no. 413387. ARJ is supported by a contract from the Spanish Junta de Andalucía (Nicolas Monardes program: C1-0001-2023). The funders did not play any role in the design, conclusions, interpretation of the study, or decision to publish.

Author Contribution

Conceptualization: ARJ and MTC. Formal analysis: AYG and GAT. Funding acquisition: ARJ and MTC. Investigation: AYG, ASG and MAT. Methodology: all authors. Project administration: ARJ and MTC. Resources: ARJ, ASG and MTC. Software: AYG, ARJ and GAT. Supervision: ARJ, GAT, and MTC. Validation: AYG, ARJ, and GAT. Visualization: AYG, ARJ, and MTC. Writing - original draft: AYG, ARJ and MTC. Writing - review & editing: all authors.

Acknowledgement

We gratefully acknowledge Alonso Panti May, Melissa Suárez Galaz, Claudia Carillo Chan, Rodolfo Chan Chan, Raymundo Matu Góngora, Bibiana Reyes Hernández, Angélica Andrade López, Rodrigo Ramos Vázquez, Rosa María Galaz Avalos, and Kevin Yam Trujillo for their technical support in sample collection, processing, and analysis. Also, we acknowledge the administrations of Rancho Santa Maria (Panabá, Yucatán), Grutas Las Sartenejas (Tekax, Yucatán), and Parque Ecoturístico Kaalmankal (Tekax, Yucatán) for their facilities for bat sampling.

Anthony SJ, Ojeda-Flores R, Rico-Chávez O, Navarrete-Macias I, Zambrana-Torrelio CM, Rostal MK, Epstein JH, Tipps T, Liang E, Sanchez-Leon M, Sotomayor-Bonilla J, Aguirre AA, Ávila-Flores RA, Medellín RA, Goldstein T, Suzán G, Daszak P, Lipkin WI (2013) Coronaviruses in bats from Mexico. J Gen Virol 94:1028–1038. https://doi.org/10.1099/VIR.0.049759-0
Balboni A, Battilani M, Prosperi S (2012) The SARS-like coronaviruses: the role of bats and evolutionary relationships with SARS coronavirus. New Microbiol 35:1–16.
Barrón-Rodríguez RJ, Parra-Laca R, Rojas-Anaya E, Romero-Espinoza JÁI, Ayala-Sumuano JT, Vázquez-Pérez JA, García-Espinosa G, Loza-Rubio E (2022) Evidence of viral communities in three species of bats from rural environment in Mexico. Acta Chiropt 24:249–264. https://doi.org/10.3161/15081109ACC2022.24.1.020
Bonilla-Aldana DK, Jimenez-Diaz SD, Arango-Duque JS, Aguirre-Florez M, Balbin-Ramon GJ, Paniz-Mondolfi A, Suárez JA, Pachar MR, Perez-Garcia LA, Delgado-Noguera LA, Sierra MA, Muñoz-Lara F, Zambrano LI, Rodriguez-Morales AJ (2021) Bats in ecosystems and their wide spectrum of viral infectious potential threats: SARS-CoV-2 and other emerging viruses. Int J Infect Dis 102:87–96. https://doi.org/10.1016/J.IJID.2020.08.050
Brierley L, Vonhof MJ, Olival KJ, Daszak P, Jones KE (2016) Quantifying global drivers of zoonotic bat viruses: a process-based perspective. The American Naturalist 187:E53. https://doi.org/10.1086/684391
Canché-Pool EB, Panti-May JA, Ruiz-Piña HA, Torres-Castro M, Escobedo-Ortegón FJ, Tamay-Segovia P, Blum-Domínguez S, Torres-Castro JR, Reyes-Novelo E (2022) Cutaneous Leishmaniasis emergence in southeastern Mexico: the case of the State of Yucatan. Trop Med Infect Dis 7:444. https://doi.org/10.3390/TROPICALMED7120444
Colunga-Salas P, Hernández-Canchola G (2021) Bats and humans during the SARS-CoV-2 outbreak: The case of bat-coronaviruses from Mexico. Transbound Emerg Dis 68:987–992. https://doi.org/10.1111/TBED.13751
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DGJC, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 25:2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045
Cui J, Li F, Shi ZL (2018) Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol 17:181–192. https://doi.org/10.1038/s41579-018-0118-9
Góes L, Ruvalcaba S, Campos A, Queiroz L, de Carvalho C, Jerez J, Durigon EL, Dávalos LI, Dominguez SR (2013) Novel bat Coronaviruses, Brazil and Mexico. Emerg Infect Dis 19:1711-1713. https://doi.org/10.3201/eid1910.130525
Haro P, Trasviña-Muñoz E, May-Concha I, López-Valencia G, Monge-Navarro F, Herrera-Ramírez C, Mercado-Rodríguez JA, Villanueva-Alonzo H, Waleckx E (2021) Historical spatial distribution of zoonotic diseases in domestic, synanthropic, and wild animals in the Mexican territory of the Yucatan Peninsula. J Trop Med 2021. https://doi.org/10.1155/2021/8699455
Hernández-Aguilar I, Lorenzo C, Santos-Moreno A, Naranjo EJ, Navarrete-Gutiérrez D (2021) Coronaviruses in bats: a review for the Americas. Viruses 13:1226. https://doi.org/10.3390/V13071226
Hernández-Aguilar I, Ramírez-Palacios LR, Lorenzo C, Santos-Moreno A (2024) Preliminary study does not demonstrate SARS-CoV-2 infection in bats from Oaxaca, México during the Covid-19 pandemic. Therya Notes 5:86–91. https://doi.org/10.12933/therya_notes-24-155
Li H, Mendelsohn E, Zong C, Zhang W, Hagan E, Wang N, Li S, Yan H, Huang H, Zhu G, Ross N, Chmura A, Terry P, Fielder M, Miller M, Shi Z, Daszak P (2019) Human-animal interactions and bat coronavirus spillover potential among rural residents in Southern China. Biosaf Health 1:84–90. https://doi.org/10.1016/J.BSHEAL.2019.10.004
Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, Wang H, Crameri G, Hu Z, Zhang H, Zhang J, McEachern J, Field H, Daszak P, Eaton BT, Zhang S, Wang L-F (2005) Bats are natural reservoirs of SARS-like Coronaviruses. Science 310:676–679
Medellin RA, Arita H, Sanchez O (2008) Identificación de los murciélagos de México. Instituto de Ecología. UNAM-CONABIO
Menachery VD. Yount BL, Debbink K, Agnihothram S, Gralinski LE, Plante JA, Graham RL, Scobey T, Ge XY, Donaldson EF, Randell SH, Lanzavecchia A, Marasco WA, Shi ZL, Baric RS (2015) A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med 21:1508–1513. https://doi.org/10.1038/nm.3985
Morse SS, Mazet JAK, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P (2012) Prediction and prevention of the next pandemic zoonosis. Lancet 380:1956–1965. https://doi.org/10.1016/S0140-6736(12)61684-5
Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR., Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK (2021) Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol 20:299–314. https://doi.org/10.1038/s41579-021-00652-2
Torres-Castro M, Muñoz-Dueñas D, Hernández-Betancourt S, Bolio-González M, Noh-Pech H, Peláez-Sánchez R, Sosa-Escalante J (2019) Infection with Toxoplasma gondii (Eucoccidiorida: Sarcocystidae) in bats of Campeche and Yucatán, Mexico. Rev Biol Trop 67:633–642. https://doi.org/10.15517/RBT.V67I3.35147
V’kovski P, Kratzel A, Steiner S, Stalder H, Thiel V (2020) Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 19:155–170. https://doi.org/10.1038/s41579-020-00468-6
Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Dempsey DM, Dutilh BE, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Nibert M, Orton RJ, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Varsani A, Zerbini FM, Davison AJ (2020) Changes to virus taxonomy and the statutes ratified by the International Committee on Taxonomy of Viruses (2020). Arch Virol 165:2737–2748. https://doi.org/10.1007/S00705-020-04752-X
Warmuth VM, Metzler D, Zamora-Gutierrez V (2023) Human disturbance increases coronavirus prevalence in bats. Sci Adv 9. https://doi.org/10.1126/SCIADV.ADD0688

No competing interests reported.

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Surveillance of SARS-like CoV in bats from Yucatán, Mexico

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