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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Cell. Infect. Microbiol.</journal-id>
<journal-title>Frontiers in Cellular and Infection Microbiology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Cell. Infect. Microbiol.</abbrev-journal-title>
<issn pub-type="epub">2235-2988</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fcimb.2022.856429</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Cellular and Infection Microbiology</subject>
<subj-group>
<subject>Original Research</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Multilocus Genotyping of <italic>Giardia duodenalis</italic> in Alpine Musk Deer (<italic>Moschus chrysogaster</italic>) in China</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Cui</surname><given-names>Zhaohui</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/1638691"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname><given-names>Qilin</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Huang</surname><given-names>Xiyao</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Bai</surname><given-names>Jiayi</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhu</surname><given-names>Bingyang</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wang</surname><given-names>Bingchen</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Guo</surname><given-names>Xiaohang</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Qi</surname><given-names>Meng</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/756041"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Li</surname><given-names>Junqiang</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref>
<uri xlink:href="https://loop.frontiersin.org/people/445966"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Food and Pharmacy College, Xuchang University</institution>, <addr-line>Xuchang</addr-line>, <country>China</country></aff>
<aff id="aff2"><sup>2</sup><institution>College of Animal Science and Technology, Tarim University</institution>, <addr-line>Alar</addr-line>, <country>China</country></aff>
<aff id="aff3"><sup>3</sup><institution>College of Veterinary Medicine, Henan Agricultural University</institution>, <addr-line>Zhengzhou</addr-line>, <country>China</country></aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Razakandrainibe Romy, Universit&#xe9; de Rouen, France</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Mohamed Mammeri, Ecole Nationale Veterinaire D&#x2019;alfort, France; Abdelmounaim Mouhajir, Universit&#xe9; de Rouen, France</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Meng Qi, <email xlink:href="mailto:qimengdz@163.com">qimengdz@163.com</email>; Junqiang Li, <email xlink:href="mailto:lijunqiangcool@126.com">lijunqiangcool@126.com</email>
</p>
</fn>
<fn fn-type="other" id="fn002">
<p>This article was submitted to Parasite and Host, a section of the journal Frontiers in Cellular and Infection Microbiology</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>20</day>
<month>04</month>
<year>2022</year>
</pub-date>
<pub-date pub-type="collection">
<year>2022</year>
</pub-date>
<volume>12</volume>
<elocation-id>856429</elocation-id>
<history>
<date date-type="received">
<day>17</day>
<month>01</month>
<year>2022</year>
</date>
<date date-type="accepted">
<day>28</day>
<month>03</month>
<year>2022</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2022 Cui, Wang, Huang, Bai, Zhu, Wang, Guo, Qi and Li</copyright-statement>
<copyright-year>2022</copyright-year>
<copyright-holder>Cui, Wang, Huang, Bai, Zhu, Wang, Guo, Qi and Li</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p><italic>Giardia duodenalis</italic> is the underlying cause of a significant number of outbreaks of gastrointestinal illness in humans and animals worldwide. The purpose of this study was to elucidate the prevalence and genetic diversity of <italic>G. duodenalis</italic> in captive alpine musk deer (<italic>Moschus chrysogaster</italic>) in China. A total of 202 fecal samples were collected from three farms in Gansu Province, China. Identification of <italic>G. duodenalis</italic> was conducted by nested PCR targeting the genes coding for SSU rRNA, &#x3b2;-giardin (<italic>bg</italic>), glutamate dehydrogenase (<italic>gdh</italic>) and triosephosphate isomerase (<italic>tpi</italic>). The overall prevalence of <italic>G. duodenalis</italic> in captive alpine musk deer in surveyed area was 19.3% (39/202). Two <italic>G. duodenalis</italic> genetic assemblages were identified, namely assemblage A and E. Mixed genotype infections (A+E) were found in 15.4% (6/39) of positive samples. Multilocus genotyping (MLG) analysis of <italic>G. duodenalis</italic> isolates revealed six novel assemblage A MLGs formed by two newly-described MLG-subtypes which belonged to sub-assemblage AI. To the best of our knowledge, this is the first report on MLG of <italic>G. duodenalis</italic> isolates in captive alpine musk deer in China. The presence of zoonotic assemblages and sub-assemblages of <italic>G. duodenalis</italic> in deer species suggests that these animals may potentially act as a reservoir of this protozoan for humans.</p>
</abstract>
<kwd-group>
<kwd><italic>Giardia duodenalis</italic>
</kwd>
<kwd>alpine musk deer</kwd>
<kwd>multilocus genotyping</kwd>
<kwd>zoonotic potential</kwd>
<kwd>China</kwd>
</kwd-group>
<counts>
<fig-count count="2"/>
<table-count count="4"/>
<equation-count count="0"/>
<ref-count count="53"/>
<page-count count="8"/>
<word-count count="3554"/>
</counts>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>    <p><italic>Giardia duodenalis</italic> (also known as <italic>Giardia lamblia</italic> and <italic>Giardia intestinalis</italic>) is the most prevalent protozoan pathogen, commonly found in the intestinal tract of humans and animals worldwide (<xref ref-type="bibr" rid="B2">Adam, 2021</xref>). Transmission of <italic>G. duodenalis</italic> infection occurs by several routes either directly (i.e., person-to-person, animal-to-animal, or zoonotic infection) or indirectly (i.e., water or food) (<xref ref-type="bibr" rid="B14">Dixon, 2021</xref>). Approximately 280 million people are considered to be infected with <italic>G. duodenalis</italic> worldwide, with infection rates at the range of 8.0&#x2013;30.0% in developing countries and 0.4&#x2013;7.5% in developed countries (<xref ref-type="bibr" rid="B17">Feng and Xiao, 2011</xref>; <xref ref-type="bibr" rid="B43">Ryan and Zahedi, 2019</xref>). Giardiasis is generally a self-limiting clinical illness in humans, whereas it can be threatening to infants, young children, the elderly, institutionalized individuals, travelers, and immunocompromised individuals (<xref ref-type="bibr" rid="B8">Cacci&#xf2; et&#xa0;al., 2018</xref>; <xref ref-type="bibr" rid="B9">Cai et&#xa0;al., 2021</xref>). Nitroimidazoles (e.g., metronidazole and tinidazole) are the most commonly drugs used to treat giardiasis, although requiring multiple doses and being often associated with adverse effects (<xref ref-type="bibr" rid="B4">Arg&#xfc;ello-Garc&#xed;a et&#xa0;al., 2020</xref>).</p>
<p>To date, according to the reservoir and genetic characteristics of the protozoan, eight <italic>Giardia</italic> species have been recognized (<xref ref-type="bibr" rid="B42">Ryan et&#xa0;al., 2019</xref>). However, most studies for both public and veterinary health have focused on the taxonomy, population genetics, and epidemiology of <italic>G. duodenalis</italic> (<xref ref-type="bibr" rid="B34">Li et&#xa0;al., 2017a</xref>; <xref ref-type="bibr" rid="B51">Xiao and Feng, 2017</xref>). Based on studies employing iso-enzymatic and nucleic acid polymorphisms, <italic>G. duodenalis</italic> is known as a multispecies complex, consisting of eight genetic assemblages (A&#x2013;H) considering different host distribution (<xref ref-type="bibr" rid="B8">Cacci&#xf2; et&#xa0;al., 2018</xref>); assemblages A and B are commonly found in humans and occasionally in other mammals; assemblages C and D are often found in canids; assemblage E mainly infects ungulates; assemblages F, G, and H are specific to cats, rodents and pinnipeds, respectively (<xref ref-type="bibr" rid="B40">Ryan and Cacci&#xf2;, 2013</xref>; <xref ref-type="bibr" rid="B9">Cai et&#xa0;al., 2021</xref>). Furthermore, putative sub-assemblages have been identified within assemblage A (AI&#x2013;III) and assemblage B (BIII and BIV) using a multilocus genotyping (MLG) approach (<xref ref-type="bibr" rid="B11">Capewell et&#xa0;al., 2021</xref>).</p>
<p>China has the largest wild and captive populations of alpine musk deer (<italic>Moschus chrysogaster</italic>) in the world, which are mainly distributed in the Qinghai Tibet Plateau, Sichuan and Gansu Province (<xref ref-type="bibr" rid="B25">Jiang et&#xa0;al., 2021</xref>). Musk, produced by adult male alpine musk deer, is an important raw material for preparations of the traditional Chinese medicine and the fragrance industry. However, illegal hunting, habitat fragmentation, and other human activities have decimated wild alpine musk deer populations in China (<xref ref-type="bibr" rid="B10">Cai et&#xa0;al., 2020</xref>). For these reasons, the alpine musk deer has been listed as an endangered species by the International Union for Conservation of Nature (IUCN) and as category I-protected wild animal in China. Although the Chinese government has encouraged enterprises to participate in programs of breeding of captive alpine musk deer, gastrointestinal infections are the most significant threats to population growth and breeding scale whose fatality rate is approximately 30% (<xref ref-type="bibr" rid="B33">Li et&#xa0;al., 2017b</xref>). Currently, little information is available on the prevalence and genetic characteristics of <italic>G. duodenalis</italic> in cervids in China.</p>
<p>Thus, the aim of the present study was to investigate the prevalence and genetic diversity of <italic>G. duodenalis</italic> in captive alpine musk deer. The findings discussed herein provide insights into the development of preventive measures against <italic>Giardia</italic> infection.</p>
</sec>
<sec id="s2">
<title>Material and Methods</title>
<sec id="s2_1">
<title>Ethics Statement</title>
<p>This study was performed with strict adherence to the recommendations of the Guide for the Care and Use of Laboratory Animals of the Ministry of Health, China. The research protocol was reviewed and approved by the Research Ethics Committee of Tarim University (approval no. ECTU 2020-0013). Farm owners&#x2019; consent was obtained prior to proceeding to fecal sample collection from selected animals.</p>
</sec>
<sec id="s2_2">
<title>Samples</title>
<p>In September 2020, 202 fecal samples were collected from three farms in Gansu Province, China (<xref ref-type="fig" rid="f1"><bold>Figure&#xa0;1</bold></xref>). Alpine musk deer animals were shed-fed and housed in separate breeding houses according to age. Fresh fecal samples were taken from the soil immediately after defecation using a sterile disposal latex glove, ensure absence of exogenous contamination. Subsequently, samples were placed individually into a disposable plastic container, recorded the date, site, age, and number. All animals from which fecal samples were obtained were apparently in good health with no signs of diarrhea at the time of sample collection. Samples were transferred to the laboratory in an insulated container on ice and stored at 4&#xb0;C prior to DNA extraction.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Sampling sites. No copyright permission was required. The figure was designed with the software ArcGIS 10.2. The map has been originally modified and assembled according to permission and attribution guidelines of the National Geomatics Center of China (<uri xlink:href="http://www.ngcc.cn">http://www.ngcc.cn</uri>).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-856429-g001.tif"/>
</fig>
</sec>
<sec id="s2_3">
<title>DNA Extraction and Genotyping</title>
<p>Genomic DNA was extracted from approximately 200 mg of each precipitated sample using the E.Z.N.A.<sup>&#xae;</sup> Stool DNA kit (Omega Bio-tek Inc., Norcross, GA, USA), according to manufacturer&#x2019;s instructions. The extracted DNA was stored at -20&#xb0;C until PCR assay. Four genes were used for <italic>G. duodenalis</italic> genotyping by nested PCR, namely SSU rRNA, &#x3b2;-giardin (<italic>bg</italic>), glutamate dehydrogenase (<italic>gdh</italic>), and triosephosphate isomerase (<italic>tpi</italic>) (<xref ref-type="table" rid="T1"><bold>Table&#xa0;1</bold></xref>). Positive (DNA from an isolate known to harbor the four surveyed loci) and negative (reagent-grade water) controls were included in each PCR amplification.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Primer sequences and reaction conditions used in nested PCR amplifications.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Target Gene</th>
<th valign="top" align="center">Primer sequences (5&#x2019;- 3&#x2019;)</th>
<th valign="top" align="center">Annealing </th>
<th valign="top" align="center">Target size </th>
<th valign="top" align="center">Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Gia2029 (AAGTGTGGTGCAGACGGACTC)</td>
<td valign="top" align="center">55&#xb0;C</td>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">SSU rRNA</td>
<td valign="top" align="left">Gia2150c (CTGCTGCCGTCCTTGGATGT)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">RH11 (CATCCGGTCGATCCTGCC)</td>
<td valign="top" align="center">59&#xb0;C</td>
<td valign="top" align="center">292 bp</td>
<td valign="top" rowspan="2" align="left">(<xref ref-type="bibr" rid="B3">Appelbee et&#xa0;al., 2003</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">RH4 (AGTCGAACCCTGATTCTCCGCCCAGG)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">AL3543 (AAATIATGCCTGCTCGTCG)</td>
<td valign="top" align="center">50&#xb0;C</td>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"><italic>tpi</italic>
</td>
<td valign="top" align="left">AL3546 (CAAACCTTITCCGCAAACC)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">AL3544 (CCCTTCATCGGIGGTAACTT)</td>
<td valign="top" align="center">50&#xb0;C</td>
<td valign="top" align="center">530 bp</td>
<td valign="top" rowspan="2" align="left">(<xref ref-type="bibr" rid="B48">Sulaiman et&#xa0;al., 2003</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">AL3545 (GTGGCCACCACICCCGTGCC)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">GDH1 (TTCCGTRTYCAGTACAACTC)</td>
<td valign="top" align="center">50&#xb0;C</td>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"><italic>gdh</italic>
</td>
<td valign="top" align="left">GDH2 (ACCTCGTTCTGRGTGGCGCA)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">GDH3 (ATGACYGAGCTYCAGAGGCACGT)</td>
<td valign="top" align="center">50&#xb0;C</td>
<td valign="top" align="center">530 bp</td>
<td valign="top" rowspan="2" align="left"> (<xref ref-type="bibr" rid="B7">Cacci&#xf2; et&#xa0;al., 2008</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">GDH4 (GTGGCGCARGGCATGATGCA)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">G7 (AAGCCCGACGACCTCACCCGCAGTGC)</td>
<td valign="top" align="center">58&#xb0;C</td>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"><italic>bg</italic>
</td>
<td valign="top" align="left">G759 (GAGGCCGCCCTGGATCTTCGAGACGAC)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">2005F (GAACGAACGAGATCGAGGTCCG)</td>
<td valign="top" align="center">55&#xb0;C</td>
<td valign="top" align="center">511 bp</td>
<td valign="top" rowspan="2" align="left"> (<xref ref-type="bibr" rid="B31">Lalle et&#xa0;al., 2005</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">2005R (CTCGACGAGCTTCGTGTT)</td>
<td valign="top" align="center"/>
<td valign="top" align="center"/>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s2_4">
<title>Sequence and Phylogenetic Analysis</title>
<p>All positive secondary PCR products from SSU rRNA, <italic>bg</italic>, <italic>gdh</italic>, and <italic>tpi</italic> genes were bi-sequenced by GENEWIZ (Suzhou, China). Nucleotide sequences were aligned and edited with DNAstar Lasergene Editseq 7.1.0 (<uri xlink:href="https://www.dnastar.com/software/lasergene/">https://www.dnastar.com/software/lasergene/</uri>) and Chromas Pro 2.1.10 (<uri xlink:href="http://technelysium.com.au/wp/chromaspro/">http://technelysium.com.au/wp/chromaspro/</uri>). Genotypes and subtypes of <italic>G. duodenalis</italic> were determined by aligning reference sequences available in NCBI GenBank database using ClustalX 2.1 (<uri xlink:href="http://www.clustal.org/">http://www.clustal.org/</uri>). To determine genetic diversity among the isolates, concatenated sequences (<italic>bg</italic>-<italic>tpi</italic>-<italic>gdh</italic>) from each isolate at the three analyzed loci were aligned with reference sequences. Neighbor-joining (NJ) analysis was performed using MEGA 7.0 (<uri xlink:href="http://www.megasoftware.net/">http://www.megasoftware.net/</uri>) to infer the phylogenetic relationships of concatenated sequences based on the Kimura-2 parameter model.</p>
</sec>
<sec id="s2_5">
<title>Nucleotide Sequence Accession Numbers</title>
<p>Representative nucleotide sequences of <italic>bg</italic> and <italic>tpi</italic> genes of <italic>G. duodenalis</italic> are available in the NCBI GenBank database under the accession numbers OM273018-OM273020, respectively.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>Prevalence and Assemblages of <italic>G. duodenalis</italic>
</title>
<p>Overall, a total of 39 samples (19.3%, 39/202) were confirmed to be <italic>G. duodenalis</italic> by PCR at the SSU rRNA locus (<xref ref-type="table" rid="T2"><bold>Table&#xa0;2</bold></xref>). Prevalence rate by region was as follows: Yuzhong A (22.2%, 8/36), Yuzhong B (24.6%, 16/65), and Zhuanglang (14.9%, 15/101). In addition, the infection was numerically more frequent in adults (&gt;1 year, 20.6%, 35/170) compared to young animals (&lt;6 month, 12.5%, 4/32). Subsequently, all <italic>G. duodenalis</italic>-positive samples were genotyped by MLG of SSU rRNA, <italic>bg</italic>, <italic>tpi</italic> and <italic>gdh</italic> genes. Two <italic>G. duodenalis</italic> genetic assemblages were identified among samples: assemblage A (72.2%, 26/39) and assemblage E (17.9%, 7/39). Mixed genotype infections (A+E) were found in 6 of 39 samples.</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>Prevalence of <italic>G. duodenalis</italic> by location in Gansu Province, China.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Farm</th>
<th valign="top" align="center">N/T (%)</th>
<th valign="top" align="center">assemblages (n)</th>
<th valign="top" align="center">SSU rRNA (n)</th>
<th valign="top" align="center"><italic>tpi</italic> (n)</th>
<th valign="top" align="center"><italic>gdh</italic> (n)</th>
<th valign="top" align="center"><italic>bg</italic> (n)</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Yuzhong A</td>
<td valign="top" align="center">8/36 (22.2)</td>
<td valign="top" align="left">A (7), E (1)</td>
<td valign="top" align="left">A (7), E (1)</td>
<td valign="top" align="left">A (3)</td>
<td valign="top" align="left">A (2)</td>
<td valign="top" align="left">A (2)</td>
</tr>
<tr>
<td valign="top" align="left">Yuzhong B</td>
<td valign="top" align="center">16/65 (24.6)</td>
<td valign="top" align="left">A (9), E (2),<break/>A+E (5)</td>
<td valign="top" align="left">A (11), E (5)</td>
<td valign="top" align="left">A (11)</td>
<td valign="top" align="left">A (1), E (2)</td>
<td valign="top" align="left">A (4), E (2)</td>
</tr>
<tr>
<td valign="top" align="left">Zhuanglang</td>
<td valign="top" align="center">15/101 (14.9)</td>
<td valign="top" align="left">A (10), E (4),<break/>A+E (1)</td>
<td valign="top" align="left">A (10), E (5)</td>
<td valign="top" align="left">A (9), E (1)</td>
<td valign="top" align="left">A (4), E (1)</td>
<td valign="top" align="left">A (7), E (3)</td>
</tr>
<tr>
<td valign="top" align="left">Total</td>
<td valign="top" align="center">39/202 (19.3)</td>
<td valign="top" align="left">A (26), E (7),<break/>A+E (6)</td>
<td valign="top" align="left">A (28), E (11)</td>
<td valign="top" align="left">A (23), E (1)</td>
<td valign="top" align="left">A (7), E (3)</td>
<td valign="top" align="left">A (13), E (5)</td>
</tr>
<tr>
<td valign="top" align="left"><bold>Age</bold>
</td>
<td valign="top" align="center"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">&lt;6 month</td>
<td valign="top" align="center">4/32 (12.5)</td>
<td valign="top" align="left">A (1), E (2),<break/>A+E (1)</td>
<td valign="top" align="left">A (1), E (3)</td>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left">E (1)</td>
<td valign="top" align="left">E (2)</td>
</tr>
<tr>
<td valign="top" align="left">&gt;1 year</td>
<td valign="top" align="center">35/170 (20.6)</td>
<td valign="top" align="left">A (25), E (5),<break/>A+E (5)</td>
<td valign="top" align="left">A (27), E (8)</td>
<td valign="top" align="left">A (22), E (1)</td>
<td valign="top" align="left">A (7), E (2)</td>
<td valign="top" align="left">A (13), E (3)</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>N, number of positives for G. duodenalis; T, total analysis samples.</p>
</fn>
</table-wrap-foot>
</table-wrap>
</sec>
<sec id="s3_2">
<title>Polymorphisms at Single Loci</title>
<p>Amplification of the <italic>bg</italic> gene was obtained from 18 of 39 <italic>G. duodenalis</italic>-positive isolates; among these, 13/18 (72.2%) of isolates were identified as belonging to genetic assemblage A and 5/18 (27.8%) of assemblage E (<xref ref-type="table" rid="T3"><bold>Table&#xa0;3</bold></xref>). Within assemblage A isolates, three subtypes were formed and designated as A1 (n=4), A2 (n=1), and A3 (n=8). Compared to the sequence MK610391, A1 sequences exhibited one single-nucleotide polymorphism (SNP) (C327T), whereas A2 sequence contained three SNPs (T302C, G308A, and C327T). A3 sequences were identical to MK610392. Moreover, the five assemblage E sequences were identical to the sequence MK610387.</p>
<table-wrap id="T3" position="float">
<label>Table&#xa0;3</label>
<caption>
<p>Multi-locus characterization of <italic>G. duodenalis</italic> isolates in alpine musk deer in China based on <italic>bg</italic>, <italic>gdh</italic> and <italic>tpi</italic> genes.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Isolate Code</th>
<th valign="top" align="center"><italic>bg</italic>
</th>
<th valign="top" align="center"><italic>tpi</italic>
</th>
<th valign="top" align="center"><italic>gdh</italic>
</th>
<th valign="top" align="center">MLG Type</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">22</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">32</td>
<td valign="top" align="left">A1 (OM273018)</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">47,80</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">AI-novel 1</td>
</tr>
<tr>
<td valign="top" align="left">65</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">71</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">78</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">79</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">81</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">86</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">A2 (OM273020)</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">Excluded</td>
</tr>
<tr>
<td valign="top" align="left">100</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">104</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">115</td>
<td valign="top" align="left">A2 (OM273019)</td>
<td valign="top" align="left">A1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">120</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">147</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">A2</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">152</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">157,172,195,207</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A2</td>
<td valign="top" align="left">AI-novel 2</td>
</tr>
<tr>
<td valign="top" align="left">163</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">E1</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">173</td>
<td valign="top" align="left">E</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">182</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">199</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">204</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
<tr>
<td valign="top" align="left">217</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">A3</td>
<td valign="top" align="left">PN</td>
<td valign="top" align="left"/>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>PN, PCR negative.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Sequence analysis of the <italic>tpi</italic> locus revealed that 23 out of 24 successfully amplified isolates were identified as assemblage A, whereas only one was classified as assemblage E. The single assemblage E sequence was 100% identical to the sequence KT922262. Among assemblage A sequences, A1 (n=12) and A3 (n=9) sequences were identical to the sequences MK639171 and MK639172, respectively. In addition, A2 (n=2) sequences showed a SNP (C21T) compared to the sequence MK639173. At the <italic>gdh</italic> locus, seven and three isolates were successfully amplified and identified as assemblage A and E, respectively. The subtypes A1 (n=3) and A2 (n=4) were consistent with the sequences MN047217 and the MK645799, respectively. Moreover, the three assemblage E sequences were identical to the sequence MK645786.</p>
</sec>
<sec id="s3_3">
<title>MLG and Phylogenetic Analysis</title>
<p>In total, seven isolates were successfully sequenced at <italic>bg</italic>, <italic>tpi</italic> and <italic>gdh</italic> loci, and formed six assemblage A MLGs after removal of sequences of mixed infection samples (<xref ref-type="table" rid="T3"><bold>Table&#xa0;3</bold></xref>). The six identified assemblage A MLGs were composed of two novel MLG-subtypes (AI-novel 1 and AI-novel 2); AI-novel 1 was found in two isolates, whereas AI-novel 2 was identified in four isolates. Phylogenetic relationships of assemblage A MLGs with reference genotypes are shown in <xref ref-type="fig" rid="f2"><bold>Figure&#xa0;2</bold></xref>. Based on phylogenetic analysis, all assemblage A MLGs identified herein were clustered in the MLG AI branch, with MLG AI-novel 1 clustered closer to MLG AI-1, whereas MLG AI-novel 2 clustered closer to MLG AI-2.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>Phylogenetic relationships among <italic>G. duodenalis</italic> assemblage A isolates inferred by neighbor-joining analysis based on concatenated datasets for <italic>bg</italic>, <italic>tpi</italic> and <italic>gdh</italic> nucleotide sequences. Bootstrap values greater than 50% from 1000 replicates were shown on nodes. The novel MLGs in this study were indicated in bold.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fcimb-12-856429-g002.tif"/>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>Six species of musk deer (<italic>Moschus</italic> spp.) have historically been bred in China, which include siberian musk deer (<italic>M. moschiferus</italic>), forest musk deer (<italic>M. berezovskii</italic>), black musk deer (<italic>M. fuscus</italic>), alpine musk deer (<italic>M. chrysogaster</italic>), himalayan musk deer (<italic>M. leucogaster</italic>), and anhui musk deer (<italic>M. anhuiensis</italic>) (<xref ref-type="bibr" rid="B15">Fan et&#xa0;al., 2018</xref>). In previous studies, deer have been considered as a major reservoir of viruses, bacteria, and parasites for humans and livestock (<xref ref-type="bibr" rid="B6">B&#xf6;hm et&#xa0;al., 2007</xref>; <xref ref-type="bibr" rid="B36">Mehrpad et&#xa0;al., 2018</xref>). In particular, a recent study has suggested the potential emergence of a new reservoir of SARS-CoV-2 viruses in free-ranging white-tailed deer, which may open new pathways for evolution, transmission to other wildlife species, and potential spillback of novel variants to humans (<xref ref-type="bibr" rid="B20">Hale et&#xa0;al., 2022</xref>).</p>
<p><italic>Giardia</italic> spp. infects a broad range of hosts including humans, livestock, companion animals, wildlife and birds (<xref ref-type="bibr" rid="B41">Ryan et&#xa0;al., 2021</xref>). However, information on the distribution, molecular characteristics and zoonotic potential of <italic>Giardia</italic> in cervids is scant. To date, <italic>G. duodenalis</italic> infections in cervids have been reported in several countries, including Australia, Bangladesh, Canada, Croatia, Italy, Japan, Netherlands, Norway, Poland, Spain, Sweden, USA and China, with the infection rates ranging from 0.6% to 24.0% (<xref ref-type="table" rid="T4"><bold>Table&#xa0;4</bold></xref>). Interestingly, the rodent-specific species <italic>Giardia microti</italic> has been isolated in roe deer (<italic>Capreolus capreolus</italic>) in Croatia (<xref ref-type="bibr" rid="B5">Beck et&#xa0;al., 2011</xref>). In the present study, the prevalence of <italic>G. duodenalis</italic> was 19.3% (39/202) in alpine musk deer, which is higher than that reported in sika deer (0.6% and 0.8%) and forest musk deer (2.2%) in China. The discrepancies in infection rates of <italic>G. duodenalis</italic> may be related to the differences in geographical location, sampling season, animal species, and sample size. To the best of our knowledge, this is the first study to isolate and characterize <italic>G. duodenalis</italic> from alpine musk deer in China using MLG.</p>
<table-wrap id="T4" position="float">
<label>Table&#xa0;4</label>
<caption>
<p><italic>Giardia duodenalis</italic> infection rates and genotypes in cervids worldwide.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="top" align="left">Location</th>
<th valign="top" align="center">Host</th>
<th valign="top" align="center">Positive % (N/T)</th>
<th valign="top" align="center">Assemblage (n)</th>
<th valign="top" align="center">Sub-Assemblage (n)</th>
<th valign="top" align="center">Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Australia</td>
<td valign="top" align="left">Sambar deer, red deer,<break/>fallow deer</td>
<td valign="top" align="center">0.6 (10/1563)</td>
<td valign="top" align="left">A (10)</td>
<td valign="top" align="left">A-I (1), A-III (9)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B28">Koehler et&#xa0;al., 2016</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Bangladesh</td>
<td valign="top" align="left">Spotted deer</td>
<td valign="top" align="center">3.3 (1/30)</td>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B27">Karim et&#xa0;al., 2021</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Canada</td>
<td valign="top" align="left">Boreal caribou</td>
<td valign="top" align="center">2.0 (3/149)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B26">Johnson et&#xa0;al., 2010</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">China</td>
<td valign="top" align="left">Sika deer</td>
<td valign="top" align="center">0.8 (5/662)</td>
<td valign="top" align="left">E (5)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B22">Huang et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Forest musk deer</td>
<td valign="top" align="center">2.2 (5/223)</td>
<td valign="top" align="left">A (2), E (3)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B46">Song et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Sika deer</td>
<td valign="top" align="center">0.6 (5/818)</td>
<td valign="top" align="left">A (2), E (3)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B35">Ma et&#xa0;al., 2021</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Alpine musk deer</td>
<td valign="top" align="center">19.3 (39/202)</td>
<td valign="top" align="left">A (22), E (5), A+E (6)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"><bold>This study</bold>
</td>
</tr>
<tr>
<td valign="top" align="left">Croatia</td>
<td valign="top" align="left">Red deer</td>
<td valign="top" align="center">1.1 (4/374)</td>
<td valign="top" align="left">A (3), D (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B5">Beck et&#xa0;al., 2011</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">24.0 (5/21)</td>
<td valign="top" align="left">A (2), D (2), <italic>G. microti</italic> (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B5">Beck et&#xa0;al., 2011</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Italy</td>
<td valign="top" align="left">Fallow deer</td>
<td valign="top" align="center">11.5 (16/139)</td>
<td valign="top" align="left">A (8)</td>
<td valign="top" align="left">A-I (8)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B30">Lalle et&#xa0;al., 2007</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Fallow deer</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (8)</td>
<td valign="top" align="left">A-III (8)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B7">Cacci&#xf2; et&#xa0;al., 2008</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Japan</td>
<td valign="top" align="left">Sika deer</td>
<td valign="top" align="center">0.7% (2/271)</td>
<td valign="top" align="left">A (2)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B52">Yamazaki et&#xa0;al., 2018</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Netherlands</td>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B50">van der Giessen et&#xa0;al., 2006</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Norway</td>
<td valign="top" align="left">Reindeer</td>
<td valign="top" align="center">5.0% (6/114)</td>
<td valign="top" align="left">A (6)</td>
<td valign="top" align="left">AI (6)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B23">Idland et&#xa0;al., 2021</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Reindeer</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (6)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B39">Robertson et&#xa0;al., 2007</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Moose</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (13)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B39">Robertson et&#xa0;al., 2007</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Red deer</td>
<td valign="top" align="center">1.7 (5/289)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B21">Hamnes et&#xa0;al., 2006</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">15.5 (45/291)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B21">Hamnes et&#xa0;al., 2006</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Reindeer</td>
<td valign="top" align="center">7.1 (11/115)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B21">Hamnes et&#xa0;al., 2006</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Moose</td>
<td valign="top" align="center">12.3 (56/455)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B21">Hamnes et&#xa0;al., 2006</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Poland</td>
<td valign="top" align="left">Red deer</td>
<td valign="top" align="center">1.6 (1/61)</td>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left">A-III (1)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B45">Solarczyk et&#xa0;al., 2012</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">4.0% (2/50)</td>
<td valign="top" align="left">A (2)</td>
<td valign="top" align="left">A-I (2)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B45">Solarczyk et&#xa0;al., 2012</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Red deer</td>
<td valign="top" align="center">17.9 (5/28)</td>
<td valign="top" align="left">B (4)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B47">Stojecki et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">22.9 (11/48)</td>
<td valign="top" align="left">B (8)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B47">Stojecki et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Moose</td>
<td valign="top" align="center">17.0 (4/23)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B47">Stojecki et&#xa0;al., 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">Spain</td>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">8.9 (19/212)</td>
<td valign="top" align="left">A (7)</td>
<td valign="top" align="left">A-II (7)</td>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B18">Garc&#xed;a-Presedo et&#xa0;al., 2013</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Roe deer</td>
<td valign="top" align="center">5.4 (12/224)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B13">Castro-Hermida et&#xa0;al., 2011b</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Deer</td>
<td valign="top" align="center">7.7 (14/181)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B12">Castro-Hermida et&#xa0;al., 2011a</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Fallow deer</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (1), E (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B32">Lebbad et&#xa0;al., 2010</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Moose</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B32">Lebbad et&#xa0;al., 2010</xref>)</td>
</tr>
<tr>
<td valign="top" align="left">USA</td>
<td valign="top" align="left">White-tailed deer</td>
<td valign="top" align="center">1.3 (1/80)</td>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B44">Santin and Fayer, 2015</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">White-tailed deer</td>
<td valign="top" align="center">1.3 (5/394)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B38">Rickard et&#xa0;al., 1999</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">White-tailed deer</td>
<td valign="top" align="center">3.8 (1/26)</td>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B49">Trout et&#xa0;al., 2003</xref>)</td>
</tr>
<tr>
<td valign="top" align="left"/>
<td valign="top" align="left">Reindeer</td>
<td valign="top" align="center"/>
<td valign="top" align="left">A (1)</td>
<td valign="top" align="left"/>
<td valign="top" align="left"> (<xref ref-type="bibr" rid="B37">Miska et&#xa0;al., 2009</xref>)</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<fn>
<p>N=number of positives for G. duodenalis; T, total analysis samples.</p>
</fn>
</table-wrap-foot>
</table-wrap>
<p>Methods based on sequence analysis of SSU rRNA, <italic>gdh</italic>, <italic>bg</italic> and <italic>tpi</italic> genes have currently been widely used for genotyping <italic>G. duodenalis</italic> isolates from human and animal samples in order to obtain high-sequencing resolution (<xref ref-type="bibr" rid="B17">Feng and Xiao, 2011</xref>). To date, molecular studies have identified <italic>G. duodenalis</italic> in fallow deer, forest musk deer, moose, red deer, reindeer, roe deer, sambar deer, spotted deer and white-tailed deer with a worldwide distribution (<xref ref-type="table" rid="T4"><bold>Table&#xa0;4</bold></xref>). In addition to zoonotic assemblages A and B, other <italic>G. duodenalis</italic> assemblages including E (mainly found in hoofed mammals) and D (mainly found in canines) have also been reported occasionally in these animal hosts (<xref ref-type="bibr" rid="B5">Beck et&#xa0;al., 2011</xref>; <xref ref-type="bibr" rid="B22">Huang et&#xa0;al., 2018</xref>), which suggests potential transmission routs of <italic>G. duodenalis</italic> assemblages between humans, livestock, companion animals and cervids. In the present study, both assemblage A and E were identified, and assemblage A was the predominant genotype. Mixed infections were observed in alpine musk deer at both assemblage and sub-assemblage levels, which may be a result of infection with <italic>Giardia</italic> parasites with different genetic profiles. Assemblages A is responsible for most giardiasis cases in humans, especially in South America and the Middle East (<xref ref-type="bibr" rid="B51">Xiao and Feng, 2017</xref>; <xref ref-type="bibr" rid="B41">Ryan et&#xa0;al., 2021</xref>). Interestingly, the host-adapted genotype assemblage E which was approximately 87% similar to assemblages A in genome, has been reported in at least 57 human giardiasis cases in Brazil, Egypt, Vietnam, Australia and New Zealand (<xref ref-type="bibr" rid="B1">Abdel-Moein and Saeed, 2016</xref>; <xref ref-type="bibr" rid="B16">Fantinatti et&#xa0;al., 2016</xref>; <xref ref-type="bibr" rid="B53">Zahedi et&#xa0;al., 2017</xref>; <xref ref-type="bibr" rid="B19">Garcia-R et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B24">Iwashita et&#xa0;al., 2021</xref>). Collectively, the presence of zoonotic assemblages of <italic>G. duodenalis</italic> in alpine musk deer in China suggests that these animals may potentially act as a reservoir of <italic>G. duodenalis</italic> for humans.</p>
<p>Moreover, in order to elucidate the genetic diversity of <italic>G. duodenalis</italic> in alpine musk deer, positive samples identified in the present were subjected for sub-genotyping by MLG. Moderate genetic variation was observed within assemblage A sequences, whereas no genetic variation was noticed within assemblage E sequences, which may be due to the low allelic sequence heterozygosity (ASH) in the genomes of assemblages A and E (<xref ref-type="bibr" rid="B29">Kooyman et&#xa0;al., 2019</xref>). In addition, the six assemblage A MLGs were composed of two novel MLG-subtypes which belonged to sub-assemblage AI. Among the three sub-assemblages within assemblage A, sub-assemblage AI is most commonly found in animals, whereas sub-assemblage AII is mostly found in humans; sub-assemblage AIII is rare and has been found in wild ruminants and two human giardiasis cases in Romania and New Zealand (<xref ref-type="bibr" rid="B17">Feng and Xiao, 2011</xref>; <xref ref-type="bibr" rid="B9">Cai et&#xa0;al., 2021</xref>; <xref ref-type="bibr" rid="B41">Ryan et&#xa0;al., 2021</xref>). In published studies, both sub-assemblage AI, AII and AIII were identified in various deer (<xref ref-type="table" rid="T4"><bold>Table&#xa0;4</bold></xref>). Further studies based on MLG analysis are necessary to gain a better understanding on the potential role of deer in the zoonotic transmission of <italic>G. duodenalis</italic>.</p>
</sec>
<sec id="s5" sec-type="conclusions">
<title>Conclusions</title>
<p>In conclusion, this is the first report of <italic>G. duodenalis</italic> in alpine musk deer with a high prevalence in China. Two <italic>G. duodenalis</italic> assemblages were identified, assemblage A and E. Moderate genetic diversity was observed within assemblage A sequences based on MLG analysis. Six assemblage A MLGs were identified which were composed of two novel MLG-subtypes belonging to sub-assemblage AI. Collectively, zoonotic assemblages of <italic>G. duodenalis</italic> identified in the present study point out that alpine musk deer may potentially act as reservoirs of this protozoan to humans.</p>
</sec>
<sec id="s6" sec-type="data-availability">
<title>Data Availability Statement</title>
<p>The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.</p>
</sec>
<sec id="s7" sec-type="ethics-statement">
<title>Ethics Statement</title>
<p>The animal study was reviewed and approved by Research Ethics Committee of Tarim University. Written informed consent was obtained from the owners for the participation of their animals in this study.</p>
</sec>
<sec id="s8" sec-type="author-contributions">
<title>Author Contributions</title>
<p>ZC, QW, XH, JB, BZ, BW, and XG performed the experiments. ZC drafted the manuscript. MQ and JL critically revised the manuscript. All authors contributed to the article and approved the submitted version.</p>
</sec>
<sec id="s9" sec-type="funding-information">
<title>Funding</title>
<p>The research was funded by the National Natural Science Foundation of China (32102689), Science and Technology Planning Project of Henan Province (222102110240), the Program for Young and Middle-aged Leading Science, Technology, and Innovation of Xinjiang Production &amp; Construction Group (2018CB034), and Scientific research project of Xuchang University (2022GJPY009 and 2022YB034).</p>
</sec>
<sec id="s10" sec-type="COI-statement">
<title>Conflict of Interest</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s11" sec-type="disclaimer">
<title>Publisher&#x2019;s Note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
</body>
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