Detection of SARS-CoV-2 variants in aircraft wastewater

By Dr. Priyom Bose, Ph.D.Reviewed by Benedette Cuffari, M.Sc.Jul 12 2022

Scientists have worked relentlessly to contain the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this end, several pharmaceutical and non-pharmaceutical strategies have been developed to prevent further transmission of SARS-CoV-2 and protect individuals from severe infection.

Study: SARS-CoV-2 Testing of Aircraft Wastewater Shows That Mandatory Tests and Vaccination Pass before Boarding Did Not Prevent Massive Importation of Omicron Variant into Europe. Image Credit: heychli / Shutterstock.com

Background

Newly emerged SARS-CoV-2 variants have been found to be transmitted through air travel and cruises from infected passengers. To limit these events from occurring, several strategies have been implemented, such as travel restrictions, quarantine periods, and compulsory vaccination to prevent the further spread of SARS-CoV-2.

To date, most available studies have focused on the impact of travel restrictions on the early phase of the COVID-19 pandemic. Although some studies have shown that these restrictions significantly delayed viral transmission, others have contradicted these observations and instead reported that travel restrictions were inadequate to preventing global transmission of SARS-CoV-2.

Many countries have reinforced various pre- and post-travel rules to restrict the spread of SARS-CoV-2 variants. Recently, the Omicron variant, which was first reported in South Africa, has become the dominant circulating strain in most countries across the world. 

Previous studies have reported the presence of a high concentration of viable SARS-CoV-2 ribonucleic acid (RNA) in stool samples of both asymptomatic and symptomatic individuals with COVID-19. As a result, the analysis of SARS-CoV-2 in wastewater has been proposed as an effective strategy to determine viral loads within communities. 

In fact, several studies have successfully isolated viral genotypes circulating within a community by sequencing the SARS-CoV-2 genome from sewage samples.

To this end, various SARS-CoV-2 strains have been identified in sewage samples that were similar to variants isolated from clinical samples. However, new SARS-CoV-2 genotypes were also found that were not reported in clinical samples.

To date, there have been limited studies demonstrating the presence of SARS-CoV-2 RNA in wastewater from passenger aircrafts. One related study has reported the successful detection of SARS-CoV-2 variants from aircraft wastewater by genome sequencing.

About the study

A new Viruses study successfully detected SARS-CoV-2 variants in the wastewater of aircrafts. Herein, researchers obtained wastewater samples from two flights traveling from Addis Ababa, Ethiopia to Marseille, France.

In this study, scientists tested both wastewater samples and passengers for the presence of SARS-CoV-2 upon disembarking to determine if the results of the wastewater analysis and passengers' SARS-CoV-2 tests were correlated. Both reverse transcription-polymerase chain reaction (RT-PCR) assay and full-length genome sequencing were utilized to detect SARS-CoV-2 variants from the samples.

Study findings

Wastewater analysis of the two flights revealed the presence of the Omicron variant, with genomic sequencing confirming the mutation patterns of this variant.

Taken together, 12 passengers of the December 24, 2021 flight tested positive for SARS-CoV-2 by a lateral flow test. Genomic sequencing of 11 of these samples confirmed the presence of the Omicron variant.

This indicates that despite fulfilling the requirement of producing a negative RT-PCR test within 72 hours of boarding and being vaccinated, one-fifth of the passengers were infected with SARS-CoV-2. These observations align with those of a recent study reporting the detection of the Omicron variant in the wastewater of a flight traveling from Johannesburg, South Africa to Darwin, Australia.

The congruent results of the COVID-19 tests of passengers and aircraft wastewater analysis indicate that this method is effective for monitoring circulating variants and assessing the risk of importing newly emerged strains. However, this process would require interrogating passengers who used toilets during the flight. 

Although the wastewater tanks were thoroughly cleaned between flights, the possibility of contamination by traces of SARS-CoV-2 RNA in the blackwater tanks from previous flights cannot be entirely omitted. However, in this case, the high viral load cannot be the result of contamination and is strongly linked to viral excretion by onboard passengers or aircraft crew.

The importation of the Omicron variant from South Africa to Europe has demonstrated that airplane traveling is a powerful entry route for new variants. Since aircraft wastewater screening can be carried out within an hour, this approach could be a more powerful tool as compared to current traveling rules of providing negative COVID-19 test results and vaccination certificates of the passengers.

Conclusions

The current study emphasized the importance of monitoring wastewater of aircrafts, as it offers important information related to the global transmission of newly emerged SARS-CoV-2 variants.

Furthermore, a negative COVID-19 test before boarding or vaccination does not confirm that passengers are not carrying the virus. Instead, the approach of analyzing aircraft wastewater is a roust tool for controlling SARS-CoV-2 importation and exportation.