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A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia.
Urushadze L
,
Babuadze G
,
Shi M
,
Escobar LE
,
Mauldin MR
,
Natradeze I
,
Machablishvili A
,
Kutateladze T
,
Imnadze P
,
Nakazawa Y
,
Velasco-Villa A
.
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Mammal-associated coronaviruses have a long evolutionary history across global bat populations, which makes them prone to be the most likely ancestral origins of coronavirus-associated epidemics and pandemics globally. Limited coronavirus research has occurred at the junction of Europe and Asia, thereby investigations in Georgia are critical to complete the coronavirus diversity map in the region. We conducted a cross-sectional coronavirus survey in bat populations at eight locations of Georgia, from July to October of 2014. We tested 188 anal swab samples, remains of previous pathogen discovery studies, for the presence of coronaviruses using end-point pan-coronavirus RT-PCR assays. Samples positive for a 440 bp amplicon were Sanger sequenced to infer coronavirus subgenus or species through phylogenetic reconstructions. Overall, we found a 24.5% positive rate, with 10.1% for Alphacoronavirus and 14.4% for Betacoronavirus. Albeit R. euryale, R. ferrumequinum, M. blythii and M. emarginatus were found infected with both CoV genera, we could not rule out CoV co-infection due to limitation of the sequencing method used and sample availability. Based on phylogenetic inferences and genetic distances at nucleotide and amino acid levels, we found one putative new subgenus and three new species of Alphacoronavirus, and two new species of Betacoronavirus.
Figure 1. Geographic location and relative proportion of bat species collected per collection site. Red circles indicate the approximate location of collection site. Pie charts indicate the relative proportion of each bat species collected per site. Size of the pie charts indicates the relative number of samples collected per site. Asterisks within the pie indicate whether individuals of that species tested positive for alpha (red) and/or beta CoVs (blue). Lack of asterisks indicates no CoV were detected in a bat species and/or site. Color codes for each bat species represented in the pie charts are indicated in the lower part of the figure.
Figure 2. Unrooted Bayesian phylogenetic tree for AlphaCoVs generated with a partial informative 411 bp fragment of the RdRp. Representative BetaCoV taxa were used in the alignment to demonstrate consistent segregation between both genera. Values at nodes represent branch support values expressed as Bayesian posterior probabilities. Scale bar indicates branch lengths. Highlighted nodes are robustly supported with colored bars indicating relevant branches encompassing taxa pertaining to a given subgenus on the left. Bars on the right indicate taxa pertaining to recognized coronavirus species according to the most recent ICTV classification scheme. Taxa highlighted in orange on the right side of the tree indicate coronavirus sequences obtained from Georgian bats. Dark red bars indicate unclassified coronavirus subgenera or species identified herein. Taxa names for all reference sequences in the tree start with their respective GenBank accession number. Animal silhouettes on the extreme right indicate the animal species from which reference sequences were recovered.
Figure 3. Unrooted Bayesian phylogenetic tree for beta CoVs generated with a partial informative 411 bp fragment of the RdRp. Representative BetaCoV taxa were used in the alignment to demonstrate consistent segregation between both genera. Values at nodes represent branch support values expressed as Bayesian posterior probabilities. Scale bar indicates branch lengths. Highlighted nodes are robustly supported with colored bars indicating relevant branches encompassing taxa pertaining to a given subgenus on the left. Bars on the right indicate taxa pertaining to recognized CoV species according to the most recent ICTV classification scheme. Taxa highlighted in orange on the right side of the tree indicate CoV sequences obtained from Georgian bats, and the dark blue bars indicate unclassified CoV species. Taxa names for all reference sequences in the tree start with their respective GenBank accession number. Animal silhouettes on the extreme right indicate the animal species from which reference sequences were recovered.
Figure 4. Distribution maps for bat species found to be CoV positive in this study compared with the geographic range of other bat species presenting highly similar CoVs across Eurasia as observed in our phylogenetic reconstructions. (A) depicts the geographic range of bat species with highly similar AlphaCoV obtained from Georgia with those reported in other countries across Eurasia. (B) depicts the geographic range of bat species with highly similar BetaCoV obtained from Georgia with those reported in other countries across Eurasia.
Allen,
Global hotspots and correlates of emerging zoonotic diseases.
2017, Pubmed
Allen,
Global hotspots and correlates of emerging zoonotic diseases.
2017,
Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Anthony,
Global patterns in coronavirus diversity.
2017,
Pubmed
Ar Gouilh,
SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world.
2018,
Pubmed
Bai,
Molecular Survey of Bacterial Zoonotic Agents in Bats from the Country of Georgia (Caucasus).
2017,
Pubmed
Chen,
RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
2020,
Pubmed
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses,
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.
2020,
Pubmed
Cui,
Origin and evolution of pathogenic coronaviruses.
2019,
Pubmed
De Benedictis,
Alpha and lineage C betaCoV infections in Italian bats.
2014,
Pubmed
Dominguez,
Detection of group 1 coronaviruses in bats in North America.
2007,
Pubmed
Drexler,
Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences.
2010,
Pubmed
Drexler,
Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS.
2014,
Pubmed
Edgar,
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
2004,
Pubmed
Falcón,
Detection of alpha and betacoronaviruses in multiple Iberian bat species.
2011,
Pubmed
Ge,
Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft.
2016,
Pubmed
Geldenhuys,
Overview of Bat and Wildlife Coronavirus Surveillance in Africa: A Framework for Global Investigations.
2021,
Pubmed
Gloza-Rausch,
Detection and prevalence patterns of group I coronaviruses in bats, northern Germany.
2008,
Pubmed
Gouilh,
SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory.
2011,
Pubmed
Gu,
Molecular phylogeny of hantaviruses harbored by insectivorous bats in Côte d'Ivoire and Vietnam.
2014,
Pubmed
Hamre,
A new virus isolated from the human respiratory tract.
1966,
Pubmed
Huelsenbeck,
MRBAYES: Bayesian inference of phylogenetic trees.
2001,
Pubmed
Jevšnik,
Coronavirus infections in hospitalized pediatric patients with acute respiratory tract disease.
2012,
Pubmed
Kahn,
History and recent advances in coronavirus discovery.
2005,
Pubmed
Kim,
Detection of Severe Acute Respiratory Syndrome-Like, Middle East Respiratory Syndrome-Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats.
2016,
Pubmed
Kohl,
Update on Potentially Zoonotic Viruses of European Bats.
2021,
Pubmed
Kumar,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
2016,
Pubmed
Lau,
Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats.
2005,
Pubmed
Lelli,
Detection of coronaviruses in bats of various species in Italy.
2013,
Pubmed
Mallapaty,
The search for animals harbouring coronavirus - and why it matters.
2021,
Pubmed
McIntosh,
Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease.
1967,
Pubmed
Memish,
Saudi Arabia and the emergence of a novel coronavirus.
2013,
Pubmed
Mendenhall,
Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan.
2019,
Pubmed
Phelps,
Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia.
2019,
Pubmed
Reusken,
Circulation of group 2 coronaviruses in a bat species common to urban areas in Western Europe.
2010,
Pubmed
Souilmi,
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.
2021,
Pubmed
Tang,
Prevalence and genetic diversity of coronaviruses in bats from China.
2006,
Pubmed
Urushadze,
Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus).
2017,
Pubmed
Wassenaar,
2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses.
2020,
Pubmed
Wilkinson,
Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses.
2020,
Pubmed
Wong,
Global Epidemiology of Bat Coronaviruses.
2019,
Pubmed
Wu,
A new coronavirus associated with human respiratory disease in China.
2020,
Pubmed
Wu,
Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases.
2016,
Pubmed
Xu,
Detection and characterization of diverse alpha- and betacoronaviruses from bats in China.
2016,
Pubmed
Zhou,
A pneumonia outbreak associated with a new coronavirus of probable bat origin.
2020,
Pubmed