Respiratory Disease Surveillance in the Middle East and Latin America during the COVID-19 Pandemic, 2020-2022

Abstract

Characterizing the epidemiology of circulating respiratory pathogens during the COVID-19 pandemic could clarify the burden of acute respiratory infections and monitor outbreaks of public health and military relevance. The US Department of Defense supported 2 regions for influenza-like illness and severe acute respiratory infections surveillance, one in the Middle East through US Naval Medical Research Unit EURAFCENT, and another in Latin America through US Naval Medical Research Unit SOUTH. During 2020‒2022, coinciding with the COVID-19 pandemic, we collected a total of 16,146 nasopharyngeal and oropharyngeal swab samples from sentinel sites in Jordan (n = 11,305) and Latin America (n = 4,841). Samples were tested for SARS-CoV-2, influenza, and other respiratory pathogens. SARS-CoV-2 was the most frequently detected pathogen during 2020; other respiratory pathogens had distinct temporal and frequency distributions according to geographic location. Our findings support the need for continued sentinel surveillance as a vital tool for assessing the burden of respiratory diseases globally.

Keywords: COVID-19; Latin America; Middle East; SARS-CoV-2; influenza; respiratory infections; severe acute respiratory syndrome coronavirus 2; surveillance; viruses; zoonoses.

Figure 1

Overall relative frequency distribution of respiratory pathogens commonly tested as part of respiratory disease surveillance in the Middle East (Jordan) and Latin America during the COVID-19 pandemic, 2020–2022. Percentages were calculated relative to the total number of common targets tested by both Fast-Track Diagnostics 33 (FTD-33; Siemens Healthineers, https://www.siemens-healthineers.com) and BioFire FilmArray Respiratory Panel 2.1 (RP 2.1; bioMérieux, https://www.biomerieux.com) assays. Samples include 3,738 from Jordan and 4,4,28 from Latin America. Others includes Chlamydia pneumoniae (0.44% in Jordan and 0.07% in Latin America), Bordetella pertussis (0.1% in Jordan and 0.05% in Latin America), and Mycoplasma pneumoniae (0.17% in Jordan and 0.02% in Latin America). AdV, adenovirus; MPV, metapneumovirus; PIV, parainfluenza virus; RSV, respiratory syncytial virus; RV/EV, rhinovirus/enterovirus.

Figure 2

Percent positivity of different respiratory pathogens associated with ILI in detected as part of respiratory disease surveillance in the Middle East (Jordan, A) and Latin America (B) during the COVID-19 pandemic, 2020–2022. In Jordan, testing ILI cases with Fast-Track Diagnostics 33 (FTD-33; Siemens Healthineers, https://www.siemens-healthineers.com) started in February 2021. During October 2020–January 2021, ILI cases were tested only for influenza and SARS- CoV-2. Others includes Chlamydia pneumoniae, Bordetella pertussis, and Mycoplasma pneumoniae. ILI, influenza-like illness; RSV, respiratory syncytial virus; RV/EV, rhinovirus/enterovirus.

Figure 3

Percent positivity of different respiratory pathogens associated with SARI detected as part of respiratory disease surveillance in the Middle East (Jordan, A) and Latin America (B) during the COVID-19 pandemic, 2020–2022. Others includes Chlamydia pneumoniae, Bordetella pertussis, and Mycoplasma pneumoniae. ILI, influenza-like illness; RSV, respiratory syncytial virus; RV/EV, rhinovirus/enterovirus; SARI, severe acute respiratory infection.