Supplementary Information for. Diagnosis of Zika virus infection on a nanotechnology platform

Transcription

1 Supplementary Information for Diagnosis of Zika virus infection on a nanotechnology platform Bo Zhang 1,7, Benjamin A. Pinsky 2,3,7, Jeyarama S. Ananta 1, Su Zhao 1, Shylaja Arulkumar 1, Hao Wan 1, Malaya K. Sahoo 2, Janaki Abeynayake 4, Jesse J. Waggoner 5, Clay Hopes 1, Meijie Tang 1 & Hongjie Dai 6 Affiliations 1 Nirmidas Biotech Inc., Palto Alto, California, USA. 2 Department of Pathology, Stanford University School of Medicine, Stanford, California, USA. 3 Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA. 4 Medical Research Institute, Colombo, Sri Lanka. 5 Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA. 6 Department of Chemistry, Stanford University, Stanford, California, USA. 7 These authors contributed equally to this work. Correspondence should be addressed to B.Z. (bo.zhang@nirmidas.com) or H.D. (hdai1@stanford.edu) This file includes: Supplementary Figure 1-7 Supplementary Table 1-5

2 Supplementary Figure 1. Titration curves for ZIKV IgG and IgA antibody on pgold and glass platforms. (a) Titration curves for ZIKV IgG generated by averaging the median fluorescence intensity of IRDye680 emission over the triplicate microarray spots at various dilution of a ZIKV IgG positive serum sample on plasmonic gold slide and glass microscope slide (Fisher Healthcare, US), from 100 times dilution to 10 million times dilution. (b) Titration curves for ZIKV IgA generated by averaging the median fluorescence intensity of IRDye800 emission over the triplicate microarray spots at various dilution of a ZIKV IgA positive serum sample on plasmonic gold slide and glass slide, from 100 times dilution to 10 million times dilution.error bars represent the standard deviation of the assay over 4 replicate assays on 2 slides.

3 Supplementary Figure 2. Multiplexed ZIKV/DENV antigen microarray on nanostructured plasmonic gold (pgold). A pgold biochip is composed of a pgold slide separated into 16 wells. Each well has identical ZIKV/DENV antigen microarray. For each microarray, ZIKV antigen and DENV antigen spots were immobilized on pgold in triplicate. During testing, human serum is applied to the microarray, where different isotypes of human antibodies against ZIKV and DENV antigens, if present, will be captured on corresponding ZIKV and DENV antigens. After a washing step, a mixture of antihuman IgG-IRDye680 conjugate and antihuman IgA-IRDye800 conjugate is applied to the microarray to label captured human IgG antibody with IRDye680 and human IgA antibody with IRDye800. Then the pgold biochip is scanned and analyzed with a fluorescence reader. Fluorescence channel and intensity at specific antigen spots are correlated to the amount of a specific antibody isotype against a particular antigen.

4 Supplementary Figure 3. Compare pgold result with commercial kit result for Dengue IgG/IgM measurement. IgG antibodies against DENV antigen were measured with the multiplexed assay on pgold (a) and Focus Dengue Virus IgG DxSelect test (c). IgM antibodies against DENV antigen were measured with the multiplexed assay on pgold (b) and Panbio Dengue IgM Capture ELISA (d). DENV IgG cutoff on pgold is defined by mean DENV IgG levels of control samples + 3SD; DENV IgM cutoff on pgold is defined by mean DENV IgM levels of control samples + 3SD. All signal levels on pgold are normalized by a reference sample.

5 Supplementary Figure 4. ROC curves for ZIKV IgG&IgA detection. (a) ROC curves for differentiation of 29 ZIKV infected patients (Group1_Z, as described in the manuscript) from 50 healthy control (Group3_H), based on ZIKV IgG measurement. (b) ROC curves for differentiation of 29 ZIKV infected patients (Group1_Z) from 50 healthy control (Group3_H), based on ZIKV IgA measurement. (c) ROC curves for differentiation of 29 ZIKV infected patients (Group1_Z) from 64 DENV infected patient (Group2_D), based on ZIKV IgG measurement. (d) ROC curves for differentiation of 29 ZIKV infected patients (Group1_Z) from 64 DENV infected patient (Group2_D), based on ZIKV IgA measurement.

6 Supplementary Figure 5. IgG/IgM/IgA antibody levels against DENV2 antigen. (a) Box plot for DENV IgG antibody level for serum specimens from three groups of patients: 64 patients with DENV infection (Group2_D); 29 patients with ZIKV infection (Group1_Z); and 50 patients with no known history of ZIKV or DENV infection (Group3_H). (b) Box plot for DENV IgM antibody level for serum specimens from three groups of patients as described in (a). (c) Box plot for DENV IgA antibody level for serum specimens from three groups of patients as described in (a). All signal levels are normalized by a reference sample.

7 Supplementary Figure 6. IgG/IgM/IgA antibody levels against DENV1, DENV3 and DENV4 antigen. (a) Box plot for DENV1 IgG/M/A antibody level for serum specimens from three groups of patients: 64 patients with DENV infection (Group2_D); 29 patients with ZIKV infection (Group1_Z); and 50 patients with no known history of ZIKV or DENV infection (Group3_H). (b) Box plot for DENV3 IgG/M/A antibody level for serum specimens from three groups of patients as described in (a). (c) Box plot for DENV4 IgG/M/A antibody level for serum specimens from three groups of patients as described in (a).

8 Supplementary Figure 7. ROC curves for ZIKV IgG&IgA detection, for ZIKV PCR+ positive samples (Group4_Z). (a) ROC curves for differentiation of 49 ZIKV infected patients (Group4_Z) from 50 healthy control (Group3_H), based on ZIKV IgG measurement. (b) ROC curves for differentiation of 49 ZIKV infected patients (Group4_Z) from healthy control (Group3_H), based on ZIKV IgA measurement. (c) ROC curves for differentiation of 49 ZIKV infected patients (Group4_Z) from 64 DENV infected patient (Group2_D), based on ZIKV IgG measurement. (d) ROC curves for differentiation of 49 ZIKV infected patients (Group4_Z) from 64 DENV infected patient (Group2_D), based on ZIKV IgA measurement.

9 Supplementary Table 1. Clinical and test info of 29 ZIKV infected patients (Group1_Z) from Colombia who were clinically diagnosed with ZIKV infection. PATIENT INFORMATION PREVIOUS HISTORY DIAGNOSIS INFORMATION Sample ID AGE SEX COUNTRY OF ORIGIN GESTATIONAL WEEK DAYs between 1ST ZIKA SYMPTOM to SAMPLE COLLECTION DENGUE DIAGNOSIS Zika M Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia NO 2 NO ACUTE ZIKA INFECTION Zika F Colombia 8 WEEKS 3 NO ACUTE ZIKA INFECTION Zika F Colombia NO 4 NO ACUTE ZIKA INFECTION Zika F Colombia 5 WEEKS 5 NO ACUTE ZIKA INFECTION Zika F Colombia NO 5 NO ACUTE ZIKA INFECTION Zika F Colombia 24 WEEKS 8 NO ACUTE ZIKA INFECTION Zika F Colombia NO 8 NO ACUTE ZIKA INFECTION Zika M Colombia NO 9 NO ACUTE ZIKA INFECTION Zika M Colombia NO 12 NO ACUTE ZIKA INFECTION Zika F Colombia 5 WEEKS 13 NO ACUTE ZIKA INFECTION Zika M Colombia NO 15 NO ACUTE ZIKA INFECTION Zika M Colombia NO 23 NO ACUTE ZIKA INFECTION Zika F Colombia 19 WEEKS 26 NO ACUTE ZIKA INFECTION Zika F Colombia 27.5 WEEKS 29 NO ACUTE ZIKA INFECTION Zika F Colombia NO 33 NO ACUTE ZIKA INFECTION Zika F Colombia 36 WEEKS 34 NO ACUTE ZIKA INFECTION Zika F Colombia 30 WEEKS 38 NO ACUTE ZIKA INFECTION Zika F Colombia 1 WEEKS 41 NO ACUTE ZIKA INFECTION Zika F Colombia 2 WEEKS 47 NO ACUTE ZIKA INFECTION Zika F Colombia 20 WEEKS 56 NO ACUTE ZIKA INFECTION Zika F Colombia 17 WEEKS 64 NO ACUTE ZIKA INFECTION Zika M Colombia NO 65 NO ACUTE ZIKA INFECTION Zika M Colombia NO 72 NO ACUTE ZIKA INFECTION Zika M Colombia NO 93 NO ACUTE ZIKA INFECTION ZIKA SYMPTOMS OTHER INFORMATION pgold test result SAMPLE ID FEVER SKIN RASH JOINT PAIN MYALGIA EYE PAIN CEPHALAGIA CONJUNCTIVITIS DIARRHEA Rapid Test result (Zika IgG) Rapid Test result (Zika IgM) ZIKV IgG ZIKV IgM ZIKV IgA Zika-01 YES YES YES YES YES YES YES NO positive positive positive Zika-02 YES YES YES YES YES YES NO NO Positive Positive Negative positive positive Zika-03 YES YES YES YES YES YES YES NO Positive Positive positive positive positive Zika-04 YES YES YES YES YES YES NO NO Positive Positive positive positive positive Zika-05 YES YES YES YES YES YES YES YES Positive Positive positive positive positive Zika-06 YES YES YES YES NO NO YES NO positive negative positive Zika-07 YES YES YES YES YES YES YES NO positive negative positive Zika-08 YES YES YES YES NO NO YES NO positive positive positive Zika-09 YES YES YES YES NO YES YES NO positive positive positive Zika-10 YES YES YES YES YES YES YES NO positive negative positive Zika-11 YES YES YES YES NO NO YES NO positive positive negative Zika-12 YES YES YES NO NO YES YES NO positive positive positive Zika-13 YES YES YES YES YES NO NO NO negative positive negative Zika-14 YES YES YES YES NO YES YES NO positive negative negative Zika-15 YES YES NO YES NO YES YES NO positive negative negative Zika-16 YES YES YES YES NO NO YES NO positive positive positive Zika-17 YES YES YES YES NO YES YES NO positive positive positive Zika-18 YES YES YES NO YES NO YES NO positive positive positive Zika-19 YES YES YES YES YES YES NO YES positive negative positive Zika-20 YES YES YES YES NO YES YES YES negative positive negative Zika-21 YES YES YES YES NO YES YES NO positive positive positive Zika-22 YES YES YES YES YES YES NO NO positive positive positive Zika-23 YES YES YES YES YES NO NO NO positive positive positive Zika-24 YES YES YES YES NO NO YES YES positive negative positive Zika-25 YES YES YES YES YES YES NO NO positive positive negative Zika-26 YES YES YES YES NO YES YES NO positive positive negative Zika-27 YES YES YES YES NO YES YES NO positive positive positive Zika-28 YES YES YES YES YES YES NO YES positive negative negative Zika-29 YES YES YES YES YES YES NO NO positive negative negative

10 Supplementary Table 2. Clinical and test info of 64 DENV infected patients (Group2_D) with a clinical diagnosis of DENV infection from Colombia, Ecuador, and Honduras, collected before the introduction of ZIKV to the Americas, as well as Sri Lanka which has had no known ZIKV cases. Sample ID Origin Clinical History IgG Reference Result IgM Reference Result PCR result Dengue-1 Colombia POS POS Dengue-2 Colombia POS POS Dengue-3 Honduras POS NEG Dengue-4 Honduras POS NEG Dengue-5 Honduras POS NEG Dengue-6 Honduras POS NEG Dengue-7 Honduras NEG NEG Dengue-8 Honduras POS NEG Dengue-9 Ecuador POS POS Dengue-10 Colombia POS POS Dengue-11 Honduras POS NEG Dengue-12 Honduras POS NEG Dengue-13 Ecuador POS POS Dengue-14 Ecuador POS POS Dengue-15 Sri Lanka Fever POS Neg Dengue-16 Sri Lanka Fever POS Neg Dengue-17 Sri Lanka Fever POS Neg Dengue-18 Sri Lanka Fever POS Dengue-19 Sri Lanka Fever POS Dengue-20 Sri Lanka Fever POS Neg Dengue-21 Sri Lanka Fever POS Neg Dengue-22 Sri Lanka Fever; low platelets POS Neg Dengue-23 Sri Lanka Fever, H ache POS Neg Dengue-24 Sri Lanka Fever; low platelets NEG Neg Dengue-25 Sri Lanka Fever NEG Neg Dengue-26 Sri Lanka Fever; low platelets NEG Dengue-27 Sri Lanka Fever; low platelets NEG Neg Dengue-28 Sri Lanka Fever; low platelets NEG Neg Dengue-29 Sri Lanka Fever NEG Neg Dengue-30 Sri Lanka Fever, H ache NEG DENV Dengue-31 Sri Lanka Fever, H ache NEG DENV Dengue-32 Sri Lanka Fever NEG Dengue-33 Sri Lanka Fever NEG Neg Dengue-34 Sri Lanka Fever; low platelets NEG Neg Dengue-35 Sri Lanka Fever; low platelets NEG Neg Dengue-36 Sri Lanka Fever; low platelets NEG Neg Dengue-37 Sri Lanka Fever NEG Neg Dengue-38 Sri Lanka Fever NEG Neg Dengue-39 Sri Lanka Fever NEG Neg Dengue-40 Sri Lanka Fever, H ache NEG Neg Dengue-41 Sri Lanka Fever NEG Dengue-42 Sri Lanka Fever; low platelets NEG Dengue-43 Sri Lanka Fever NEG Neg Dengue-44 Sri Lanka Fever, H ache NEG DENV Dengue-45 Sri Lanka Fever, H ache NEG Neg Dengue-46 Sri Lanka Fever NEG Neg Dengue-47 Sri Lanka Fever, H ache NEG Neg Dengue-48 Sri Lanka Fever POS Neg Dengue-49 Sri Lanka Fever NEG Neg Dengue-50 Sri Lanka Fever, H ache POS Neg Dengue-51 Sri Lanka Fever POS Neg Dengue-52 Sri Lanka Fever, Mayalgia POS Neg Dengue-53 Sri Lanka Fever; Low Platelets POS Neg Dengue-54 Sri Lanka Fever, Abdominal pain POS Neg Dengue-55 Sri Lanka Fever, Mayalgia POS DENV Dengue-56 Sri Lanka Fever, Mayalgia POS Dengue-57 Sri Lanka Fever; Low platelets POS Neg Dengue-58 Sri Lanka Fever, cough, Chest pain POS DENV Dengue-59 Sri Lanka Fever, Mayalgia POS Dengue-60 Sri Lanka Fever; Low platelets POS Neg Dengue-61 Sri Lanka Fever; Low platelets POS DENV Dengue-62 Sri Lanka Fever, Mayalgia POS Neg Dengue-63 Sri Lanka Fever, Abdominal pain POS Neg Dengue-64 Sri Lanka Fever; Low platelets POS Neg

11 Supplementary Table 3. Clinical and test info of 49 ZIKV infected patients (Group4_Z) from Dominican Republic who were confirmed with ZIKV infection by laboratory ZIKV RT-PCR test. Sample ID Age Sex Country of Origin Pregnancy (Trimester) Days between Zika symptom to sample collection LightMix Modular Zika Virus Real Time PCR Assay EURROIMMUN Anti-ZIKV ELISA (IgM) EURROIMMUN Anti-ZIKV ELISA (IgG) EuroImmun Anti-DENV ELISA (IgM) EuroImmun Anti-DENV ELISA (IgG) Zika Male Dominican Republic No 6 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 3 Detected Neg Pos Pos Pos Zika Female Dominican Republic No 3 Detected Neg Equiv Neg Pos Zika Female Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Male Dominican Republic No 1 Detected Neg Neg Neg Pos Zika Male Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Male Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Male Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 2 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 6 Detected Neg Equiv Neg Pos Zika Female Dominican Republic 1St Trimester 2 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 3 Detected Neg Equiv Neg Pos Zika Female Dominican Republic No 4 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 2 Detected Neg Equiv Neg Pos Zika Female Dominican Republic No 4 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 6 Detected Neg Pos Pos Pos Zika Female Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 1 Detected Neg Neg Equiv Pos Zika Female Dominican Republic No 3 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 4 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 4 Detected Equiv Neg Neg Pos Zika Male Dominican Republic No 3 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 3 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 2 Detected Neg Pos Neg Pos Zika Male Dominican Republic No 3 Detected Neg Neg Equiv Pos Zika Female Dominican Republic No 4 Detected Neg Neg Neg Pos Zika Male Dominican Republic No 5 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 4 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 4 Detected Neg Neg Neg Pos Zika Male Dominican Republic No 3 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 3 Detected Neg Pos Pos Pos Zika Male Dominican Republic No 2 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 4 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 2 Detected Pos Neg Neg Pos Zika Male Dominican Republic No 4 Detected Neg Neg Neg Pos Zika Female Dominican Republic 1st Trimester 1 Detected Neg Pos Neg Pos Zika Female Dominican Republic No 1 Detected Neg Neg Neg Pos Zika Female Dominican Republic No 1 Detected Neg Pos Zika Female Dominican Republic No 1 Detected Pos Pos Zika Female Dominican Republic No 4 Detected Neg Pos Zika Female Dominican Republic No 3 Detected Equiv Pos Zika Female Dominican Republic 2nd Trimester 4 Detected Equiv Pos Zika Male Dominican Republic No 4 Detected Neg Neg Zika Female Dominican Republic No 3 Detected Neg Pos Zika Female Dominican Republic No 3 Detected Neg Neg Zika Female Dominican Republic No 3 Detected Neg Equiv Zika Female Dominican Republic No 3 Detected Neg Pos Zika Male Dominican Republic No 2 Detected Neg Pos Zika Female Dominican Republic 1st Trimester 4 Detected Pos Pos

12 Supplementary Table 4. ZIKV infection diagnostic table summarizing ZIKV IgG/IgA test sensitivity and specificity, for different cohort of Zika samples: Group1_Z: 29 patients from DENV endemic Colombia (purchased from Medical Research Networx, LLC) who were clinically diagnosed (people showing ZIKV symptoms who lived or had travelled to regions with ZIKV transmission confirmed by RT-PCR) with ZIKV infection 2-93 days post symptom onset during the recent outbreak in Colombia. Group4_Z: 49 patients from DENV endemic Dominican Republic (purchased from Boca Biolistics) confirmed to be acute ZIKV infection (2-6 days post symptom onset) by laboratory ZIKV RT-PCR tests. Group1_Z Group4_Z ZIKV IgG test ZIKV IgA test ZIKV IgG test ZIKV IgA test Sensitivity against Dengue samples 89.7% 69.0% 42.9% 16.3% Specificity against Dengue samples 98.4% 98.4% 98.4% 98.4% Sensitivity against Control samples 93.1% 69.0% 77.6% 16.3% Specificity against Control samples 100.0% 100.0% 100.0% 100.0%

13 Supplementary Table 5. ZIKV IgG/IgA test intra assay and inter assay reproducibility. 5 samples, from low to high ZIKV IgG/IgA levels were tested. Each sample was tested 2 times per assay run, over 5 days. Reproducibility: IgG Sample N ZIKV IgG level Intra assay CV % Inter assay CV % Low positive Medium positive Medium positive High positive High positive Reproducibility: IgA Sample N ZIKV IgA level Intra assay CV Inter assay CV Low positive Medium positive Medium positive High positive High positive