New SARSCoV2 Variants of concern: What are their Implications for Covid19 response in Kenya

By John Kiragu (MPH Ongoing)

New strains of SARSCoV2

There are multiple strains of the SARSCoV2 virus that are circulating globally. The new strains have arisen from the mutational changes of the Spike region of the SARSCoV2 virus. Therefore, the new strains of the SARSCoV2 virus are having a different type of Spike region that cannot be recognized and neutralized by the immune antibodies developed from the initial Covid19 vaccines or from the SARCoV2 infection. The new strains arising from viral mutations are likely to present an unending Covid19 pandemic, reduced efficacy, and effectiveness of Covid19 vaccines, and continued re-escalation of Covid19 restrictions and protocols. For example, the emergence of the variant strains of the SARSCoV2 virus was alarming in the United Kingdom necessitating the UK government to issue a new set of lockdown measures including stay-at-home orders and closure of schools on 5th January 2021.

Are the new strains of SARCoV2 virus more dangerous than the initial strain? Some of the new strains have been estimated to be more contagious. For example, a recent study estimated that the 501Y strain variants are 75 % more transmissible hence more contagious(5).

Some of the new strains include the B.1.1.7 lineage (a.k.a. 20I/501Y.V1 Variant of Concern (VOC) 202012/01) which is emerged in U.K on September 2020. This strain is more contagious and has spread to several countries including United States and Canada (CDC 2020).

Another strain is the B.1.351 lineage (a.k.a. 20H/501Y.V2) which was first discovered in Nelson Mandela Bay in South Africa in October 2020. By late December 2020, this variant strain was the predominant strain of the SARSCoV2 virus in Zambia. This strain has been cited to be capable of evading neutralization by the antibodies produced for the initial SARS-CoV2 viral strains (CDC 2020).

The third strain of Concern is the P.1 lineage (a.k.a. 20J/501Y.V3) SARSCoV2 virus which arose from the S protein mutation just like the B.1.351 lineage and the B.1.1.7 lineage. It was first reported in Japan from four travelers coming from Brazil. There is evidence suggesting that this strain can evade the immune response generated previously through Covid19 vaccination or developed from natural infection (CDC 2020).

In Kenya, no new strains of SARSCoV2 have been identified. However, this does not rule out that any of the listed variant strains of SARSCoV2 are circulating in Kenya or new strains have independently developed in Kenya(6). The new strains would be identified by whole-genome sequencing of the cluster of Covid19 cases however a recent issue brief by KEMRI cites that there was insufficient sequencing data for Kenya between October 2020 and January 2021 that could have enabled the detection of Variant Strains of Concern on Covid19 disease(5).

Implications of the SARSCoV2 multiple strains of Concern

  1. The Covid-19 Vaccines may not work well

The Spike region is the main antigenic component of the SARSCoV2. Therefore, only those antibodies that are specific to it can neutralize it(4). A variant of the Spike region means that existing antibodies from the natural infection or from the Covid19 vaccination cannot work. This implies that the Covid19 vaccines are not the magical bullets in stopping the Covid19 Pandemic-causing SARSCoV2 virus both internationally and locally. Public health measures have to remain in place to slow the spread of any strain of the SARSCoV2 virus. This has a huge bearing on the continued protection of vulnerable populations such as people with comorbid conditions and health workers. A study on a cohort of 12541 Health workers exposed to Covid19 disease showed that an initial Covid19 infection among health workers reduced the risk of getting re-infected with Covid19 disease within the ensuing 6 months after recovery from the disease(7). Therefore, there is currently no evidence to suggest that natural immunity to Covid19 is happening or has happened. This means that the infection prevention and control (IPC) measures to protect Health workers should be sustained until further studies establish that Covid19 vaccines can confer long life immunity.

2. Covid-19 diagnostic Molecular testing protocols

Covid-19 testing is a key strategy for the containment of the SARSCoV2 virus. The real-time reverse transcriptase Polymerase chain reaction (RT-PCR) test is the gold standard for Covid19 testing as recommended by the WHO. The SARSCoV2 virus has several structural components important targets for RT-PCR testing including the Spikes(S), the envelope (E), the Nucleocapsid (N), and the genetic materials responsible for replication such as the Open Reading frames (ORF).

Figure showing SARS- CoV 2 Structure.  Contributed by Rohan Bir Singh, MD; Made with

To test for the presence of SARS-CoV2 viral infection which causes Covid19 disease, at least two molecular targets should be included in the assay for analysis(8).  This strategy enhances the specificity of the test by avoiding the genetic drifting of the SARSCoV2 virus and potential for cross-reaction with another endemic coronavirus. Currently, there is no evidence that any two combinations of the molecular gene targets are superior or others(8). Therefore, different countries have RT PCR tests targeting a different combination of SARSCoV2 genes. For example, the Ministry of Health Kenya recommends the use of the N2 gene and the E gene analysis for the Gene Xpert RT PCR test in the detection of the SARSCoV2 virus as indicated in the COVID-19 Antigen Rapid Diagnostic Testing Interim Guide by the MOH Kenya(9).

SARSCoV2 variants of concerns especially from the mutational changes of Spike protein have an implication on the Covid19 molecular testing locally and internationally. For example, KEMRI recommends against the use of diagnostic SARSCoV2 molecular tests that target the Spike (S region alone) region alone.  This is because it is evidently unstable and variable. Therefore, this implies that both private and public laboratories that carry out diagnostic testing for SARSCoV2 infection in Kenya should purpose to review their protocols for genomic surveillance. In addition, there is a pressing need to increase the capacity to collect data for genomic surveillance among the Kenyan Covid19 cases and deaths(6). This is the only way to reliably tell whether there are SARSCoV2 variants of concerns already developed in Kenya or being imported into the country.  Given that coronaviruses are prone to mutation(2), further studies need to be done to investigate if other structural regions of SARSCoV2 such as the membrane or the envelope regions are also likely to mutate the same way as the Spike region.

3. Covid19 Disease Reinfection among the recoveries

It is possible for an individual who recovered from the Covid19 disease to be re-infected by the SAR- CoV2 virus of the variant strains. A case study of a patient who was re-infected with variant SARSCoV2 strain despite having antibodies for the first infection. The 29-Year-old woman was immune-competent, was first infected in March during the first wave in Brazil, and developed the symptoms of Covdi19 disease. She also developed signs and symptoms for covid19 disease during the reinfection on December 19th, 2020. The SARSCoV2 strains during the first and second episodes of the infection were different(10). The authors argue that it is possible to be re-infected with a different strain of SARSCOV2 and develop the disease. Given that the patient described above had developed an immune response against the initial strain of the SARSCOV2 virus, acquiring the SARCOV2 infection for a second time means that the emerging strains of the virus are able to escape the immune system and are not neutralized by the memory antibodies.

This has a huge implication for Kenya where 83% (82,350) of the Covid19 cases have recovered as at 17th January 2021(NERC MOH COVID19 UPDATE: Brief No 299). The Kenyan Ministry of Health, the county government and other health partners should continue to sensitize and mobilize the Kenyan public in strict adherence to Covid19 protocols even as the Kenyan economy continues to resume normalcy. The guard on Covid19 protocols should not be let down especially in schools and other public places.

Another case study describes the reinfection of health workers following a nosocomial outbreak. The viral strains that re-infected the HWs were different from the initial strains. The HWs were noted to develop milder symptoms during the re-infection episode compared to the initial one. Despite the HWs developing strong humoral (a type of immune response that produces antibodies ) immunity in form of antibodies after the initial infection, the HWs still got re-infected with the variant strains. The authors conclude that cases like these imply that life-long immunity to SARSCoV2 is unlikely which has huge implications on the current vaccines(10).

Conclusion and Recommendations

Multiple strains of the SARSCoV2 virus, the Covid19 disease-causing novel coronavirus, are in circulation within the population internationally. However, the local spread of the variant strains of concern has not been established. Therefore, genomic surveillance in Kenya needs to be stepped up through increased capacity for whole-genome sequencing on cases and deaths of Covid19 disease in line with the recommendations given by KEMRI(5).

SARSCoV2 Variants of concern have huge implications on the Covid19 vaccines, Covid19 Testing  and the persistent population susceptibility to reinfection with Covid19 disease as argued in this article. Thus, Covid19 vaccines should not be seen as magic-bullets for stopping the pandemic.

Despite the emergence of new strains of Covid19, with a possibility of having some of them developing or being imported into the Kenyan population, the existing public health Covid19 containment and mitigations protocols remain the cornerstone of slowing the spread of Covid19 disease and should be reinforced rather than introducing new measures which is also in line with recommendations by KEMRI(5).


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  5. Kemri Kenya. Emergence of new SARS-CoV-2 Variants of Concern : Should Kenya Review its Port of Entry Requirements for International Travelers ? 2021
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  8. Guide I. REPUBLIC OF KENYA COVID-19 Antigen Rapid Diagnostic Testing Interim Guide. 2020;1–16.
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  10. Selhorst P, Van Ierssel S, Michiels J, Mariën J, Bartholomeeusen K, Dirinck E, et al. Symptomatic SARS-CoV-2 reinfection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response. Clin Infect Dis. 2020;32(0).

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John Kiragu

A student in Masters' of Public Health focusing on Health Economics, Health Policy and Planning at the School of Public Health_University of Nairobi.
Practicing RN with a Bachelors' Degree in Nursing Sciences from the same University. A founder for Kenyan-based Health-Tech Startup company implementing a digital platform to improve maternal health outcomes.


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