What is the stability of SARS-CoV-2 strains in human biological fluids?

By Bhavana KunkalikarAug 24 2022Reviewed by Aimee Molineux

In a recent study posted to the bioRxiv* preprint server, researchers assessed the stability of ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage in human biological fluids.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

The SARS-CoV-2 virus is majorly transmitted from infected individuals via respiratory droplets, while virus-laden excretions can potentially be a source of infection. Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 has evolved into novel variants of concern (VOCs) which display increased transmissibility, infectivity, and fitness. However, extensive research is required to understand the stability of these VOCs in human biological fluids.

About the study

In the present study, researchers investigated and compared the stabilities of SARS-CoV-2 VOCs and the ancestral lineage in biological fluids.

The team cultured Vero E6-transmembrane serine protease 2 (TMPRSS2) cells in Dulbecco’s Modified Eagle Medium (DMEM). Four distinct SARS-CoV-2 variants were used in the study: (1) USA-WA/2020 (WA-1): isolated from the COVID-19 patient identified in the US in January 2020, (2) human CoV (hCoV)-19/England/204820464/2020 (Alpha VOC): isolated in the UK in November 2020, (3) hCoV-19/South Africa/KRISPK005325/2020 (Beta VOC): isolated in South Africa in November 2020, and (4) hCoV-19/USA/NY-MSHSPSP-PV44476/2021 (Omicron VOC): isolated in New York in November 2021. Viral stock titers were subsequently estimated via end-point titration.  

Furthermore, the team assessed the amino acid substitutions in SARS-CoV-2 Alpha and Beta VOCs by mapping sequencing reads per the WA-1 consensus sequence. This was followed by an analysis using the low-frequency variant detector program to assess non-synchronous substitutions. The consensus sequences were further extracted for each individual variant from the read mappings, which were then aligned with sequences published in the Global Initiative on Sharing All Influenza Data (GISAID) database to inspect the identified mutations manually. 

Results

The study results highlighted that the consequence sequence derived from the SARS-CoV-2 WA-1 strain was completely identical to the reference sequence from the GISAID database apart from one synonymous mutation noted at position 1912 from C to T. Additionally, viral stock corresponding to the Alpha VOC was 100% homologous to the reference sequence and displayed various amino acid substitutions in the spike protein as compared to the WA-1 strain. The team also observed an amino acid substitution at position three from aspartic acid to leucine of the SARS-CoV-2 nucleocapsid protein.

The viral stock derived from the Beta VOC was homologous with the reference sequence and comprised various amino acid substitutions within the spike protein compared to the WA-1 strain. Furthermore, two additional substitutions were observed in the viral stock of the Beta VOC in comparison to the reference sequence. The consensus nucleotide sequence in the Omicron stock was 100% identical to the reference sequence. The Omicron VOC showed 31 amino acid substitutions, three insertions, and six deletions in the spike protein, along with various deletions and substitutions in other structural proteins compared to the QA-1 strain.

The liquid nasal mucus samples showed that the WA-1 strain was comparatively more stable than the Alpha VOC in summer, indoor, and spring/fall environments. Moreover, the Beta VOC was more stable than the Alpha VOC in summer, spring/fall, and indoor conditions. Notably, there was a considerable difference in the rates of viral decay corresponding to WA-1 and Beta in indoor conditions. Also, compared to the Beta VOC, the Alpha VOC and WA-1 strain were more stable in winter conditions.

In liquid sputum, the WA-1 strain was more stable than the Alpha VOC in indoor, summer, spring/fall, and winter conditions. Additionally, the WA-1 strain showed more stability than the Beta VOC under indoor, summer, spring/fall, and winter conditions in liquid sputum. Altogether, the Alpha and Beta VOCs displayed comparable stabilities under all the conditions assessed in liquid sputum.

The liquid saliva samples highlighted that the Alpha VOC and the WA-1 strain were comparatively more stable than the Beta VOC in winter environments. Moreover, the half-life values estimated for WA-1 were higher than those in the Alpha and Beta VOCs in winter conditions. However, the team found no difference in half-lives among the three VOCs in medium, sputum, nasal mucus, and saliva dried on a stainless steel surface. Moreover, Omicron VOC was less stable than the WA-1 strain in spring/fall conditions in medium and liquid nasal mucus.

Overall, the study findings showed that the SARS-CoV-2 Alpha, Beta, and Omicron variants displayed lesser stability in human biological fluids than in the ancestral lineage. The researchers believe the present study highlighted the potential risk of SARS-CoV-2 transmission via contaminated biological fluids.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources