About

Yvonne Maldonado is a professor in the Department of Pediatrics with a focus on Infectious Diseases and Health Research and Policy at Stanford University. Her research and academic work are centered on infectious diseases, contributing to the understanding and treatment of infectious conditions within pediatric populations. As a faculty member, she is involved in teaching and mentoring students, and her expertise supports the university's broader efforts in health research and policy.

Research topics

• Medicine
• Internal medicine
• Virology
• Pathology
• Immunology
• Computer Science
• Sociology
• Psychology
• Gastroenterology
• Gender studies
• Gerontology
• Psychiatry

Selected publications

• Estimating the generation time for SARS-CoV-2 transmission using United States household data, December 2021–May 2023

  Scientific Reports · 2026-04-11

  articleOpen access

  Generation time, representing the interval between infection events in primary and secondary cases, is important for understanding disease transmission dynamics including predicting the effective reproduction number (Rt), which informs public health decisions. While previous estimates of SARS-CoV-2 generation times have been reported for early Omicron variants, there is a lack of data for subsequent sub-variants, such as XBB. We estimated SARS-CoV-2 generation times using data from the Respiratory Virus Transmission Network – Sentinel (RVTN-S) household transmission study conducted across seven U.S. sites from December 2021 to May 2023. The study spanned three Omicron sub-periods dominated by the sub-variants BA.1/2, BA.4/5, and XBB. We employed a Susceptible-Exposed-Infectious-Recovered (SEIR) model with a Bayesian data augmentation method that imputes unobserved infection times of cases to estimate the generation time. The estimated mean generation time for the overall Omicron period was 3.5 days (95% credible interval, CrI: 3.3–3.7). During the sub-periods, the estimated mean generation times were 3.8 days (95% CrI: 3.4–4.2) for BA.1/2, 3.5 days (95% CrI: 3.3–3.8) for BA.4/5, and 3.5 days (95% CrI: 3.1–3.9) for XBB. Our study provides estimates of generation times for the Omicron variant, including the sub-variants BA.1/2, BA.4/5, and XBB. These up-to-date estimates specifically address the gap in knowledge regarding these sub-variants and are consistent with earlier studies. They enhance our understanding of SARS-CoV-2 transmission dynamics by aiding in the prediction of Rt, offering insights for improving COVID-19 modeling and public health strategies.

  PublisherOA PDFDOI

• Estimating the generation time for SARS-CoV-2 transmission using United States household data, December 2021–May 2023

  UNC Libraries · 2026-04-23

  articleOpen access
  PublisherDOI

• Estimated Burden of COVID-19 Illnesses, Medical Visits, Hospitalizations, and Deaths in the US From October 2022 to September 2024

  JAMA Internal Medicine · 2026-01-05 · 4 citations

  articleOpen access

  Importance: Since 2020, COVID-19 has dramatically impacted the US population and health care system. Reporting requirements, circulating variants, testing practices, and population immunity from vaccination and previous infections evolved as the COVID-19 pandemic progressed. Evidence-based public health policy and resource allocation decisions require current estimates of disease burden. Objective: To estimate the age group-specific burden of COVID-19-associated illnesses, outpatient visits, hospitalizations, and deaths in the US from October 2022 to September 2024. Design, Setting, and Participants: In this cross-sectional study, hierarchical Bayesian modeling, adjusting for underdetection of SARS-CoV-2 due to testing practices and test sensitivity, was applied to hospitalization data from the population-based COVID-19 Hospitalization Surveillance Network (COVID-NET) database, which includes 89 counties and jurisdictional equivalents in 12 states covering approximately 10% of the US population. Data from 94 363 participants from October 2022 to September 2023 (surveillance period, 2022-2023) and from 72 176 participants from October 2023 to September 2024 (surveillance period, 2023-2024) were included, and probabilistic mathematical multiplier models estimated counts of deaths, outpatient visits, and symptomatic illnesses incorporating literature and study-based multipliers. Data were modeled from April 2024 to September 2025. Exposures: COVID-NET patients with a laboratory-confirmed COVID-19-associated hospitalization, defined as a positive SARS-CoV-2 test result within 14 days before or during hospitalization. Main Outcomes and Measures: Estimated national counts with 95% uncertainty intervals (UIs) of outpatient visits, illnesses, hospitalizations, and deaths by age group. Results: In 2022-2023, there were an estimated 43.6 million (95% UI, 25.3-64.0 million) COVID-19-associated illnesses, 10.0 million (95% UI, 7.0-13.1 million) outpatient visits, 1.1 million (95% UI, 0.9-1.4 million) hospitalizations, and 101 300 (95% UI, 73 600-132 500) deaths. In 2023-2024, there were an estimated 33.0 million (95% UI, 20.2-49.0 million) COVID-19-associated illnesses, 7.7 million (95% UI, 5.5-9.9 million) outpatient visits, 879 100 (95% UI, 738 600-1 039 000) hospitalizations, and 100 800 (95% UI, 64 000-140 400) deaths. In 2023-2024, people 65 years and older comprised 17.7% of the total US population but accounted for 47.9% (95% UI, 27.1-66.9) of COVID-19-associated illnesses, 64.3% (95% UI, 53.1-73.4) of outpatient visits, 67.6% (95% UI, 65.9-69.2) of hospitalizations, and 81.2% (95% UI, 70.2-90.6) of deaths. Conclusions and Relevance: In this cross-sectional study, despite declining from the first to the second surveillance period, the COVID-19 burden continued to have a large impact in the US, particularly among adults 65 years and older, underscoring the ongoing importance of prevention measures.

  PublisherOA PDFDOI

• 56 Positive SARS-CoV-2 symptomatology despite persistently negative molecular testing: Insights from a Multicenter Household Transmission Study

  Journal of Clinical and Translational Science · 2025-03-25

  articleOpen access

  Objectives/Goals: We describe the prevalence of individuals with household exposure to SARS-CoV-2, who subsequently report symptoms consistent with COVID-19, while having PCR results persistently negative for SARS-CoV-2 (S[+]/P[-]). We assess whether paired serology can assist in identifying the true infection status of such individuals. Methods/Study Population: In a multicenter household transmission study, index patients with SARS-CoV-2 were identified and enrolled together with their household contacts within 1 week of index’s illness onset. For 10 consecutive days, enrolled individuals provided daily symptom diaries and nasal specimens for polymerase chain reaction (PCR). Contacts were categorized into 4 groups based on presence of symptoms (S[+/-]) and PCR positivity (P[+/-]). Acute and convalescent blood specimens from these individuals (30 days apart) were subjected to quantitative serologic analysis for SARS-CoV-2 anti-nucleocapsid, spike, and receptor-binding domain antibodies. The antibody change in S[+]/P[-] individuals was assessed by thresholds derived from receiver operating characteristic (ROC) analysis of S[+]/P[+] (infected) versusS[-]/P[-] (uninfected). Results/Anticipated Results: Among 1,433 contacts, 67% had ≥1 SARS-CoV-2 PCR[+] result, while 33% remained PCR[-]. Among the latter, 55% (n = 263) reported symptoms for at least 1 day, most commonly congestion (63%), fatigue (63%), headache (62%), cough (59%), and sore throat (50%). A history of both previous infection and vaccination was present in 37% of S[+]/P[-] individuals, 38% of S[-]/P[-], and 21% of S[+]/P[+] (P<0.05). Vaccination alone was present in 37%, 41%, and 52%, respectively. ROC analyses of paired serologic testing of S[+]/P[+] (n = 354) vs. S[-]/P[-] (n = 103) individuals found anti-nucleocapsid data had the highest area under the curve (0.87). Based on the 30-day antibody change, 6.9% of S[+]/P[-] individuals demonstrated an increased convalescent antibody signal, although a similar seroresponse in 7.8% of the S[-]/P[-] group was observed. Discussion/Significance of Impact: Reporting respiratory symptoms was common among household contacts with persistent PCR[-] results. Paired serology analyses found similar seroresponses between S[+]/P[-] and S[-]/P[-] individuals. The symptomatic-but-PCR-negative phenomenon, while frequent, is unlikely attributable to true SARS-CoV-2 infections that go missed by PCR.

  PublisherOA PDFDOI

• Symptoms, Viral Loads, and Rebound Among COVID-19 Outpatients Treated With Nirmatrelvir/Ritonavir Compared With Propensity Score–Matched Untreated Individuals

  UNC Libraries · 2025-03-18

  articleOpen access

  BACKGROUND: Nirmatrelvir/ritonavir (N/R) reduces severe outcomes from coronavirus disease 2019 (COVID-19); however, rebound after treatment has been reported. We compared symptom and viral dynamics in individuals with COVID-19 who completed N/R treatment and similar untreated individuals. METHODS: We identified symptomatic participants who tested severe acute respiratory syndrome coronavirus 2-positive and were N/R eligible from a COVID-19 household transmission study. Index cases from ambulatory settings and their households contacts were enrolled. We collected daily symptoms, medication use, and respiratory specimens for quantitative polymerase chain reaction for 10 days during March 2022-May 2023. Participants who completed N/R treatment (treated) were propensity score matched to untreated participants. We compared symptom rebound, viral load (VL) rebound, average daily symptoms, and average daily VL by treatment status measured after N/R treatment completion or 7 days after symptom onset if untreated. RESULTS: Treated (n = 130) and untreated participants (n = 241) had similar baseline characteristics. After treatment completion, treated participants had greater occurrence of symptom rebound (32% vs 20%; P = .009) and VL rebound (27% vs 7%; P < .001). Average daily symptoms were lower among treated participants without symptom rebound (1.0 vs 1.6; P < .01) but not statistically lower with symptom rebound (3.0 vs 3.4; P = .5). Treated participants had lower average daily VLs without VL rebound (0.9 vs 2.6; P < .01) but not statistically lower with VL rebound (4.8 vs 5.1; P = .7). CONCLUSIONS: Individuals who completed N/R treatment experienced fewer symptoms and lower VL but rebound occured more often compared with untreated individuals. Providers should prescribe N/R, when indicated, and communicate rebound risk to patients.

  PublisherDOI

• High HBV seroprotection rates in infants born to people with HIV and HBV infection in sub-Saharan Africa

  Vaccine X · 2025-11-21

  articleOpen access

  There is little data on hepatitis B surface antibody (anti-HBs) responses in HIV-exposed, uninfected (HEU) infants born to people living with HIV and hepatitis B virus infection (HBV) (HEU-HBV). We examined anti-HBs titers in infants in a post-hoc analysis of the HIV Prevention Trials Network (HPTN) 046 trial. Thirty-three infants were tested for anti-HBs at 6 and 12 months. Of these, 84.8 % had a protective response (anti-HBs >10 IU/ml) at 6 months, and 97 % had anti-HBs >10 IU/ml at 12 months. Infants with low birth weight ([LBW] ≤2500 g) had lower median anti-HBs titers at 6 and 12 months (472 IU/mL and 48 IU/mL, respectively) compared to infants without LBW, although this was not statistically significant. Anti-HBs titers at 6 and 12 months in HEU-HBV are similar to those in HIV unexposed, uninfected (HUU) infants.

  PublisherDOI

• Review of "The Impacts of Viral Interaction on Household Transmission of Respiratory Viruses"

  2025-04-15

  peer-reviewOpen access1st authorCorresponding
  PublisherOA PDFDOI

• The Path Forward for Vaccine Policy in the United States

  New England Journal of Medicine · 2025-07-30 · 5 citations

  article
  PublisherDOI

• Social vulnerability and the risk of respiratory virus infection in households: a case-ascertained study

  Research Square · 2025-06-30

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• P-634. Effect of Pre-existing OPV-induced immunity on development of canonical and non-canonical poliovirus virulence mutations

  Open Forum Infectious Diseases · 2025-01-29

  articleOpen accessSenior author

  Abstract Background Preventing vaccine-derived polio is crucial, yet polio evolution and transmission mechanisms remain unclear. Our previous study in Mayan infants found that preexisting OPV-induced polio antibodies did not affect S3 immunogenicity. We now explore if viral mutations differ in those with and without preexisting antibodies. Using NGS, we identify and characterize vaccine poliovirus’ mutation patterns from stool sample isolates post one and two OPV doses. We hypothesize that OPV-induced intestinal immunity will correlate with increased mutations after the 2nd dose compared to the 1st. S1 Canonical Mutations vs. Mutation Rates Post 1st and 2nd Dose of 116 OPV Isolates Methods 179 OPV samples from a previous study were used. Participants received an OPV dose at study weeks 1 and 9 with stool samples collected at weeks 0, 1, 2, 4, 6, 8, 9, 10, 14, 16, and 17. A multiplex qPCR was used to determine serotype positivity. PCR amplicons created from stool viral RNA were purified and sequenced. Sequences were analyzed using the Illumina workflow nf-core/viralrecon (ver 2.5) and R (ver. 4.2.2). S2 Canonical Mutations vs. Mutation Rates Post 1st and 2nd Dose of 82 OPV Isolates Results 303 isolates were sequenced: 127 serotype 1 (S1), 91 serotype 2 (S2) and 85 serotype 3 (S3); 35 from week 0, 187 from weeks 1-8 (post dose 1: D1) and 81 from weeks 9-17 (post dose 2: D2). S1 and S2 in D2 showed significantly higher mutation rates (% of samples with mutation(s) at a given genome location) at all positions (S1 p = 0.0014, S2 p < 2.2e-16), while S3 showed no difference (p = 0.9899). For canonical mutations, S1 D2 had higher mutations at G480A (D1 65.3% vs. D2 68.6%) and A2795G (D1 8.5% vs. D2 10.5%), but 0% at A2438T while D1 had 6%; no mutations were seen at T525C and T2879C. For S2, D2 had higher mutations at A481G (D1 11.4% vs. D2 16.7%), with no mutations at T2909C in either set. In S3, D2 showed higher mutations at T472C (D1 36.6% vs. D2 46.4%), but lower mutations at C2493T (D1 26.9% vs. D2 16.7%) and T2034C (D1 3.8% vs. D2 0%). S3 Canonical Mutations vs. Mutation Rates Post 1st and 2nd Dose of 70 OPV Isolates Conclusion Overall, isolates post the 2nd OPV dose showed significantly higher mutation rates for S1 and S2, but not for S3. Preexisting antibodies may be associated with higher mutation rates and long-term likelihood of neurovirulent reversion. Serotype differences may be related to shedding patterns and other serotype specific characteristics. Further studies are planned to understand the impact of pre-existing intestinal immunity on polio viral mutation and evolution. Disclosures Yvonne A. Maldonado, MD, Pfizer: Grant/Research Support|Pfizer: Member, DSMB

  PublisherOA PDFDOI

Recent grants

• Global Epidemiology of Infectious Diseases

  NIH · $3.5M · 2002–2027

• NIH Grant R01AI031475

  NIH · $734k · 1997

• NIH Grant R01AI068577

  NIH · $2.4M · 2013

Frequent coauthors

• Clea Sarnquist

  Stanford University

  99 shared

• Elizabeth D. Barnett

  Colorado State University

  64 shared

• Flor M. Muñoz

  Texas Children's Hospital

  58 shared

• Jonathan Altamirano

  Stanford University

  57 shared

• Avinash K. Shetty

  Manipal Academy of Higher Education

  54 shared

• Jeffrey Luther

  49 shared

• Wilbert H. Mason

  Kaiser Permanente Fontana Medical Center

  49 shared

• Mark Sawyer

  University of Tasmania

  49 shared