---
title: "Sarcocystis neurona genotypes in California sea lions with polyphasic rhabdomyositis"
id: "plos-one-3-molecular-characterization-of-sarcocystis-neurona-genotypes-in-california-sea"
canonical_url: "https://medichelpline.com/clinical-feed/plos-one-3-molecular-characterization-of-sarcocystis-neurona-genotypes-in-california-sea"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "PLOS ONE (Medicine)"
source_url: "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274"
published_at: "2026-08-28T14:00:00.000Z"
evidence_level: "Journal Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Sarcocystis neurona genotypes in California sea lions with polyphasic rhabdomyositis
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/plos-one-3-molecular-characterization-of-sarcocystis-neurona-genotypes-in-california-sea
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** PLOS ONE (Medicine)
- **Source URL:** [Original Journal Publication](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274)
- **Published At:** 2026-08-28T14:00:00.000Z
- **Evidence Rating:** Journal Feed
## Executive GIST (TL;DR)
- A syndrome of **polyphasic rhabdomyositis** associated with **Sarcocystis neurona** has been described in free-ranging California sea lions (CSLs); its pathogenesis remains poorly understood. - This study screened archived skeletal muscle from 25 CSLs with moderate to severe S. neurona–associated rhabdomyositis for parasite DNA and performed multilocus sequence typing (MLST). - DNA screening used a nested PCR targeting the multi-copy **ITS1** locus to confirm S. neurona, followed by MLST across six polymorphic loci (SnSAG1/5/6, SnSAG3, SnSAG4, sn3, sn7, sn9). - From 25 cases, investigators identified 15 distinct **S. neurona genotypes**; six matched genotypes previously reported in other hosts and nine were novel to date. - The most frequently detected genotypes were **IIg/j** (6/25, 24%), **Ib/c/d/gg** (3/25, 12%), **IIi** (2/25, 8%), **IIIl/m/o** (2/25, 8%), and **VIIr** (2/25, 8%). - One new surface antigen type (XV) and five new microsatellite types (nn, oo, pp, qq, rr) were reported. - Genotypes previously implicated in severe disease in other marine mammals (e.g., Ia, Ib/c/d/gg, IIg/j, IIi, VIy, IIIl/m/o) were present among CSLs, but many genotypes were unique to CSLs in this sample. - The geographic sampling spanned a ~450-km central California coastline (San Francisco to Morro Bay); cases were collected randomly (2–4 animals/year) from 2017–2024 and were animals that died or were euthanized during care. - Authors conclude the high genotype diversity in a small sample suggests parasite genotype alone may not drive the CSL rhabdomyositis syndrome and support a potential host-driven or immune-mediated mechanism. - Study limitations include small sample size, potential under-detection of mixed infections with MLST, and that archived samples were used rather than prospectively collected material.
## Clinical Analysis & Structured Key Points
[ Skip to main content ](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#main-content) Advertisement * [plos.org](https://plos.org/) * [Create account](https://community.plos.org/registration/new) * [Sign in](https://journals.plos.org/user/secure/login?page=%2Fplosone%2Farticle%3Fid%3D10.1371%2Fjournal.pone.0357274) * * About * Browse * Publish * [](https://journals.plos.org/plosone/ "PLOS One") * Search [advanced search](https://journals.plos.org/plosone/search) * [Browse Topics](https://journals.plos.org/plosone/subjectAreaBrowse) Browse Subject Areas ? Click through the PLOS taxonomy to find articles in your field. For more information about PLOS Subject Areas, click [here](https://github.com/PLOS/plos-thesaurus/blob/master/README.md "Link opens in new window"). [](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274) [](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274) * 0 [Save](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#savedHeader) [Total Mendeley and Citeulike bookmarks.](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#savedHeader) * 0 [Citation](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#citedHeader) [Paper's citation count computed by Dimensions.](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#citedHeader) * 29 [View](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#viewedHeader) [PLOS views and downloads.](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#viewedHeader) * 0 [Share](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#discussedHeader) [Sum of Facebook, Twitter, Reddit and Wikipedia activity.](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274#discussedHeader) Open Access Peer-reviewed Research Article # Molecular characterization of _Sarcocystis neurona_ genotypes in California sea lions (_Zalophus californianus_) with polyphasic rhabdomyositis * Alene G. Pohly, Roles Investigation, Visualization, Writing – original draft Current address: Arizona Veterinary Diagnostic Laboratory, 2831 N Freeway, Tucson, AZ, USA 85705 Affiliation Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, 1 Shields Ave, Davis, California, United States of America [ ![ORCID logo](https://journals.plos.org/resource/img/orcid_16x16.png) https://orcid.org/0009-0007-9149-0760 ](https://orcid.org/0009-0007-9149-0760 "ORCID Registry") ⨯ * Devinn M. Sinnott, Roles Conceptualization, Investigation, Methodology, Project administration, Writing – review & editing Affiliation Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, 1 Shields Ave, Davis, California, United States of America [ ![ORCID logo](https://journals.plos.org/resource/img/orcid_16x16.png) https://orcid.org/0000-0001-7890-4833 ](https://orcid.org/0000-0001-7890-4833 "ORCID Registry") ⨯ * Margaret E. Martinez, Roles Conceptualization, Resources, Writing – review & editing Affiliation The Marine Mammal Center, Bunker Rd, Sausalito, California, United States of America ⨯ * Cara L. Field, Roles Conceptualization, Resources, Writing – review & editing Affiliation The Marine Mammal Center, Bunker Rd, Sausalito, California, United States of America ⨯ * Pádraig J. Duignan , Roles Conceptualization, Methodology, Project administration, Resources, Writing – review & editing * E-mail: duignanp@tmmc.org (PD); kshapiro@ucdavis.edu (KS) Affiliation The Marine Mammal Center, Bunker Rd, Sausalito, California, United States of America ⨯ * Karen Shapiro Roles Conceptualization, Methodology, Project administration, Resources, Supervision, Writing – review & editing * E-mail: duignanp@tmmc.org (PD); kshapiro@ucdavis.edu (KS) Affiliation Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, 1 Shields Ave, Davis, California, United States of America [ ![ORCID logo](https://journals.plos.org/resource/img/orcid_16x16.png) https://orcid.org/0000-0003-2678-3851 ](https://orcid.org/0000-0003-2678-3851 "ORCID Registry") ⨯ # Molecular characterization of _Sarcocystis neurona_ genotypes in California sea lions (_Zalophus californianus_) with polyphasic rhabdomyositis * Alene G. Pohly, * Devinn M. Sinnott, * Margaret E. Martinez, * Cara L. Field, * Pádraig J. Duignan, * Karen Shapiro ![PLOS](https://journals.plos.org/resource/img/logo-plos-full-color.svg) x * Published: August 28, 2026 * * [Article](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274) * [Authors](https://journals.plos.org/plosone/article/authors?id=10.1371/journal.pone.0357274) * [Metrics](https://journals.plos.org/plosone/article/metrics?id=10.1371/journal.pone.0357274) * [Comments](https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0357274) * [Media Coverage](http://plos.altmetric.com/details/doi/10.1371/journal.pone.0357274) * [Peer Review](https://journals.plos.org/plosone/article/peerReview?id=10.1371/journal.pone.0357274) * [Abstract](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#abstract0) * [Introduction](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec001) * [Methods](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec002) * [Results](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec003) * [Discussion](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec004) * [Supporting information](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec005) * [Acknowledgments](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#ack) * [References](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#references) * [Reader Comments](https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0357274) * [Figures](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274) ## Abstract A unique clinical syndrome characterized by polyphasic rhabdomyositis associated with _Sarcocystis neurona_ has been reported in both free-ranging and managed care California sea lions (CSLs; _Zalophus californianus_). The pathogenesis of this disease is poorly understood. Specific _S. neurona_ genotypes have been associated with more severe sarcocystosis and mortality in other marine mammals; however, _S. neurona_ genotypes infecting CSLs with rhabdomyositis have not yet been investigated. The objective of this study was to characterize genotypes of _S. neurona_ from CSLs with rhabdomyositis and to compare these with genotypes described in other marine and terrestrial hosts. Archived skeletal muscle samples from 25 affected free-ranging CSLs were screened for _S. neurona_ DNA using polymerase chain reaction (PCR) targeting a multi-copy locus (ITS1), followed by genotype characterization using a PCR-based multilocus sequence typing approach targeting six polymorphic loci. Among these 25 CSLs, 15 different _S. neurona_ genotypes were identified. Of these, six have been previously identified in southern sea otters (_Enhydra lutris nereis_) and/or other hosts, but the remaining nine have not been reported in any host to date. This study, although limited in sample size, demonstrates a wide diversity of _S. neurona_ genotypes infecting free-ranging CSLs affected with rhabdomyositis, some shared with other hosts in the region, but many others that appear to be unique to sea lions. ## Figures ![Table 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.t001) ![Fig 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g001) ![Fig 2](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g002) ![Table 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.t001) ![Fig 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g001) ![Fig 2](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g002) ![Table 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.t001) ![Fig 1](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g001) ![Fig 2](https://journals.plos.org/plosone/article/figure/image?size=inline&id=10.1371/journal.pone.0357274.g002) **Citation:** Pohly AG, Sinnott DM, Martinez ME, Field CL, Duignan PJ, Shapiro K (2026) Molecular characterization of _Sarcocystis neurona_ genotypes in California sea lions (_Zalophus californianus_) with polyphasic rhabdomyositis. PLoS One 21(8): e0357274. https://doi.org/10.1371/journal.pone.0357274 **Editor:** Vikrant Sudan, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), INDIA **Received:** April 30, 2026; **Accepted:** August 14, 2026; **Published:** August 28, 2026 **Copyright:** © 2026 Pohly et al. This is an open access article distributed under the terms of the [Creative Commons Attribution License](http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. **Data Availability:** All relevant data are within the paper and its [Supporting Information](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#sec005) files. **Funding:** The author(s) received no specific funding for this work. **Competing interests:** The authors have declared that no competing interests exist. ## Introduction The genus _Sarcocystis_ represents a diverse group of apicomplexan parasites with a wide reported host range. _Sarcocystis_ spp. life cycles are heteroxenous, typically involving a carnivorous definitive host that ingests the infected tissues of an herbivorous or omnivorous prey species (intermediate host) [[1](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref001),[2](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref002)]. Sexual replication occurs within the gastrointestinal tract of definitive hosts that then shed sporocysts in the feces [[1](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref001), [2](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref002)]. Intermediate hosts become infected after ingesting sporocysts in fecally-contaminated food or water, with subsequent asexual replication of the parasite occurring in several tissues throughout the body, eventually forming quiescent sarcocysts encysted in skeletal muscle [[1](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref001), [2](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref002)]. _Sarcocystis neurona_ is an important pathogen in veterinary medicine, affecting many domestic and wildlife species. The definitive host of _S. neurona_ in North America is the Virginia opossum (_Didelphis virginiana_) [[3](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref003),[4](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref004)]. Many terrestrial and aquatic species have been reported to serve as intermediate hosts including equids, nine-banded armadillos (_Dasypus novemcinctus_), skunks (_Mephitis mephitis_), sea otters (_Enhydra lutris_), and harbor porpoises (_Phocoena phocoena_) [[5](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref005)–[7](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref007)]. _Sarcocystis neurona_ has been best studied as the most common etiologic agent of Equine Protozoal Myeloencephalitis (EPM), a severe neurologic disease of horses [[5](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref005)]. Marine mammals are believed to become infected with _S. neurona_ following the land-to-sea transport of infective sporocysts from coastal watersheds inhabited by opossums into the ocean via surface water runoff [[7](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref007)]. _Sarcocystis neurona_ has been reported as a major cause of encephalitis in marine mammals, including Pacific harbor seals (_Phoca vitulina_ _richardsii_), Steller sea lions (_Eumetopias jubatus_), and southern sea otters (SSO, _Enhydra lutris nereis_), leading to stranding and death [[8](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref008)–[11](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref011)]. The intramuscular stages of _S. neurona_ (sarcocysts) have been identified for decades in California sea lions (CSLs; _Zalophus californianus_) [[12](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref012)] as a primarily incidental finding. Since the early 2000’s, a syndrome has emerged of disseminated polyphasic rhabdomyositis that may vary in clinical expression leading to generalized muscle wasting, severe respiratory distress, or megaesophagus depending on the muscle groups affected and ultimately result in stranding and mortality from malnutrition, renal failure (myoglobinuric nephropathy) or secondary infections [[13](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref013)–[15](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref015)], TMMC unpublished data]. Histologic lesions of polyphasic rhabdomyositis include myocytes in various stages of inflammation, degeneration, necrosis, regeneration, and scarring indicative of a chronic or ongoing injury to the skeletal muscle. The pathogenesis of this condition is poorly understood, although an immune-mediated component has been proposed [[14](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref014)]. In SSOs and other marine mammals, specific _S. neurona_ genotypes have been associated with greater disease severity and mortality (e.g., XIIIhh, IIg/j, Ib/c/d/gg) [[11](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref011),[16](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref016)]. _Sarcocystis neurona_ genotypes in CSLs with rhabdomyositis have not yet been investigated and the role of parasite genotype as a driver of this disease in this marine host is unknown. The objectives of this study were to characterize the genotypes of _S. neurona_ present in CSLs affected with polyphasic rhabdomyositis and to compare these genotypes to those reported in other marine and terrestrial mammals along the Pacific coast of North America. ## Methods This study included CSLs that live-stranded along a 450-kilometer (280-mile) length of the central California coastline between San Francisco in the north to Morro Bay in the south, and were admitted to The Marine Mammal Center (TMMC; Sausalito, CA) for assessment. Strandings of the animals included in this study occurred through most of the year (February through October) and did not appear to be geographically clustered. Samples were only collected from animals that died in transport or while in care as a result of _Sarcocystis_ - associated infection (generalized rhabdomyositis, megaesophagus, respiratory complications, myoglobinuria, protozoal cardiomyositis, meningoencephalitis, or combinations thereof) or that were euthanized under clinical veterinary oversight due to poor prognosis or moribund status based on diagnosis of the above listed morbidities. In all CSLs, _S. neurona_ was identified as either the primary cause of death or a contributor to death based on gross and histologic findings. Only cases with a moderate or severe diagnosis, as previously defined [[14](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref014)] were included. Medical records at TMMC were searched to generate a list of CSLs with previously confirmed clinical and histopathologic evidence of moderate to severe _S. neurona_ –associated rhabdomyositis and that had archived frozen skeletal muscle samples (diaphragm, tongue, or other skeletal muscle) available for testing. Due to resource limitations, the study was limited to 25 cases. Two to four animals per year from 2017 to 2024 were randomly selected for a total of 25 cases. Postmortem examination and sample collection were performed by trained veterinary pathologists (PJD, MEM) and necropsy staff at TMMC. Diaphragm, tongue, or unspecified skeletal muscle samples from these 25 CSLs were collected at the time of necropsy by TMMC under authorized permits (NOAA CI #24359 [for the years of 2023 and 2024] and #18786−06 [for years including and prior to 2022]). The archived muscle samples were obtained as part of routine surveillance and biobanking during postmortem examination and were not collected specifically for this study. DNA was extracted in triplicate from one muscle sample (diaphragm, tongue, or unspecified skeletal muscle) for each CSL using a Qiagen DNeasy Blood and Tissue kit (Qiagen; Redwood City, CA) according to the manufacturer’s instructions with one modification: 180 µl buffer ATL and 30 µl proteinase K were added to each sample to incubate overnight at 56˚C to enhance tissue digestion. Extracted DNA samples for each CSL were screened for _S. neurona_ DNA using a sensitive pan-apicomplexan nested PCR assay targeting the multi-copy ITS1 locus using previously described primers and cycling conditions [[16](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref016)] followed by Sanger sequencing. Forward and reverse sequences were trimmed, aligned, and compared to known reference sequences available in GenBank using BLAST ( ). After confirming the presence of _S. neurona_ DNA (>99% identity) in each CSL, one replicate of extracted DNA per animal was genotyped using a nested or hemi-nested PCR-based multilocus sequence typing (MLST) approach targeting six polymorphic loci including three surface antigens (SnSAG1/5/6, SnSAG3, SnSAG4) and three microsatellite markers (sn3, sn7, sn9). These assays were performed using previously described primers, cycling conditions, and sequence analysis methods [[7](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref007),[17](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0357274#pone.0357274.ref017)]. The relative proportion of each genotype identified in CSLs with rhabdomyositis was calculated for the total cases included in this study (n = 25). Genotypes were then compared to previously published _S. neurona_ genotypes characterized from other hosts along the Pacific coast of the United States and Canada including sea otters, harbor seals, Guadalupe fur seals (_Arctocephalus townsendi),_ Steller sea lions, Northern fur seals (_Callorhinus ursinus_), Northern elephant seals (_Mirounga angustirostris_), Pacific white-sided dolphins (_Aethalodelphis obliquidens_), horses, opossums, and a
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