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Influenza, RSV and SARS-CoV-2 surveillance in rural Zambia from 2019-2021

Morris Sianyinda • May 16, 2023

Influenza, RSV and SARS-CoV-2 surveillance in rural Zambia from 2019-2021

 Morris Sianyinda¹ Edgar Simulundu1, Mutinta Hamahuwa1, Pamela Sinywimaanzi1, Mathias Muleka1, Passwell Munachoonga1, Hellen Matakala1, Juliet Morales2, Katherine Fenstermacher3, Richard Rothman3, Andrew Pekosz4, Mwaka Monze5, Phil Thuma1, Catherine Sutcliffe2,6
1Macha Research Trust, Zambia; 2Dept International Health, Johns Hopkins Bloomberg School of Public Health (JHBSPH); 3Dept Emergency Medicine, Johns Hopkins School of Medicine; 4Dept Molecular Microbiology and Immunology, JHBSPH; 5University Teaching Hospital, Zambia; 6Dept Epidemiology, JHBSPH,

Background
•    Respiratory infections are a major cause of morbidity and mortality globally but are relatively understudied in sub-Saharan Africa, particularly in rural areas
•    Surveillance for respiratory viruses, including influenza A, influenza B, and respiratory syncytial virus (RSV) was initiated in December 2018 in Macha, Zambia as part of the Johns Hopkins Center for Excellence in Influenza Research and Surveillance (CEIRS)
•    In 2020, SARS-CoV-2 emerged and caused a global pandemic, with mitigation measures disrupting circulation of respiratory pathogens
The ongoing surveillance in Macha provided the opportunity to understand the burden of respiratory pathogens before
Objectives
1.    To assess the burden of influenza A virus, influenza B virus, RSV and SARS COV-2 in Macha viruses in Macha before and during the COVID-19 pandemic before and during the COVID-19 pandemic
2.    To assess the burden of other respiratory
Materials and Methods
AREA VIEW OF MACHA

MACHA HOSPITAL

Setting: Macha is located in Southern Province, Zambia and is a rural area (population density: 25-45 residents per km2).

•       Surveillance:

•       Respiratory surveillance was initiated in Dec 2018 at Macha Hospital

•       All patients attending the outpatient clinic were screened for influenza-like illness (ILI; fever + cough/sore throat)

•       An age-stratified sample of patients with ILI were enrolled each week

•       A nasopharyngeal swab was collected

•       Laboratory testing:

•       Swabs were tested onsite for RSV, influenza A/B virus, and SARS-CoV-2 using the GeneXpert platform

•       Swabs were shipped to Johns Hopkins and tested for rhinovirus/enterovirus, parainfluenza virus, metapneumovirus, human coronaviruses (non-SARS-CoV-2), and adenovirus using the BioFire or Genmark ePlex respiratory panel

•       Analysis: Monthly and annual pathogen prevalence among outpatients with ILI was estimated using survey sampling weights for 2019, 2020, and 2021

Results

•       The number of OPD visits was similar in 2019 and 2020 but decreased in 2021 due to a decrease in visits in the middle of the year (Fig 1A)

•       The proportion of OPD patients with ILI decreased from 16.9% in 2019 to 6.9% in 2021 (Fig 1B)

Figure 1: Outpatient visits and influenza-like-illness, 2019-2021



  • Patients with ILI were enrolled: 555 in 2019; 463 in 2020; and 417 in 2021
  • In 2019, influenza and RSV were detected in distinct parts of the year: RSV in the beginning; influenza A virus in the middle; and influenza B virus in the later part of the year
  •  In 2020,no cases of influenza virus and only a few RSV cases were detected
  •   In 2021 the viruses returned and at a similar level and timing to 2019
  •   The first SARS-CoV-2 infection in Macha was identified in December 2020, and SARS-CoV-2 was detected at low levels throughout 2021    

Figure 2: Prevalence of influenza, RSV, and SARS-CoV-2 among outpatients with influenza-like illness, 2019-2021

 graph

  • The prevalence of influenza virus and RSV was highest among children (Fig 3A-C)
  • The prevalence of SARS-CoV-2 was highest among adults (Fig 3D)

 

Figure 3: Age-stratified pathogen, 2019-2021prevalence among outpatients with influenza-like illness

Other respiratory pathogens were detected throughout 2019-2021 with no distinct patterns (Fig 4)

Figure 4: Prevalence of other respiratory viruses among outpatients with influenza-like illness, 2019-2021

CONCLUSION

  • In summary, this area has a significant burden of respiratory infections
  • COVID-19 mitigation measures reduced the burden of influenza and RSV in 2020
  • Once initial measures were eased in late 2020, they returned to prior levels in 2021 and co-circulated with SARS-CoV-2

Acknowledgements

This work was supported by NIH contract HHSN272201400007C.

We would like to thank the Macha Research Trust, Johns Hopkins University, University Teaching Hospital and Macha Hospital teams for their assistance with the study.

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