By Maria Keridon
Topic: Could mutations of SARS-CoV-2 suppress diagnostic detection? // SARS-CoV-2 evolution during treatment of chronic infection
During rounds of viral replication inside their hosts, mutations accumulate and can alter characteristics of the virus. Although SARS-CoV-2 is a more slowly mutating virus than Influenza or HIV (Adashek and Kurzrock, 2020) several variants have already been labelled to be ‘of concern’ by the WHO. A primary concern is that people who have been previously infected with the virus or gained immunity through vaccination could be infected with new strains that evade the acquired immune responses of these individuals. By the same mechanisms, treatments that are based on antibodies, such as convalescent plasma or monoclonal antibodies, could become obsolete.
Viral evolution could also impair our ability to track and contain the spread of SARS-CoV-2 if it begins to affect diagnostic tests. To avoid both of these scenarios, it should be investigated how these escape variants arise and what preventative measures can be taken.
New research suggests vaccines can protect against variants of concern (VOCs)
Following reports of several vaccines significantly losing efficacy in regions where new variants have emerged and become dominant, like South Africa and Brazil (Garcia-Beltran et al., 2021), concerns have been raised whether the hopes of returning to normality after large-scale vaccination efforts would be justified. Discussions were mostly centered around the impact of this viral evolution on vaccines.
Numerous studies have looked into how antibodies found in blood sera of either previously infected or vaccinated individuals interact with emerging viral variants. The results show that in order to gain protection from new variants, individuals with previous infection require one mRNA vaccine dose to boost their antibody response, but two vaccine doses are necessary for a similar broadly protective response in previously non-infected individuals (Stamatatos et al., 2021; Reynolds et al. 2021). Additionally, Geers et al. (2021) have shown that even variants which quite readily escape neutralising antibodies, do not escape T cell responses, and therefore some levels of protection are maintained. Non-neutralising antibodies and T cell responses are essential parts of the immune response to infectious agents, but it is specifically high neutralising antibody titres, which have been associated with a lack of infectious virus shedding (van Kampen et al. 2021).
Correlates of protection have not yet been determined for SARS-CoV-2 infection (Abdool Karim et al., 2021). In simpler terms, it is not fully known what properties of the immune response, such as the titre of antibodies, are really required to protect from COVID-19 in both mild and severe form. Because of this, it can be difficult to predict which new variants will prove to be more dangerous and which will really evade acquired immunity from vaccines or infection.
So far, when investigating efficacy of vaccines in the UK against the newly dominant Delta variant compared to Alpha, it has been found that all vaccines show only slight reductions in efficacy in fully vaccinated people, but that difference in efficacy is more pronounced when comparing partially vaccinated individuals (Lopez Bernal et al., 2021). This further confirms the necessity of ensuring that individuals follow through with second vaccine doses when required. However, there have been found significant reductions in the efficacy of the ChAdOx1 nCoV-19 (AstraZeneca) vaccine against the Beta variant to only 10.4% (Madhi et al., 2021), making this VOC perhaps more alarming if it spreads extensively in places where this vaccine has been used in a large proportion of the population.
The virus faces stronger selective forces as a larger fraction of the population obtain immunity either by natural infection or vaccination, driving evolution of immune evasion (Ribbes, Chaccour and Moncunill, 2021). In order to stay ahead and be timely in detecting when SARS-CoV-2 variants truly begin to evade vaccine-induced protection, we need to still carefully monitor the spread of virus via testing. However, our testing methods are also at risk of losing their sensitivity as the virus evolves and this may become an issue especially when immune responses of vaccinated individuals starts to wane.
Evolution of SARS-CoV-2 may cause it to go undetected by diagnostic tests
Two of the most important and widely used methods of detecting SARS-CoV-2 are reverse transcription polymerase chain reaction (RT-PCR) tests and various types of immunoassays, also known as antigen tests. RT-PCR tests rely on short primers that recognise and bind to defined regions in the viral genome, enabling the replication of the viral genomic material, if present in the sample, to be replicated to high enough copy numbers to be detectable. Immunoassays involve antibodies which recognise small regions of viral proteins. Nevertheless, the results of both of these diagnostic tools could be faulty as the virus mutates in the small regions recognised by the tests, leading to higher numbers of false negative tests (Adashek and Kurzrock, 2021). This has already happened in Brittany, France, where individuals presenting with severe COVID-19 symptoms did not test positive with standard PCR test kits, but infection was later confirmed post mortem by analysis of tissue and blood (Cohen, 2021).
If new variants cause false negative tests at higher rates, then negative test results could accelerate the spread of the virus as individuals would behave assuming they are not infectious (West, Montori and Sampathkumar, 2020). And as long as they do not present with severe disease, the cases will go undetected. As a result, the epidemic waves could be very hard to detect before the extensive spread of these variants.
The spike (S) protein on the viral surface is a very common diagnostic target, as it contains sequences unique to SARS-CoV-2 (Adashek and Kurzrock, 2021). It is also highly immunogenic and therefore is prone to adapting to host responses by mutation (Adashek and Kurzrock, 2021). Therefore, it is important that diagnostic tools increasingly also target the nucleocapsid (N) protein and others, which have been found to be less mutable than the S protein. Immunoassays are recommended to contain polyclonal antibodies, therefore targeting more than one site of the virus, decreasing the possibility of sequence variation (Adashek and Kurzrock, 2021). Other researchers have investigated whole viral genomes to find the least mutable genomic regions of SARS-CoV-2, which could provide broad RT-PCR primers that are less likely to lose detection efficiency (Jain et al., 2021).
As with immune evasion monitoring, there needs to be surveillance of the efficacy of diagnostic tools against new emerging variants. Continuous sequencing efforts and reconfiguring of diagnostic tools is essential to avoid new variants silently spreading in populations (Adashek and Kurzrock, 2021). Although the properties which make variants evade immune responses, drugs, and diagnostic tools can be different from each other, monitoring of all these characteristics is important to reduce new epidemic waves as SARS-CoV-2 evolves.
Viral evolution within hosts may be the key to predicting global trends
To stay ahead of viral evolution, we need to be able to predict what new VOCs might look like and how these may arise. Significant sequencing efforts are constantly made, allowing to map the spread of the virus on a global scale. Massive datasets are being generated, which give useful information to monitor the spread of the virus and new variants globally. New tools, which speed up phylogenetic studies of related sequences, could soon permit ‘molecular contact tracing’, helping connect cases and infection clusters based on genomic sequences (Turakhia et al., 2021).
The evolution of the virus within individuals has not yet been thoroughly studied, but could provide an understanding of how variants escaping the immune responses arise (Ko et al., 2021), or even help predict how the virus might evolve on a global scale. For example, the same viral mutations that have been commonly observed in immunocompromised individuals over the course of prolonged infections have been found in several VOCs (Ribes, Chaccour, Moncunill, 2021).
Numerous reports have been made of immunocompromised people developing persistent SARS-CoV-2 infections, giving more opportunities for the virus to evolve (Choi et al., 2020). Moreover, there are examples of persistent asymptomatic shedding of infectious virus from these individuals (Avanzato et al., 2020). The evolution of the virus has been found to be especially triggered by treatment with convalescent plasma, leading to variants which escape neutralising antibodies contained in the treatment serum (Kemp et al. 2021). However, immune escape variants may not necessarily be transmitted, as was shown by Kemp et al. (2021) who reported that mutation D796H in the S2 subunit enabled SARS-CoV-2 to evade antibodies while also causing defects in the infection process. This highlights the importance of determining the requirements for efficient viral shedding and how they are related to immune evasion mutations. These findings unfortunately suggest that stricter infection prevention measures may be necessary in immunocompromised patients, regardless of disease severity. Mandatory isolation could be extended to more than 10-14 days following a positive test, especially if undergoing convalescent plasma or antibody-based therapies (Kemp et al. 2021).
The worldwide sequencing efforts have already given insights regarding the progression of the pandemic and the evolution of SARS-CoV-2. In the continued pandemic, this must be kept up and perhaps even improved upon, to make sure that the tools to combat outbreaks, namely diagnostics, vaccines, and medicines, remain efficacious. The pandemic certainly has proven that scientists worldwide can keep up with the challenges of this virus, and so governments and research institutions must continue to provide resources to make their work possible.
Abdool Karim, S. S. (2021) Vaccines and SARS-CoV-2 variants: the urgent need for a correlate of protection. The Lancet, 384, 8, pp. 1263-1264.
Adashek, J. and Kurzrock, R. (2021) Balancing clinical evidence in the context of a pandemic. Nature Biotechnology, 39(3), pp. 274-275.
Avanzato, V., Matson, M., Seifert, S., Pryce, R., Williamson, B., Anzick, S., Barbian, K., Judson, S., et al. . (2020) Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer. Cell, 183, 7, pp. 1901-1912.
Cho, B., Choudhary, M.C.,, Regan, J., Sparks, J.A.,, Padera, R.F., Qiu, X., Solomon, I.H.,, Kuo, H.H. et al. (2020) Persistence and Evolution of SARS-CoV-2 in an immunocompromised Host. New England Journal of Medicine, 383, 23, pp. 2291-2293.
Cohen, J., 2021. Latest Covid-19 Variant Discovered In France Isn’t Detected By Standard PCR Tests. [online] Forbes. Available at: https://www.forbes.com/sites/joshuacohen/2021/03/17/latest-covid-19-variant-discovered-in-france-isnt-detected-by-standard-pcr-tests/?sh=380164967e18 [Accessed 23 July 2021].
Garcia-Beltran, W., Lam, E., St. Denis, K., Nitido, A., Garcia, Z., Hauser, B., Feldman, J., Pavlovic, M. et al. (2021) Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell, 184, pp. 2372-2383.
Geers, D., Shamier, M., Bogers, S., den Hartog, G., Gommers, L., Nieuwkoop, N., Schmitz, K., Rijsbergen, L., et al. (2021) SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees. Science Immunology, 6 (59), eabj1750.
Kemp, S., Collier, D., Datir, R., Ferreira I., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Michochova, P. et al. (2021) SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592, pp. 277-282.
Ko, S., Mokhtari, E., Mudvari, P., Stein, S., Stringham, C., Wagner, D., Ramelli, S., Ramos-Benitez, M. et al. (2021) High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19. PLoS Pathogens, 17(4), e1009431.
Lopez Bernal, J., Andrews, N., Gower, C., Gallagher, E., Simmons, R., Thelwall, S., Stowe, J., Tessier, E. (2021) Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant. New England Journal of Medicine, DOI: 10.1056/NEJMoa2108891.
Madhi, S., Baillie, V., Cutland, C., Voysey, M., Koen, A., Fairlie, L., Padayachee, S., Dheda, K., et al., (2021). Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine, 384(20), pp.1885-1898.
Reynolds, C., Pade, C., Gibbons, J., Butler, D., Otter, A., Menacho, K., Fontana, M., Smit, A. et al. (2021) Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose. Science, 372, pp.1418-1423.
Ribes, M., Chaccour, C. and Moncunill, G. (2021) Adapt or perish: SARS-CoV-2 antibody escape variants defined by deletions in the Spike N-terminal Domain. Signal Transduction and Targeted Therapy, 6, 164.
Stamatatos, L., Czartoski, J., Wan, Y., Homad, L., Rubin, V., Glantz, H., Neradilek, M., Seydoux, E. et al. (2021) mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection. Science, 372, pp. 1413-1418.
Turakhia, Y., Thornlow, B., Hinrichs, A. S., De Maio, N., Gozashti, L., Lanfear, R., Haussler, D. and Corbett-Detig, R. (2021) Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic. Nature Genetics, 53, pp. 809-816.
van Kampen, J., van de Vijver, D., Fraaji, P., Haagmans, B., Lamers, M., Okba, N., van de Akker, J., Endeman, H. et al. (2021) Duration and key determinants of infectious virus shedding in hospitalized patients with coronavirus disease-2019 (COVID-19). Nature Communications, 12, 267.
West, C., Montori, V. and Sampathkumar, P. (2020) COVID-19 Testing: The Threat of False-Negative Results. Mayo Clinic Proceedings, 95(6), pp. 1127-1129.