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Volume 28, Supplement—December 2022
SUPPLEMENT ISSUE
Surveillance

Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020–2021

David C. Shih1, Rachel Silver1Comments to Author , Olga L. Henao, Aynalem Alemu, Allan Audi, Godfrey Bigogo, Josh M. Colston, Elijah P. Edu-Quansah, Timothy A. Erickson, Andargachew Gashu, G. Burgess Gbelee, Sarah M. Gunter, Margaret N. Kosek, Gorbee G. Logan, Joy M. Mackey, Adrianna Maliga, Russell Manzanero, Gerhaldine Morazan, Francis Morey, Flor M. Munoz, Kristy O. Murray, Thelma V. Nelson, Maribel Paredes Olortegui, Pablo Penataro Yori, Shannon E. Ronca, Francesca Schiaffino, Adamu Tayachew, Musse Tedasse, Mesfin Wossen, Denise R. Allen, Pawan Angra, Amanda Balish, Madeline Farron, Marta Guerra, Amy Herman-Roloff, Victoria J. Hicks, Elizabeth Hunsperger, Lilit Kazazian, Matt Mikoleit, Peninah Munyua, Patrick K. Munywoki, Angella Sandra Namwase, Clayton O. Onyango, Michael Park, Leonard F. Peruski, David E. Sugerman, Emily Zielinski Gutierrez, and Adam L. Cohen
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (D.C. Shih, R. Silver, O.L. Henao, D.R. Allen, P. Angra, A. Balish, M. Farron, M. Guerra, V.J. Hicks, L. Kazazian, M. Mikoleit, A.S. Namwase, M. Park, L.F. Peruski, D.E. Sugerman, A.L. Cohen); Ethiopian Public Health Institute, Addis Ababa, Ethiopia (A. Alemu, A. Gashu, A. Tayachew, M. Tedasse, M. Wossen); Kenya Medical Research Institute, Kisumu, Kenya (A. Audi, G. Bigogo); University of Virginia, Charlottesville, Virginia, USA (J.M. Colston, M.N. Kosek, P. Penataro Yori, F. Schiaffino); African Field Epidemiology Network, Monrovia, Liberia (E.P. Edu-Quansah); Texas Children’s Hospital, Houston, Texas, USA (T.A. Erickson, S.M. Gunter, A. Maliga, F.M. Munoz, K.O. Murray, S.E. Ronca); Baylor College of Medicine, Houston (T.A. Erickson, S.M. Gunter, J.M. Mackey, A. Maliga, F.M. Munoz, K.O. Murray, S.E. Ronca); National Public Health Institute of Liberia, Monrovia (G.B. Gbelee, T.V. Nelson); Ministry of Health, Monrovia (G.G. Logan); Ministry of Health and Wellness, Belmopan, Belize (R. Manzanero, G. Morazan, F. Morey); Asociación Benéfica Prisma, Iquitos, Peru (M. Paredes Olortegui); US Centers for Disease Control and Prevention, Nairobi, Kenya (A. Herman-Roloff, E. Hunsperger, P. Munyua, P.K. Munywoki); US Centers for Disease Control and Prevention, Kisumu, Kenya (C.O. Onyango); US Centers for Disease Control and Prevention, Guatemala City, Guatemala (E. Zielinski Gutierrez)

Main Article

Table 1

Summary of methods used for COVID-19 incorporation into acute febrile illness surveillance systems in Belize, Kenya, Ethiopia, Peru, and Liberia, 2020–2021*

Category Belize Kenya† Ethiopia Peru Liberia
Surveillance start dates
AFI 2020 Jan 2006 Jan 2021 Feb 2021 Feb 2018 Dec
COVID-19 integration
 2020 Mar
2020 May
2021 Feb
2021 Feb
2021 Apr
No. sites
 11
 2
 4‡
 5
 2
Inclusion criteria
Age >60 d All ages >5 y >10 y >2 y (AFI), >5 y (COVID-19)
Documented body temperature or history of fever Axillary, oral, or rectal T >38°C or new fever <7 d before exam Axillary T >38°C and <5 d of acute fever Axillary, oral, or rectal T >38°C and fever for 2–14 d before exam Axillary, oral, or rectal T >38°C and new fever <14 d before exam Axillary, oral, or rectal T >37.5°C or fever <7 d before exam
Afebrile patients
 >2 respiratory symptoms and high risk for or suspected SARS-CoV-2 infection or >2 GI symptoms
 None
 None
 None
 None
Exclusion criteria
Surveillance protocol procedures Previously enrolled within the past 7 d or declined follow up for disease outcomes Previously enrolled Previously enrolled None Previously enrolled within past year
Chief complaint on arrival or during hospitalization
 Injury, trauma, or known cause of fever; returning with known cause of fever
 Injury or trauma
 Injury, trauma, focal infection, localizing symptoms, obstetric- or surgery-related cases
 Focal infection or fever onset >24 h after hospitalization (inpatients only)
 Injury, trauma, focal infection, returning with known cause of fever
Data use methods§
Collection REDCap and paper-based form Windows-based platform Paper-based form REDCap Paper-based form
Management
 REDCap
 Microsoft SQL servers
 Microsoft Excel
 Microsoft Access
 Epi Info
Specimens
Blood, NP/OP swabs, feces, eschar swabs
 Blood, NP/OP swabs;¶ urine
 Blood, NP/OP swabs¶
 Blood, nasal MT swabs, saliva
 Blood, NP swabs¶
COVID-19 testing methods Singleplex RT-PCR,# BioFire FilmArray respiratory panel** RT-PCR# Singleplex PCR# CDC COVID-19 assay#†† TaqPath COVID-19 CE-IVD RT-PCR#‡‡

*Data are sorted by COVID-19 integration month. AFI, acute febrile illness; GI, gastrointestinal; MT, mid-turbinate; NP, nasopharyngeal; OP, oropharyngeal; RT-PCR, reverse transcription PCR; T, temperature. †Data are from Kenya’s population-based infectious disease surveillance sites with survey-defined catchment areas. ‡Of 5 designated sites, only 4 were operational because of security issues. §REDCap (https://www.project-redcap.org); Microsoft Excel, Access, SQL Server, and Windows-based platform (https://www.microsoft.com); Epi Info (https://www.cdc.gov/epiinfo). ¶Additional specimens collected after COVID-19 surveillance integration into regular AFI surveillance activities. #Tests performed specifically for SARS-CoV-2. **BioFire (https://www.biofiredx.com). ††2019 nCoV Real-Time RT-PCR Diagnostic Panel, Centers for Disease Control and Prevention (https://www.cdc.gov/coronavirus/2019-ncov/lab/testing.html). ‡‡TaqPath COVID-19 CE-IVD RT-PCR kit, Thermo Fisher Scientific (https://www.thermofisher.com).

Main Article

1These first authors contributed equally to this article.

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