Guidance: Strategies for STI Screening and Treatment During COVID-19

Guidance: Strategies for STI Screening and Treatment During COVID-19

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Lead authors: Daniela DiMarco, MD, MPH,1 and Marguerite Urban, MD, with the Medical Care Criteria Committee, November 2020

The COVID-19 pandemic has caused many disruptions in routine and preventive sexual health services traditionally provided via in-person care. Enhanced cleaning and expanded use of personal protective equipment, social distancing, and stay-at-home orders are just a few changes that have become the “new normal.” Public health clinics, the foundation of sexual health services in many areas of New York State (NYS), have also been affected by reassignment of clinical and nonclinical staff to COVID-19 work. Some clinics that remain open have implemented telehealth services and “priority visits” for in-person care to continue providing sexual health care to the patients at highest risk. At the height of the pandemic, many preventive services were placed on hold, including vaccine visits and screening for sexually transmitted infections (STIs).

Rapid Antiretroviral Therapy (ART) Initiation During COVID-19

Purpose of This Guideline

Alarming increases in STIs: The NYS Department of Health (NYSDOH) AIDS Institute (AI) has released preliminary analysis of data collected from January to March 2020 revealing an alarming increase in cases of gonorrhea prior to pandemic-related reductions in healthcare services across the state [NYSDOH AI 2020]. Compared with the same time period in 2019, cases of gonorrhea in NYS, excluding New York City (NYC), increased by 34%; in the Capital District and Monroe County cases increased by 68% and 75%, respectively [NYSDOH AI 2020]. It is expected that when visit and testing volumes return to normal, incidence of STIs such as gonorrhea, syphilis, and chlamydia will increase overall.

To help combat rising numbers and move toward ending the HIV and STI epidemics, innovative prevention and treatment strategies must be implemented and carried on throughout the duration of the COVID-19 pandemic. The purpose of this guidance is to provide clinicians in NYS with best practices and resources for provision of STI screening and treatment during times when in-person care is disrupted or otherwise unavailable. This guidance provides resources to aid care providers and clinics in creating flexible care delivery models that can be modified as COVID-19 prevalence and restrictions shift over time. Of note, home collection for STI testing may be continued beyond the current pandemic to increase reach statewide and help overcome barriers, including access and stigma.

Telehealth vs. In-Person Visits

There are many possible permutations of care models that can be customized based on local COVID-19 prevalence and associated local restrictions, clinic capacity, and patient needs. Local data and policies can guide clinicians in determining whether care should be delivered through 100% telemedicine, 100% in-person visits, or through a hybrid approach. When visits are limited, priorities for in-person care will have to be identified; such priorities may include STI symptoms that do not fit a predefined syndrome, sexual assault, abdominal pain or pelvic inflammatory disease, HIV contact, syphilis or contact with syphilis, and pregnancy. In-person preventive care, such as STI screening and immunizations, may be deferred. Triage can be performed by telephone using a predetermined algorithm to ensure the best pathway for the patient. Several resources exist to assist clinicians with operationalizing sexual health services via telemedicine, some of which are outlined in Box 1: Resources for Telemedicine and STD Clinic Operations During COVID-19, below, and the National Coalition of STD Directors (NCSD) has an extensive catalog of resources specific to STD clinics during COVID-19. The NYSDOH AI Clinical Education Initiative (CEI) Sexual Health Center of Excellence is available to assist with development of triage algorithms tailored to specific practice locations; visit the CEI website for more information or to request training or technical assistance.

Box 1: Resources for Telemedicine and STD Clinic Operations During COVID-19
National Coalition of STD Directors STD Clinic Resources (see “Telemedicine & Express Visits” and “Clinic Operations”)
U.S. Centers for Disease Control and Prevention Dear Colleague Letter (4/6/2020): Providing effective care and prevention when facility-based services and in-person patient-clinician contact are limited
Kaiser Family Foundation Telemedicine in Sexual and Reproductive Health
New York City Department of Health and Mental Hygiene
New York State Department of Health AIDS Institute, CEI Strategies for Provision of Telemedicine Services for HIV, STIs, HCV, and Drug User Health in NYS during the COVID-19 Pandemic

Recent regulatory changes have expanded the video options approved for telemedicine use, and some insurance companies, including the Centers for Medicare and Medicaid Services and some private insurers, have adjusted reimbursement rates for virtual visits. See U.S. Department of Health and Human Services Telehealth: Delivering Care Safely During COVID-19 for information about telehealth-related regulatory changes related to COVID-19. The NYSDOH has also released Guidance and FAQs regarding telehealth for Medicaid providers.

Screening and Diagnostic Testing

Comprehensive STI testing generally includes collection of several different specimens (urine, blood, and genital/extragenital swabs) and testing for gonorrhea, chlamydia, syphilis, HIV, and possibly others, such as trichomoniasis, hepatitis C virus, and hepatitis B virus. At present, there are no in-home STI tests that are approved by the U.S. Food and Drug Administration, although some laboratories have been validated to process home-collected specimens. In-home collection of self-obtained specimens for laboratory processing is an option with limited availability in NYS. Self-collection of specimens entails having patients independently collect their own rectal or vaginal swab, urine sample, or finger stick for a dried blood spot. Self-collection can be performed in the clinic (e.g., during an express visit) or at home with an in-home collection kit obtained by mail or picked up from a clinic.

Box 2: Selected Resources for Laboratory Testing

There are several instructional handouts, posters, and videos available to demonstrate how to self-obtain specimens (oropharyngeal, vaginal, rectal, and urine) for STI testing (see Box 3, below). Some test manufacturers also have instructional handouts for self-collection available. For swabs from vaginal, rectal, or oropharyngeal sites, a certain contact time is needed for optimal performance of nucleic acid amplification testing (NAAT); the package insert for the specific test being used is a good place to find this information. When a urine specimen is to be sent for STI testing, the timing, method of collection, and required specimen volume should be verified in advance with the laboratory that will perform the test. First morning urine sample, not clean-catch, less than 24 hours old, and specific volume are among the collection specifications that a laboratory may require, along with specifications regarding transport methods.

Box 3: Resources for Self-Collection of Specimens and Home Test Kits for STI Testing
National Coalition of STD Directors
California Prevention Training Center Self-Swab Instructional Poster for Rectal, Throat, and Vaginal Specimens
San Francisco City Clinic Patient Instructions for Self-Collected Specimens in handout and video form for urine, vaginal, rectal, and pharyngeal samples (see screening drop-down; handouts in English and Spanish)
Trillium Health testing@home Mail-in Program (for New York State residents only)

Screening: Screening can be performed expediently with an express clinic visit when in-person care is possible; patients can self-collect specimens using validated protocols to minimize face-to-face contact time between patient and care provider. There are mail-in commercial screening kits that offer bundled STI/HIV/syphilis/viral hepatitis testing through combinations of urine, swabs, and dried blood spot specimens, although the cost is generally $100 to $200. The Kaiser Family Foundation provides an up-to-date list of such kits, and availability can be filtered by state. Currently, there is one clinical organization in NYS providing mail-in STI testing statewide at no cost to patients: the Trillium Health testing@home program.

Clinicians can contact their laboratory partners to determine whether they accept (and are validated for) home-collected specimens and may be able to design their own test kits to distribute to patients; test kits would need to be picked up by or mailed to the patient in this scenario. Resources from NCSD can assist clinicians with designing an STI home-collection screening program and kit (see Box 3: Resources for Self-Collection of Specimens and Home Test Kits for STI Testing, above). Of note, in NYS, there are no approved in-home collection options for screening tests for syphilis, viral hepatitis, and 4th-generation HIV testing, but a patient could have their blood drawn for these tests when dropping off other home-collected specimens at their local laboratory. This requires leaving the home but minimizes contact with the healthcare system.

For in-home rapid HIV testing, the NYSDOH and the NYC Department of Health and Mental Hygiene (DOHMH) have HIV home test giveaway programs in partnership with OraSure (for more information, see NYS Home Test Giveaway or NYC home test giveaway). The in-home rapid HIV test is also available for purchase commercially for about $40. Although this test is not ideal for individuals taking HIV pre-exposure prophylaxis, because it does not detect early infection, it can be considered if there are no other testing options [CDC 2020a].

Diagnostic testing: In an April 2020 Dear Colleague Letter, the U.S. Centers for Disease Control and Prevention (CDC) recommended a syndromic management approach for provision of STI care via telemedicine during the COVID-19 pandemic [CDC 2020b]. When using this strategy to direct treatment, diagnostic testing can be reserved for individuals with refractory symptoms despite treatment. In that scenario, diagnostic testing should be performed in person along with an examination if possible. As an alternative, STI testing can be accomplished with in-home self-obtained samples, as discussed above. When 4th-generation HIV, syphilis, or viral hepatitis testing is needed, patients may proceed directly to the laboratory with a care provider order already in place. Additionally, some agencies offer in-home collection of blood and urine specimens for laboratory-processed tests.

In the case of a concomitant HIV diagnosis, please see Guidance: Rapid Antiretroviral Therapy (ART) Initiation During COVID-19 (NYSDOH AI).

Treatment: Syndromic Management and Expedited Partner Therapy

Both the CDC and the NYC DOHMH have provided specific guidance for management of STIs based on a patient’s presenting STI syndrome, such as urethritis or vaginitis [CDC 2020b; NYC Health 2020b, 2020a]. For gonorrhea and syphilis, in-person treatment with a parenteral antibiotic-containing regimen is preferred over oral medications because of concerns about antibiotic resistance and treatment efficacy [Workowski, et al. 2015]. When in-person treatment cannot be provided, the CDC and the NYC DOHMH guidance recommend use of oral medications that can be prescribed electronically to the patient’s pharmacy or picked up at the clinic. See Box 4: Resources for Syndromic Management of STIs During COVID-19 Care Disruptions for links to these treatment tables.

Expedited partner therapy (EPT) should be offered to patients with a diagnosis of chlamydia, trichomoniasis, or gonorrhea [NYS Senate]. EPT is not recommended for partner management for patients with syphilis. For more information on EPT, please see the following:

Updates to NYS regulations on EPT based on the expansion of the 2019 law are anticipated soon. Self-reported asymptomatic contacts can be treated empirically via telehealth with electronic prescription as well.

Box 4: Resources for Syndromic Management of STIs During COVID-19 Care Disruptions
U.S. Centers for Disease Control and Prevention
New York City Department of Health and Mental Hygiene


The U.S. Preventive Services Task Force recommends that behavioral counseling for STI risk reduction, even if brief, should be provided to individuals seeking care [USPSTF, et al. 2020]. This Grade B recommendation applies to all sexually active adolescents and adults with increased STI risk. Counseling can be provided virtually in-person services must be minimized (see the NYSDOH AI guidelines on STI care for more information on syphilis, gonorrhea and chlamydia, and human papillomavirus prevention). Pre-exposure prophylaxis (PrEP) should be offered to individuals with ongoing risk of exposure to HIV (see the NYSDOH AI guideline PrEP to Prevent HIV and Promote Sexual Health).


Patients receiving syndromic management or alternative treatment regimens should be reminded to contact their care provider if symptoms persist or if they have any difficulty obtaining prescribed medications. Clinics should follow up by phone with patients who receive syndromic treatment to determine if further evaluation is needed when symptoms persist. Consider an in-person visit, testing, or both for patients in whom treatment fails. Patients should be encouraged to seek routine screening when it becomes safe to do so.

1University of Rochester School of Medicine and Dentistry, Infectious Diseases Division


CDC. PrEP during COVID-19: Dear colleague May 15, 2012. 2020a May 15. [accessed 2020 Oct 6]

CDC. STD treatment options: Dear colleague April 6, 2020. 2020b Apr 6. [accessed 2020 Oct 6]

NYC Health. Presumptive oral treatment of uncomplicated anogenital gonorrhea infection in the absence of ready access to injectable treatment during the COVID-19 crisis, New York City, 2020. 2020a Apr. [accessed 2020 Oct 6]

NYC Health. Syndromic management of anogenital discharges and ulcers during the COVID-19 outbreak, New York City, 2020. 2020b Apr 19. [accessed 2020 Oct 6]

NYS Senate. New York State Public Health Law Article 23: Control of Sexually Transmitted Diseases. [accessed 2020 Oct 6]

NYSDOH AI. Health advisory: Gonorrhea increasing in Monroe County and counties within the Capital District Region. 2020 Jul 14. [accessed 2020 Oct 6]

USPSTF, Krist AH, Davidson KW, et al. Behavioral counseling interventions to prevent sexually transmitted infections: US Preventive Services Task Force recommendation statement. JAMA 2020;324(7):674-681. [PMID: 32809008]

Workowski KA, Bolan GA, CDC. Sexually transmitted diseases treatment guidelines, 2015. MMWR Recomm Rep 2015;64(RR-03):1-137. [PMID: 26042815]