Collection of various sample types from patients with rare/emerging or exotic viruses and Rickettsia for molecular and serological diagnostic test development and validation purposes.

Infectious diseases present one of the most significant health and security
challenges to the global community. Due to increased mobility, climate change
and advanced technology we see and detect increasing amount of
rare/(re)emerging and exotic diseases. All important questions arising with an
emerging infection (like source and route of transmission, infectivity of
patients, recommendation of safety measures for health care personal and
distribution in an animal reservoir or vectors) require high quality and
validated laboratory diagnostic assays. To be able to detect and distinguish
pathogens we need to have knowledge about their RNA or DNA sequence, genetic
diversity and antibody kinetics as well as suitable and well verified/validated
diagnostic tests. Before implementation into daily diagnostics a test has to be
verified/validated on a representative sample set and using verified positive
controls. However these samples are scarce and an international standard
material which could aid standardisation and harmonisation of results rarely
exist [1].
To investigate the patient*s infection, commonly a blood sample is taken for
pathogen detection. The test used can be a PCR or for a test demonstrating the
presence of specific antibodies/antigens. The use of saliva and urine for the
diagnosis for many viral infections has been reported, however, it is often not
performed in the broad routine diagnostics. Sampling of blood requires
medically trained personal and can cause discomfort to the patient. Therefore,
the sampling by non-invasive methods (e.g. saliva, urine, faeces) might be a
very valuable alternative for investigating a disease. This is supported by the
report on continuing viremia in urine or semen of yellow fever infected
patients, extending the period for the use of more specific molecular detection
techniques and sequencing. Additionally, carriage in semen provides important
information as it can lead to sexual transmission, like was found for Ebola and
Zika virus [2]. Zika virus was also isolated from rectal swabs [3] pointing out
another route of dissemination and potential sexual transmission. Diagnoses of
several tick-borne emerging pathogens such as tick-borne encephalitis virus and
Rickettsiae spp currently rely on changes in specific antibody detection in
convalescent blood samples, consequently delaying diagnosis for weeks. In
addition, interpretation of these serology results is complicated by extensive
cross-reactivity of antibodies and aspecific reactions. To optimise serological
tools for Rickettsia, PCR confirmation on early specimen (eschar swab and
whole blood) is essential as a gold standard. . Furthermore the length of
persistence for (neutralizing) antibodies especially for newly emerged
pathogens is not known.

A recent review summarizes the current knowledge about the various sample types
used for some of the recently emerged viruses like Dengue, Chikungunya, Ebola,
other Flaviviruses like Zika, West Nile and Yellow Fever and other viruses
causing haemorrhagic fever [2] and clearly highlights the knowledge gaps
regarding presence and persistence of these pathogens in various body fluids.
The gaps and importance of the above knowledge gaps described was also
recognised at the European level and the PREPARE project, which is an EU funded
network for harmonized large-scale clinical research studies on infectious
diseases, was initiated (one of the work packages is focusing on arboviruses).
Therefore, we propose a study in which patients with strong clinical suspicion
or confirmed infection with a rare/emerging/exotic virus including Rickettsiae
spp infection will be approached to donate various sample types (Appendix 1).
These samples will be used for two purposes: 1, to create a panel of samples
which can be used for diagnostic test development and validation; 2, to gain
knowledge about carriage and to test suitability for diagnostic use e.g. the
presence (and duration), quantity of these pathogens and antibodies in various
bodily fluids. Furthermore, parallel to this application, a non-WMO proposal
was being prepared (entitled: Blood donation by volunteers to validate
diagnostic tests for infectious diseases; MEC-2021-0039 ) which serves as a
complementary to this effort. All these add a prospective approach to the
already approved non-WMO protocol (2015-306) which allows the use of patient
residual material for research and improvement of diagnostics.
As a tertiary care center with well-known expertise in tropical medicine,
Erasmus MC is well equipped to test and diagnose patients with rare or emerging
pathogens as they are often referred. The Viroscience department is one of the
national reference laboratories and WHO collaborating center for *Emerging and
Dangerous Pathogens of international importance, including outbreaks of
Arboviruses, Viral Haemorrhagic Fevers and novel and emerging infectious
diseases* hence we are experienced in diagnosing these pathogens. An important
part of our responsibilities is commitment to preparedness. Material and
knowledge gained from this study would be shared with our international network
but only following the appropriate Material Transfer Agreement (MTA) leading to
improved diagnostic worldwide. All these taken together represent a unique
opportunity to conduct this study.

REFERENCES
1. NIBSC.
2. Niedrig M, Patel P, El Wahed AA, Schadler R, Yactayo S. Find the right
sample: A study on the versatility of saliva and urine samples for the
diagnosis of emerging viruses. BMC Infect Dis 2018; 18:707.
3. Botto-Menezes CHA, Neto AM, Calvet GA, et al. Zika Virus in Rectal Swab
Samples. Emerg Infect Dis 2019; 25:951-4.

1, to create a sample pool for future diagnostic test development and
validation;
2, to compare various sample types in molecular and serodiagnostic tests of
rare/emerging or exotic viruses and Rickettsial infections in order to test
their suitability for diagnostic use and study length of persistence.

Single center observational study

This study entails minimal harm. Most sampling is non-invasive, although still
the sampling procedures would probably represent some level of patient burden.
Enrolled patients will be asked to provide a standard specimen set consisting
of blood (separated in whole blood, dry blood spots, serum), urine, faeces,
saliva) and as optional specimen the following: sweat, tears, breast milk,
vaginal swab/semen, post-partum placenta biopsy, eschar swab. Follow-up samples
will be asked either until patient is discharged from hospital or at follow-up
control appointments if they will be scheduled due to original illness. Only
adults will be approached, minimal patient information, travel and vaccination
records, symptom onset and other relevant comorbidities like suppressed status
will be asked in a questionnaire. In order to be enrolled in the study, the
patient will need to give informed consent and will have an all-time opt-out
option.