Effects of COVID-19 on the laboratory turn-around time of vaccine-preventable disease surveillance: the case of measles in South Sudan

The impact of the COVID-19 pandemic on measles surveillance in the World Health Organisation African Region, 2020

Introduction

following the declaration of the COVID-19 pandemic, many countries imposed restrictions on public gatherings, health workers were repurposed for COVID-19 response, and public demand for preventive health services declined due to fear of getting COVID-19 in health care settings. These factors led to the disruption in health service delivery, including childhood immunization, in the first months of the pandemic. Measles surveillance supported with laboratory confirmation, is implemented in the African Region as part of the strategies towards attaining measles elimination. World Health Organisation developed guidelines to assist countries to continue to safely provide essential health services including immunization and the surveillance of vaccine preventable diseases during the pandemic.

Methods

we analysed the measles case-based surveillance and laboratory databases for the years 2014 to 2020, to determine the impact of the COVID-19 pandemic on measles surveillance, comparing the performance in 2020 against the preceding years.

Results

the weekly reporting of suspected measles cases declined starting in April 2020. Twelve countries had more than 50% decline in both the number of reported cases as well as in the number of specimens collected in 2020, as compared to the mean for the years 2014-2018. In 2020, only 30% of the specimens from suspected measles cases arrived at the national laboratory within 3 days of collection. At Regional level, 86% of the districts reported suspected measles cases in 2020, while the non-measles febrile rash illness rate was 2.1 per 100,000 population, which was the lowest rate documented since 2014. Only 11 countries met the targets for the two principal surveillance performance indicators in 2020 as compared to an average of 21 countries in the years 2014-2019.

Conclusion

the overall quality of measles surveillance has declined during the COVID pandemic in many countries. Countries should implement immediate and proactive measures to revitalise active surveillance for measles and monitor the quality of surveillance. We recommend that countries consider implementing specimen collection and testing methods that can facilitate timely confirmation of suspected measles cases in remote communities and areas with transportation challenges.

SARS-CoV-2 direct real-time polymerase chain reaction testing in laboratories with shortage challenges

Aim: In our study, we propose the use of direct real-time polymerase chain reaction (RT-PCR), this test does not require extraction or a preheating step, which saves a lot of cost, labor, processing time and provides a solution for supply shortage. Materials & methods: We assayed 185 nasopharyngeal samples stored in viral transport media. The indirect method was done with RNA extraction step, and the direct RT-PCR was done without an extraction step, both assays were evaluated on a commercially validated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kit targeting E gene. Results: Our assay showed a sensitivity of 79%, a specificity of 100% and the agreement between methods was 72%. Conclusion: Overall, this simple direct RT-PCR approach can be utilized as a qualitative diagnostic tool for emergency SARS-CoV-2 surveillance in countries with limited resources and may help laboratories to continue testing and at greater frequency despite supply shortages, although with delay in cycle threshold value in comparison with indirect RT-PCR.