Dr. Jake Scott is a board-certified infectious diseases specialist. He provides general infectious diseases care in the inpatient and outpatient settings and his special interests include COVID-19, coccidiomycosis, multidrug-resistant organisms, HIV, and HIV pre-exposure prophylaxis. He works with patients from diverse backgrounds to provide compassionate, high-quality care aligned with their needs.

Dr. Scott was born and raised in the Bay Area and was inspired to pursue a career in medicine after working as an HIV test counselor in San Francisco. He studied literature and creative writing in college and values the narrative aspect of medicine and the importance of drawing out the story behind the diagnosis.

One of Dr. Scott’s passions is teaching. He regularly works with Stanford residents and students and has lectured on various infectious disease-related topics, such as COVID-19, fever of unknown origin, and the dangers of antibiotic overuse, especially as it contributes to the rising threat of multidrug-resistant infections. He is also committed to expanding awareness of infectious diseases outside of the hospital and university through public presentations in the community and media interviews.
He is the medical director of the Antimicrobial Stewardship Program at Stanford Health Care – ValleyCare in Pleasanton and is a member of the Infection Control Committee and the Stanford Vaccine Clinical Advisory Committee.

In his spare time, Dr. Scott enjoys rock climbing, hiking, and spending time with his wife and two young children.

Clinical Focus

  • Infectious Disease

Academic Appointments

Boards, Advisory Committees, Professional Organizations

  • Member, Infectious Diseases Society of America (2013 - Present)
  • Member, Society for Healthcare Epidemiology of America (SHEA) (2015 - Present)

Professional Education

  • Fellowship: UCLA Division of Infectious Diseases (2016) CA
  • Fellowship, UCLA Infectious Diseases Fellowship, CA (2016)
  • Residency: Kaiser Permanente Oakland Internal Medicine Residency (2014) CA
  • Medical Education: University of Vermont College of Medicine (2011) VT
  • Board Certification: American Board of Internal Medicine, Infectious Disease (2016)
  • Board Certification: American Board of Internal Medicine, Internal Medicine (2014)

All Publications

  • Prevalence of Emergent Dolutegravir Resistance Mutations in People Living with HIV: A Rapid Scoping Review. Viruses Chu, C., Tao, K., Kouamou, V., Avalos, A., Scott, J., Grant, P. M., Rhee, S. Y., McCluskey, S. M., Jordan, M. R., Morgan, R. L., Shafer, R. W. 2024; 16 (3)


    Dolutegravir (DTG) is a cornerstone of global antiretroviral (ARV) therapy (ART) due to its high efficacy and favorable tolerability. However, limited data exist regarding the risk of emergent integrase strand transfer inhibitor (INSTI) drug-resistance mutations (DRMs) in individuals receiving DTG-containing ART.We performed a PubMed search using the term "Dolutegravir", last updated 18 December 2023, to estimate the prevalence of VF with emergent INSTI DRMs in people living with HIV (PLWH) without previous VF on an INSTI who received DTG-containing ART.Of 2131 retrieved records, 43 clinical trials, 39 cohorts, and 6 cross-sectional studies provided data across 6 clinical scenarios based on ART history, virological status, and co-administered ARVs: (1) ART-naïve PLWH receiving DTG plus two NRTIs; (2) ART-naïve PLWH receiving DTG plus lamivudine; (3) ART-experienced PLWH with VF on a previous regimen receiving DTG plus two NRTIs; (4) ART-experienced PLWH with virological suppression receiving DTG plus two NRTIs; (5) ART-experienced PLWH with virological suppression receiving DTG and a second ARV; and (6) ART-experienced PLWH with virological suppression receiving DTG monotherapy. The median proportion of PLWH in clinical trials with emergent INSTI DRMs was 1.5% for scenario 3 and 3.4% for scenario 6. In the remaining four trial scenarios, VF prevalence with emergent INSTI DRMs was ≤0.1%. Data from cohort studies minimally influenced prevalence estimates from clinical trials, whereas cross-sectional studies yielded prevalence data lacking denominator details.In clinical trials, the prevalence of VF with emergent INSTI DRMs in PLWH receiving DTG-containing regimens has been low. Novel approaches are required to assess VF prevalence with emergent INSTI DRMs in PLWH receiving DTG in real-world settings.

    View details for DOI 10.3390/v16030399

    View details for PubMedID 38543764

    View details for PubMedCentralID PMC10975848

  • Clinical course and management of COVID-19 in the era of widespread population immunity. Nature reviews. Microbiology Meyerowitz, E. A., Scott, J., Richterman, A., Male, V., Cevik, M. 2023


    The clinical implications of COVID-19 have changed since SARS-CoV-2 first emerged in humans. The current high levels of population immunity, due to prior infection and/or vaccination, have been associated with a vastly decreased overall risk of severe disease. Some people, particularly those with immunocompromising conditions, remain at risk for severe outcomes. Through the course of the pandemic, variants with somewhat different symptom profiles from the original SARS-CoV-2 virus have emerged. The management of COVID-19 has also changed since 2020, with the increasing availability of evidence-based treatments in two main classes: antivirals and immunomodulators. Selecting the appropriate treatment(s) for patients with COVID-19 requires a deep understanding of the evidence and an awareness of the limitations of applying data that have been largely based on immune-naive populations to patients today who most likely have vaccine-derived and/or infection-derived immunity. In this Review, we provide a summary of the clinical manifestations and approaches to caring for adult patients with COVID-19 in the era of vaccine availability and the dominance of the Omicron subvariants, with a focus on the management of COVID-19 in different patient groups, including immunocompromised, pregnant, vaccinated and unvaccinated patients.

    View details for DOI 10.1038/s41579-023-01001-1

    View details for PubMedID 38114838

    View details for PubMedCentralID 10208005

  • Higher-Dose Fluvoxamine and Time to Sustained Recovery in Outpatients With COVID-19: The ACTIV-6 Randomized Clinical Trial. JAMA Stewart, T. G., Rebolledo, P. A., Mourad, A., Lindsell, C. J., Boulware, D. R., McCarthy, M. W., Thicklin, F., Garcia Del Sol, I. T., Bramante, C. T., Lenert, L. A., Lim, S., Williamson, J. C., Cardona, O. Q., Scott, J., Schwasinger-Schmidt, T., Ginde, A. A., Castro, M., Jayaweera, D., Sulkowski, M., Gentile, N., McTigue, K., Felker, G. M., DeLong, A., Wilder, R., Rothman, R. L., Collins, S., Dunsmore, S. E., Adam, S. J., Hanna, G. J., Shenkman, E., Hernandez, A. F., Naggie, S. 2023


    The effect of higher-dose fluvoxamine in reducing symptom duration among outpatients with mild to moderate COVID-19 remains uncertain.To assess the effectiveness of fluvoxamine, 100 mg twice daily, compared with placebo, for treating mild to moderate COVID-19.The ACTIV-6 platform randomized clinical trial aims to evaluate repurposed medications for mild to moderate COVID-19. Between August 25, 2022, and January 20, 2023, a total of 1175 participants were enrolled at 103 US sites for evaluating fluvoxamine; participants were 30 years or older with confirmed SARS-CoV-2 infection and at least 2 acute COVID-19 symptoms for 7 days or less.Participants were randomized to receive fluvoxamine, 50 mg twice daily on day 1 followed by 100 mg twice daily for 12 additional days (n = 601), or placebo (n = 607).The primary outcome was time to sustained recovery (defined as at least 3 consecutive days without symptoms). Secondary outcomes included time to death; time to hospitalization or death; a composite of hospitalization, urgent care visit, emergency department visit, or death; COVID-19 clinical progression scale score; and difference in mean time unwell. Follow-up occurred through day 28.Among 1208 participants who were randomized and received the study drug, the median (IQR) age was 50 (40-60) years, 65.8% were women, 45.5% identified as Hispanic/Latino, and 76.8% reported receiving at least 2 doses of a SARS-CoV-2 vaccine. Among 589 participants who received fluvoxamine and 586 who received placebo included in the primary analysis, differences in time to sustained recovery were not observed (adjusted hazard ratio [HR], 0.99 [95% credible interval, 0.89-1.09]; P for efficacy = .40]). Additionally, unadjusted median time to sustained recovery was 10 (95% CI, 10-11) days in both the intervention and placebo groups. No deaths were reported. Thirty-five participants reported health care use events (a priori defined as death, hospitalization, or emergency department/urgent care visit): 14 in the fluvoxamine group compared with 21 in the placebo group (HR, 0.69 [95% credible interval, 0.27-1.21]; P for efficacy = .86) There were 7 serious adverse events in 6 participants (2 with fluvoxamine and 4 with placebo) but no deaths.Among outpatients with mild to moderate COVID-19, treatment with fluvoxamine does not reduce duration of COVID-19 Identifier: NCT04885530.

    View details for DOI 10.1001/jama.2023.23363

    View details for PubMedID 37976072

  • Use of biomarkers to individualize antimicrobial therapy duration: a narrative review. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases Scott, J., Deresinski, S. 2022


    BACKGROUND: Reducing the overuse of antimicrobials is imperative for the sake of minimizing antimicrobial-associated adverse effects, optimizing resource utilization, and curtailing the rise in multidrug-resistant organisms. Biomarkers reflect host responses to infection and may assist with minimizing unnecessary antimicrobial usage.OBJECTIVES: To review the literature pertaining to the performance of biomarkers specifically used to guide the duration of antimicrobial therapy (AMT).SOURCES: Randomized controlled trials (RCTs), observational studies, and meta-analyses assessing biomarker-guided approaches to AMT decision-making and their impact on duration of therapy were reviewed.CONTENT: Several RCTs and real-world observational studies have shown that a procalcitonin (PCT)-guided strategy can help clinicians individualize the duration of AMT, particularly for non-critically ill patients hospitalized with suspected respiratory tract infections when using a PCT cutoff of <0.25 mug/L and critically ill patients with respiratory tract infections or undifferentiated sepsis when using a PCT cutoff of <0.5 mug/L or ≥80% decline in peak level. C-reactive protein (CRP) is a non-specific marker of inflammation that may also assist with earlier discontinuation of AMT, though data are limited. Hematological biomarkers are prone to variance between individuals and are often influenced by medications and non-infectious conditions, making them less reliable for the purposes of AMT decision-making. Novel biomarkers, such as multi-protein signatures and host gene expression tests, have shown promise as tools to better differentiate between bacterial and non-bacterial infections; clinical studies are needed to determine whether they can be used to help optimize the duration of AMT.IMPLICATIONS: Studies have demonstrated that PCT, when utilized appropriately, can help guide clinicians to individualize and often reduce the duration of AMT, especially for patients hospitalized with respiratory tract infections and intensive care unit (ICU) patients with suspected respiratory tract infections or sepsis. The impact of utilizing other biomarkers is less clear and requires further study.

    View details for DOI 10.1016/j.cmi.2022.08.026

    View details for PubMedID 36096429

  • Covid-19 vaccines, immunity, and boosters. BMJ (Clinical research ed.) Richterman, A., Scott, J., Cevik, M. 1800; 375: n3105

    View details for DOI 10.1136/bmj.n3105

    View details for PubMedID 34930779

  • Covid-19 vaccination: evidence of waning immunity is overstated British Medical Journal Scott, J., Richterman, A., Cevik, M. 2021

    View details for DOI 10.1136/bmj.n2320

  • Characteristics and outcomes of coronavirus disease patients under nonsurge conditions, northern California, USA, March–April 2020 Emerging Infectious Diseases Ferguson, J., Rosser, J., Quintero, O., Scott, J., Subramanian, A., Gumma, M., Rogers, A., Kappagoda, S. 2020


    Limited data are available on the clinical presentation and outcomes of coronavirus disease (COVID-19) patients in the United States hospitalized under normal-caseload or nonsurge conditions. We retrospectively studied 72 consecutive adult patients hospitalized with COVID-19 in 2 hospitals in the San Francisco Bay area, California, USA, during March 13-April 11, 2020. The death rate for all hospitalized COVID-19 patients was 8.3%, and median length of hospitalization was 7.5 days. Of the 21 (29% of total) intensive care unit patients, 3 (14.3% died); median length of intensive care unit stay was 12 days. Of the 72 patients, 43 (59.7%) had underlying cardiovascular disease and 19 (26.4%) had underlying pulmonary disease. In this study, death rates were lower than those reported from regions of the United States experiencing a high volume of COVID-19 patients.

    View details for DOI 10.3201/eid2608.201776

  • Recurrent Multifocal Mycoplasma orale Infection in an Immunocompromised Patient: A Case Report and Review. Case reports in infectious diseases Ketchersid, J., Scott, J., Lew, T., Banaei, N., Kappagoda, S. 2020; 2020: 8852115


    A young woman with mixed connective tissue disease complicated by erosive arthritis, secondary hypogammaglobulinemia due to rituximab, and a history of many infectious complications developed multiple nonhealing wounds, polyarticular joint pain, and leukocytosis. Radiographic studies demonstrated multiple scattered areas of osteomyelitis and complex abscesses. Purulent fluid drained from multiple sites did not yield a microbiologic diagnosis by standard culture technique, but Mycoplasma orale was ultimately identified using 16S ribosomal RNA gene amplification and sequencing. We describe this unique case and review the literature.

    View details for DOI 10.1155/2020/8852115

    View details for PubMedID 32850161

  • Treatment optimization for HIV/HCV co-infected patients. Therapeutic advances in infectious disease Scott, J. A., Chew, K. W. 2017; 4 (1): 18-36


    Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections affect millions of persons around the globe and cause profound morbidity and mortality. A major intersection exists between these two epidemics, with HCV infection being more common in persons with HIV than in the general population, largely due to shared routes of transmission. HCV co-infection increases risk for liver- and non-liver-related morbidity and mortality, making HCV treatment a priority in HIV co-infected persons, but the treatment of HCV in co-infected patients has been daunting for multiple reasons. Until recently, HCV treatment has frequently been deferred due to the low rates of cure, significant adverse effects, burdensome duration of therapy and drug-drug interactions with HIV antiretroviral medications. Untreated HCV has resulted in significant health consequences for the millions of those infected and has led to multiple downstream impacts on our healthcare systems around the world. The development of a remarkable number of new HCV direct-acting agents (DAAs) that are significantly more efficacious and tolerable than the previous interferon-based regimens has transformed this important field of medicine, with the potential to dramatically reduce the burden of infection and improve health outcomes in this population. This review will summarize the epidemiology and clinical impact of HIV/HCV co-infection and current approaches to the treatment of HCV in HIV/HCV co-infected patients.

    View details for DOI 10.1177/2049936116681279

    View details for PubMedID 28357062

  • Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome in Older Adults. Clinics in geriatric medicine Scott, J., Goetz, M. B. 2016; 32 (3): 571-83


    Improved survival with combination antiretroviral therapy has led to a dramatic increase in the number of human immunodeficiency virus (HIV)-infected individuals 50 years of age or older such that by 2020 more than 50% of HIV-infected persons in the United States will be above this age. Recent studies confirm that antiretroviral therapy should be offered to all HIV-infected patients regardless of age, symptoms, CD4+ cell count, or HIV viral load. However, when compared with HIV-uninfected populations, even with suppression of measurable HIV replication, older individuals are at greater risk for cardiovascular disease, malignancies, liver disease, and other comorbidities.

    View details for DOI 10.1016/j.cger.2016.02.010

    View details for PubMedID 27394024

  • Maternal decidual macrophages inhibit NK cell killing of invasive cytotrophoblasts during human pregnancy. Biology of reproduction Co, E. C., Gormley, M., Kapidzic, M., Rosen, D. B., Scott, M. A., Stolp, H. A., McMaster, M., Lanier, L. L., Bárcena, A., Fisher, S. J. 2013; 88 (6): 155


    Human pregnancy is an immunological paradox. Semiallogeneic (fetal) placental cells (extravillous cytotrophoblasts [CTBs]) invade the uterine lining (decidua), which contains a unique decidual natural killer (dNK) cell population, identified by the cell surface phenotype CD56(bright) CD16(-) CD3(-) and CD14(+) CD206(+) macrophages (dMac). Previous reports suggested that human dNK cells are not a threat to the fetoplacental unit because they are anergic. In contrast, here we showed that purified and exogenously stimulated dNK cells are capable killers of cellular targets, including semiallogeneic CTBs. However, dMacs in the decidual leukocyte (DL) population restrained dNK killing through a transforming growth factor beta1 (TGF-beta1)-dependent mechanism. Our findings support a new model whereby dNK cells, capable of killing CTBs, are prevented from doing so by neighboring macrophages, thus protecting the fetal cells from NK cell attack. We speculate that this mechanism would inhibit dNK cell-mediated killing, even under conditions where high levels of cytokines may stimulate dNK cells, which could pose a threat to the developing placenta.

    View details for DOI 10.1095/biolreprod.112.099465

    View details for PubMedID 23553431

    View details for PubMedCentralID PMC4070869