Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Abstract

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

The critical importance of vouchers in genomics

“…We surveyed the NCBI list of vertebrate genomes (focusing on reference/representative genomes of each species) with an assembly publication date up to January 1, 2020 ( https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/vertebrates ) and coverage of 30X or greater. Although we focused on reviewing vertebrate genomes, the lack of vouchers is a problem among genetic sequences submitted from many different types of organisms ( Leray et al, 2019 ; Pleijel et al, 2008 ; Peterson et al, 2007 ; Lendemer et al, 2020 ; Colella et al, 2021 ; Schoch et al, 2020 ; Thompson et al, 2021 ; Beaz-Hidalgo et al, 2015 ; Chakrabarty, 2010 ; Chakrabarty et al, 2013 ). When available, we also cross-checked the original publications reporting genome assemblies for references to a deposited voucher specimen.…”

“…The failure to associate voucher information with genome assemblies can lead to many real-world problems, such as slowing our understanding of emerging diseases (e.g., identifying the animal host of SARS-CoV-2 [ Thompson et al, 2021 ]) to complicating clinical analyses because of the use of misidentified species ( Beaz-Hidalgo et al, 2015 ).…”

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

“…The global scale of EIDs, exemplified by the current SARS-CoV-2 pandemic, calls for an intentional shift away from current reactive responses to EIDs, toward more proactive models that encourage early detection, identification, monitoring, and prevention (e.g., Documentation, Assessment, Monitoring, Action [DAMA] protocol [ 6 , 49 ]; Fig 1 ), possible by expanding One Health approaches to include the Global Museum [ 23 – 28 ]. To this end, we must invest in expanded biorepository capacity, quality, and expertise to meet the needs of EID research, an approach to building infrastructure that has not yet been normalized across disciplines [ 4 – 5 ].…”

“…Through mutual sharing of best practices in a virtual community of practice, biorepository personnel can standardize and prioritize the types of materials and preservations most useful to EID research. Likewise, the EID community can better integrate biorepository data standards into specimen collection and sampling procedures [ 5 , 21 , 76 – 78 ]. Darwin Core ( dwc.tdwg.org ) stable identifiers, for example, represent a common vocabulary intended to facilitate the sharing of information about biological diversity and specimens [ 79 ].…”

Connecting molecular sequences to their voucher specimens

“…This ensures that the results are repeatable and that the identification of the organism can be verified. It also means that other information, that perhaps do not fit within the data model for sequences, can still be made available, linked to the specimen (Thompson et al, 2021). These specimen vouchers are often kept in herbaria and museums where they are curated and stored for the long-term.…”