A biochemist who leads the development of new instruments and online services.
Associate Professor of Pediatrics
Participatory systems for surveillance of acute respiratory infection give real-time information about infections circulating in the community, yet to-date are limited to self-reported syndromic information only and lacking methods of linking symptom reports to infection types. We developed the GoViral platform to evaluate whether a cohort of lay volunteers could, and would find it useful to, contribute self-reported symptoms online and to compare specimen types for self-collected diagnostic information of sufficient quality for respiratory infection surveillance. Volunteers were recruited, given a kit (collection materials and customized instructions), instructed to report their symptoms weekly, and when sick with cold or flu-like symptoms, requested to collect specimens (saliva and nasal swab). We compared specimen types for respiratory virus detection sensitivity (via polymerase-chain-reaction) and ease of collection. Participants were surveyed to determine receptivity to participating when sick, to receiving information on the type of pathogen causing their infection and types circulating near them. Between December 1 2013 and March 1 2014, 295 participants enrolled in the study and received a kit. Of those who reported symptoms, half (71) collected and sent specimens for analysis. Participants submitted kits on average 2.30 days (95 CI: 1.65 to 2.96) after symptoms began. We found good concordance between nasal and saliva specimens for multiple pathogens, with few discrepancies. Individuals report that saliva collection is easiest and report that receiving information about what pathogen they, and those near them, have is valued and can shape public health behaviors. Community-submitted specimens can be used for the detection of acute respiratory infection with individuals showing receptivity for participating and interest in a real-time picture of respiratory pathogens near them.
Internet connectivity has opened the door to new techniques for disease detection worldwide
New detection technologies are rapidly emerging for home-based and point of care diagnosis; they harness real-time polymerase chain reaction as well as newer techniques for high sensitivity and specificity molecular detection
While nasal swabs are easy to use, the non-invasive nature of oral specimen collection makes it an easier and more convenient and thus preferable alternative to nasal swabs
In sum, while there have been some efforts to use nasal swabs for self-collection of specimens and surveillance of acute respiratory infection at scale, the work reported here adds to these existing efforts by considering important questions of utility of different specimen types, linking of individual participatory symptom reports to specimen types, and how the resulting surveillance information can be used at an individual level. To address these needs, we developed the GoViral platform. This platform is designed to acquire community generated diagnostic samples and couple them with other contemporaneous information such as participatory syndromic reports. Thus, GoViral enables us to test: 1) the types of samples that individuals are able to and willing to generate in their own homes in a timely fashion when they have an acute respiratory infection along with and appropriate processing methods, 2) how user-generated diagnostic information corresponds to self-reported symptoms and 3) reception and use of the information by the public. Herein we report results from an initial deployment during the 2013-2014 influenza season
A cohort of lay volunteers was recruited in Massachusetts. Recruitment was open throughout the study period (November 1, 2013 to April 30, 2014). We used a convenience sample in order to rapidly recruit participants and evaluate the platform during this first season (thus anticipating participants to be skewed towards those who have access to Internet), permitting investigation via a more representative sampling during subsequent years. Enrollment was driven largely by announcements on local radio stations and word of mouth. Paid online advertisements and social media were also used as means of recruiting volunteers to the study. The study size was limited by our ability to recruit and engage participants. In order to register, volunteers signed an electronic consent form and reported their email address, name and mailing address, gender and age. Volunteers were immediately sent a kit (see section below) to keep at home. Users were instructed that if they became sick with symptoms of a cold or flu, they should perform the specimen collection and rapid test within 48 hours of experiencing symptoms. Participants who returned a kit were sent a replacement, allowing them to report a second illness (second illness was included if the specimen was provided at least 2 weeks after the initial specimen). GoViral participants were also registered for Flu Near You and reported symptoms through weekly surveys, as has been previously described
The protocol was approved by the Boston Children’s Hospital Institutional Review Board.
Each kit (Figure 1) included an Oragene OM-505 Saliva collection tube (DNA Genotek Inc.), flocked nasal swab with viral collection media (part number 407C, Diagnostic Hybrids), and a lateral flow immunoassay rapid test (CerTest Biotec). The CerTest rapid test tested for Influenza A, Influenza B, RSV, and adenovirus. For the nasal specimen, we selected a nasal swab rather than a nasopharyngeal swab because it is easier to collect for the individual, and a previous study has demonstrated that they are comparable in sensitivity when using molecular diagnostic tests
Participants were instructed to collect a nasal sample by inserting the flocked nasal swab approximately 2.5 cm into one nostril and rotating. The swab was then placed in transport media for testing. 2 mL of saliva in transport media was collected. A second nasal swab mixed with reagent was collected and then the reagent was used as per instructions for the rapid test
Specimens received were excluded (both the pair of nasal and saliva specimens) if they were received and had leaked due to poor packaging or appeared to not have any saliva added. We tested samples on both the GenMark Respiratory Viral Panel, and Biofire FilmArray Respiratory Panel. Both offer a multiplex panel for respiratory pathogens. They however differ in the DNA/RNA extraction methods used, in the measured sensitivity and specificity (for nasopharyngeal specimens), and workflow parameters, such as hands-on time, time to result, and relative ease of use. Previous studies have compared these molecular multiplex platforms including laboratory developed molecular methods (PCR)
Prior to detection on the Genmark assay, DNA/RNA were extracted from the samples using the MagNA Pure extraction protocol. Details of this and further procedure are reported in the Supplementary Information section. The Genmark Panel includes: Influenza A (Subtype to Influenza A H1, Influenza A H3 and Influenza A 2009 H1N), Influenza B, Respiratory Syncytial Virus (RSV) A, Respiratory Syncytial Virus (RSV) B, Parainfluenza Virus (PIV) 1, Parainfluenza Virus (PIV) 2, Parainfluenza Virus (PIV) 3, Human Metapneumovirus (hMPV), Human Rhinovirus (HRV), Adenovirus B/E and Adenovirus C. Viral targets in the FilmArray are Influenza A (Influenza A H1, Influenza A H3, Influenza A 2009 H1N1), Influenza B, Respiratory Syncytial Virus (RSV), Coronavirus HKU1, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, Parainfluenza Virus (PIV) 1, Parainfluenza Virus (PIV) 2, Parainfluenza Virus (PIV) 3, Parainfluenza Virus (PIV) 4, Human Metapneumovirus (hMPV), Human Rhinovirus/Enterovirus and Adenovirus. The result is not binary, a threshold cycle (
Specimens were processed following the procedure found in the FilmArray Respiratory Panel Instruction Booklet. The FilmArray RP contains its own extraction procedure and internal controls within each pouch. In the FilmArray, DNA/RNA is extracted from the sample through physical agitation and chemical disruption of the cells with beads. Possible results include Detected, Not Detected, Equivocal (Influenza A only) and Invalid.
In order to gauge if diagnostic test results or flu risk actually influence individuals to change behaviors, participants were sent a survey at the completion of the study period. One of two versions of the survey was sent depending on whether the participant had sent in diagnostic samples. Participants were asked about their preventative behaviors and the difficulty of the specimen collection protocols (all questions and responses in Table S1).
Analyses were performed using R version 2.15.1 (R Development Core Team, Vienna, Austria). Key outcomes of interest were self-reported symptoms (participants could report any of fever, cough, sore throat, shortness of breath, chills, fatigue, nausea, diarrhea, body aches and headache), and diagnostic results for each of the nasal and saliva specimens via both the Genmark and BioFire systems for each set of specimens sent in. Timing of specimen collection compared to symptom onset was noted in order to understand the potential of self-collection. Univariate comparisons between symptoms and diagnostic results were performed, but sample size was too low to warrant further analyses.
Between November 1, 2013 and April 30, 2014, 295 participants enrolled in the study and received a kit. During the study period we also sent a second kit to participants who already completed one kit, allowing for second illnesses to be captured. Among the cohort of enrolled study participants, 167 individuals reported any symptoms during the study time frame, and from those individuals 71 pairs of diagnostic samples were returned (1 returned nasal sample had no accompanying saliva sample), and sent for nucleic acid analysis. Participants submitted kits an average of 3.29 (95% CI: 2.39, 4.18) days after symptom onset (Figure 2). People ages 20 to 77 signed up and received kits (Figure 3), and 70% of signups were women. Kits were returned by individuals ranging in age from 20 to 70.
Out of the 71 pairs of samples tested, 35 sets of samples tested positive in at least one specimen on both systems, 31 were negative on both and there were 5 cases in which both the saliva and nasal specimens tested on one system did not detect a virus detected in at least one specimen using the other system: Influenza A was detected in one nasal specimen by Genmark (and not on the FilmArray), Coronavirus was detected in one saliva sample detected by Genmark (and not on the FilmArray), Coronavirus detected in one nasal sample by FilmArray (and not on the Genmark), Coronavirus detected in one saliva sample by FilmArray (and not the Genmark), RSV was detected in both a nasal and saliva samples from one person on the FilmArray (and not on the Genmark). The distribution of samples and viruses detected in at least one specimen (saliva or nasal) on both systems are illustrated in Figures 4a and b. In 10 cases, there was a difference between results for the nasal and saliva specimen pairs on at least one of the systems, but the same pathogen was also detected in the other system (Table S2).
Rapid immunoassays performed by the users were not useful in identifying the specimens that were positive with influenza, RSV or adenovirus. None of the rapid tests returned alongside any of the 71 returned pairs of specimens demonstrated positive results for any pathogens, even ones that were determined positive by the PCR-based methods.
Of people who reported The CDC (Centers for Disease Control and Prevention)’s “influenza-like illness” (ILI) symptom profile (fever and cough or sore throat) two out of twelve of tested positive for influenza, five out of twelve did not test positive for anything on the panel and five out of twelve tested positive for other viruses (Coronavirus, hMPV and RSV). The full summary of symptom profiles by pathogen is provided in Table S3.
Results of the survey are reported in Table S1. Overall, it was found that i) most participants who sent in a kit did not seek any interventions from healthcare professionals for their illness (86.7%), ii) it was harder for people to produce the nasal sample than the saliva sample, and iii) beyond finding out their own diagnosis, most individuals reported that they would find it also useful to know what others in their area have had near them (83.3% for those who sent in kits, 93.7% for those who did not).
Our study seeks to specifically study user preferences and specimen types towards building a scalable method connecting self-reported symptoms to infection type for understanding community prevalence of respiratory infections. Multiple initial findings are offered: diagnostic samples can be generated by the public demonstrated by the high user participation rate (half of the people who reported any symptoms at all completed the kit and sent in specimens), and initial validation of oral specimens as compared with nasal specimens can be used for the identification of upper respiratory pathogens, along with reports of greater comfort and preference for oral specimens. While we anticipate the participation rate is biased upwards based on the types of people who may have agreed to participate in the study, it indicates that while sick at home, people are willing and able to complete the specimen collection. Influenza A, RSV, Coronavirus (3 subtypes), hMPV and HRV were detected from saliva and nasal samples, with high concordance between the nasal and saliva samples measured on two different detection methods. Pairing symptom profiles with the detected viruses showed that most people who self-report the common ILI profile did not have influenza. Through our survey, we found that most individuals who became ill and returned a sample did not seek healthcare, such as going to a clinic or the hospital. Overall, saliva collection was reported to be easier than the nasal swab specimen collection. Rapid immunoassays did not show value for community use, compared to the PCR detection of community-acquired specimens. Beyond the expected lower sensitivity and specificity of the rapid tests, the specifications for these tests have been determined using nasopharyngeal swabs on children, thus the performance on specimens from adults and using nasal swabs can be attributed to this difference. The different assays, GenMark and BioFire FilmArray, demonstrated similar performance with some false negatives on both saliva and nasal specimens from each system as compared to the other. We also found that individuals would find it useful to know what pathogens were detected in other people in the community. Regarding finding out their own diagnosis, most common reasons cited for desiring this information included concern for exposure to others, especially by those who also mentioned they work in healthcare. The results presented here suggest methods for achieving these preferences, and with further studies involving more and diverse groups the power of these conclusions will increase.
There are many aspects of the study which can be improved and future research should address. One limitation of this study was the small and non-representative sample of volunteers. Based on the Internet or mobile requirement for participation, as well as a self-selective nature of interest, participants of this study are similar demographically to those in other participatory systems
This study represents an advance with respect to the field of participatory public health surveillance systems. To-date, reports in the literature of online participatory studies have been limited to self-reported syndromic information only. Some studies have combined self-reported influenza symptoms with serology to understand attack rates in the population. However, linkage to symptoms has been limited in self-sampling studies, and although other studies have demonstrated that individuals can obtain a nasal swab specimen from themselves, we report here that individuals prefer saliva and initial results indicate that it can potentially provide a feasible medium for acute upper respiratory infection detection. Finally, via the results of our survey, it is indicated that participatory information (crowdsourced) can be used to generate context-specific, rapid information for disease surveillance that has the potential to impact public health behaviors.
Going forward, further study of data from the GoViral surveillance method offers potential benefits such as understanding household transmission characteristics, enabling evaluation of the relationship between reported symptom profiles and viral etiology as well as spatio-temporal distribution of upper respiratory infection, duration of symptoms and its relation to viral etiology, and impact of these efforts on an individual’s public health and healthcare seeking behavior. Beyond a cohort approach here, community specimen collection can be used during seasonal outbreak or pandemic investigations. Future work will increase the number and representatively of study participant demographics, as well as employ next-generation detection technologies to improve sensitivity and speed of generating the diagnostic results.
All authors have confirmed that they have no financial, personal or professional competing interests to report.
Work/studying from home
3 (10%)
Extra hand washing
18 (62%)
Got a vaccine
19 (65%)
Avoiding contact with others
8 (28%)
Didn’t take any
2 (7%)
Work/studying from home
14 (10%)
Extra hand washing
63 (44%)
Got a vaccine
106 (74%)
Avoiding contact with others
20 (14%)
Didn’t take any
21 (15%)
No
12 (43%)
1-2 days
10 (36%)
3 days
3 (11%)
1 week
1 (4%)
10 days
1 (4%)
Can’t remember
1 (4%)
Yes
4 (13%)
No
26 (87%)
Filling out the online form
20 (69%)
Using nasal swab
4 (14%)
Saliva collection
5 (17%)
Filling out the online form
5 (20%)
Using nasal swab
12 (46%)
Saliva collection
9 (35%)
Within 1 day
11 (37%)
Within 2 days
9 (30%)
Within a week
4 (13%)
Just finding out at end of season is fine
6 (20%)
Within 1 day
34 (25%)
Within 2 days
33 (24%)
Within a week
26 (19%)
Just finding out at end of season is fine
45 (33%)
Yes
25 (83%)
No
5 (17%)
Yes
132 (94%)
No
9 (6%)
Just for information/curiosity
6/27 (22%)
Take appropriate precautions for self/others
11/27 (41%)
Tell doctor
3/27 (11%)
Doctor and activities
5/27 (19%)
Nothing
2/27 (7%)
Just for information/curiosity
34/110 (31%)
Take appropriate precautions for self/others
51/110 (46%)
Tell doctor
14/110 (13%)
Doctor and activities
3/110 (3%)
Nothing
8/110 (7%)
Sample Type
Genmark Result
FilmArray Result
Nasal
Infl A 2009 H1N1 Ct=136.2Infl A Ct=115
none
Saliva
Infl A 2009 H1N1 Ct=137.3
FLA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=226.3
CORONA
Saliva
Corona 229E Ct=141.4
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=264.2
CORONA
Saliva
Corona 229E Ct=235.7
CORONA
Nasal
Infl A 2009 H1N1 Ct=347Infl A Ct=201.3
FLA
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
Corona HKU1 Ct=243.3
CORONA
Saliva
Corona HKU1 Ct=279
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
negative
EN-RH
Saliva
negative
EN-RH
Nasal
Corona NL63 Ct=6.9
CORONA
Saliva
Corona NL63 Ct=16.5
CORONA
Nasal
Infl A 2009 H1N1 Ct=348Infl A Ct=155
FLA
Saliva
Infl A 2009 H1N1 Ct=80.2Infl A Ct=208
FLA
Nasal
Infl A 2009 H1N1 Ct=210Infl A Ct=225
FLA
Saliva
negative
none
Nasal
Infl A 2009 H1N1 Ct=160Infl A Ct=97.6
none
Saliva
negative
FLA
Nasal
Corona 229E Ct=9.1
none
Saliva
Corona 229E Ct=5.8
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona HKU1 Ct=269
CORONA
Saliva
Corona HKU1 Ct=240
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
RSV A Ct=176
RSVI
Saliva
RSV A Ct=152
RSVI
Nasal
negative
none
Saliva
negative
CORONA
Nasal
Corona 229E Ct=202Corona HKU1 Ct=279
CORONA
Saliva
Corona 229E Ct=4.3Corona HKU1 Ct=169
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=197.2
CORONA
Saliva
Corona 229E Ct=206.5
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=206
CORONA
Saliva
Corona 229E Ct=207
CORONA
Nasal
Corona HKU1 Ct=184
none
Saliva
negative
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona HKU1 Ct=153
CORONA
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
Corona HKU1 Ct=213
CORONA
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
CORONA NL63 Ct=5.3
CORONA
Saliva
negative
CORONA
Nasal
negative
CORONA
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
Infl A 2009 H1N1 Ct=229Infl A Ct=233
FLA
Saliva
Infl A 2009 H1N1 Ct=312Infl A Ct=253
FLA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona HKU1 Ct=3.8
none
Saliva
Corona HKU1 Ct=91.4
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=105
none
Saliva
Corona 229E Ct=197
CORONA
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
HRV Ct=180
EN-RH
Nasal
negative
none
Saliva
Corona 229E Ct=5.8
none
Nasal
negative
none
Saliva
negative
none
Nasal
negative
none
Saliva
negative
none
Nasal
RSV A Ct=201
RSVI
Saliva
RSV A Ct=137
RSVI
Nasal
Corona NL63 Ct=16.5
CORONA
Saliva
negative
CORONA
Nasal
HRV Ct=17.1
EN-RH
Saliva
HRV Ct=25.4
EN-RH
Nasal
negative
none
Saliva
negative
none
Nasal
Infl A H3 Ct=148 Infl A Ct=32.4
FLA
Saliva
Infl A H3 Ct=161 Infl A Ct=46.1
FLA
Nasal
negative
none
Saliva
negative
none
Nasal
Corona 229E Ct=167
CORONA
Saliva
Corona 229E Ct=48
CORONA
Nasal
hMPV Ct=140
HMPV
Saliva
hMPV Ct=120
HMPV
Nasal
HRV Ct=14.6
EN-RH
Saliva
HRV Ct=9.6
EN_RH
Nasal
Infl A H3 Ct=81.6 Infl A Ct=12
none
Saliva
negative
none
Nasal
Infl A H3 Ct=147 Infl A Ct=67.6
FLA
Saliva
negative
none
Nasal
HRV Ct=157
EN-RH
Saliva
HRV Ct=7
EN-RH
Nasal
HRV Ct=212
EN-RH
Saliva
HRV Ct=148
EN-RH
Nasal
negative
none
Nasal
HRV Ct=141
EN-RH
Saliva
HRV Ct=128
EN-RH
Nasal
HRV Ct=26.7
EN-RH
Saliva
HRV Ct=17.3
EN-RH
Symptoms Reported
Influenza A (8)
Coronavirus (17)
HMPV (1)
HRV (7)
RSV (2)
Negative (31)
fever only (1)
0.0
0.00
0.00
0.0
0.0
3.2
cough only (7)
25.0
5.9
0.00
28.6
0.0
6.5
sore throat only (16)
12.5
41.2
0.00
28.6
0.0
19.4
none (19)
0.0
23.5
0.00
14.3
0.0
45.2
cough and sore throat (11)
37.5
11.8
0.00
28.6
50.0
9.7
fever, cough and sore throat (4)
0.0
5.9
100.0
0.00
0.0
6.5
fever and cough (4)
25.0
0.00
0.00
0.00
50.0
3.2
fever and sorethroat (4)
0.00
11.8
0.00
0.00
0.0
6.5
We thank Matthew Biggerstaff for his helpful comments.