#16,026
Although SARS-CoV-2 had produced more than a thousand variants in its first year of circulation, it wasn't until mid-December of 2020 that we learned for the first `functionally' superior variant; B.1.1.7 (aka `Alpha' or `UK') variant.
Over time, B.1.1.7 was shown to be not only more transmissible than the `wild type' COVID, but has also been linked into increased hospitalization as well.
In the six months since then, hundreds of new variants have emerged, and while most are of little consequence, nearly a dozen have shown enhanced capabilities and have been designated as VOIs (Variants of Interest) or VOCs (Variants of Concern) by global and national public health agencies.
The World Health Organization currently lists 4 VOCs (Variants of Concern) and 7 VOIs (Variants of Interest), and continues to monitor dozens more.
While B.1.1.7 was the first rising star, and remains the most widespread of all the variants, some of the newer challengers are threatening its dominance.
Early concerns were focused on B.1.351 (Beta) and P.1 (Gamma), but over the last 2 months B.1.617.2 (Delta) has taken the spotlight having ravaged India, and recently routed the previously dominant Alpha variant in the UK.
Some recent blogs on Delta's transmissibility, immune evasion, and suspected increased severity include:
UK: Updated Risk Assessment On Delta Variant As Daily Cases Rise To Highest Since February
CDC: Delta Variant Rapidly Gaining Ground In the United States
While it is nothing that anyone wants to hear - unless a newer, even more biologically `fit' variant emerges to challenge it - the immediate future of the COVID pandemic appears to lie with the Delta variant. It is, by every measure, simply more transmissible than any of the other variants out there.
The good news is that those who are fully vaccinated appear to be at far less of a risk of infection - or serious illness if infected - than those who are not. Vaccine effectiveness is appears reduced, but still offers significant protection.
But with Delta on the ascendant, and less than 10% of the world's population fully vaccinated, the pandemic still has plenty of room to run. And the longer that goes on, the more opportunities there will be for something even more daunting to emerge.
All of which brings us to a new Rapid Communications, published late this week in Eurosurveillance, by researchers at the World Health Organization, the London School of Hygiene and Tropical Medicine, and Imperial College London, that looks at the relative transmissibility of the VOIs and VOCs they are currently monitoring.
This report warns that Delta is poised to become dominant globally, and that it may require more intensive public health interventions to control. They also warn that Delta may not be the last variant we have to deal with.
Due to its length, I've only posted some excerpts from this data-rich report. Follow the link to read it in its entirety. I'll have a brief postscript when you return.
Rapid communication Open Access
Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021
Finlay Campbell1 , Brett Archer1 , Henry Laurenson-Schafer1 , Yuka Jinnai1 , Franck Konings1 , Neale Batra1 , Boris Pavlin1 , Katelijn Vandemaele1 , Maria D Van Kerkhove1 , Thibaut Jombart1,2,3 , Oliver Morgan1 , Olivier le Polain de Waroux1
Recent months have seen the emergence and rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants associated with increased transmissibility, including the World Health Organization (WHO)-designated variants of concern (VOC) Alpha (hereafter referred to using the Phylogenetic Assignment of Named Global Outbreak (Pango) lineage designation B.1.1.7), Beta (B.1.351), Gamma (P.1) and Delta (B.1.617.2), as well as multiple variants of interest (VOI) [1]. By 3 June 2021, B.1.1.7 had been reported from at least 160 countries, B.1.351 from 113 countries, P.1 from 64 countries and B.1.617.2 from 62 countries [1]. We present an analysis of the effective reproduction number and global spread of SARS-CoV-2 variants with data available by 3 June 2021.
Effective reproduction number estimates
We analysed 1,722,652 SARS-CoV-2 sequences uploaded to the Global Initiative On Sharing All Influenza Data (GISAID) hCoV-19 database [2], considering only VOC or VOI reported at least 25 times in at least three countries (see Supplementary Tables S1 and S2 for sequence numbers per variant per country). GISAID sequences used for this work are acknowledged in Supplement 2. We used a multinomial logistic model of competitive growth to estimate the effective reproduction number of each variant relative to that of the non-VOC/VOI viral population for each reporting country. We assumed that the generation time of VOC/VOI remained unchanged compared with previously circulating variants. Further details on the methods, as well as an exploration of the sensitivity of our results to the assumption of an unchanged generation time, can be found in the Supplementary Material.
Despite differences between countries, our analysis showed a statistically significant increase in the pooled mean effective reproduction number relative to non-VOC/VOI of B.1.1.7 at 29% (95% confidence interval (CI): 24–33), B.1.351 at 25% (95% CI: 20–30), P.1 at 38% (95% CI: 29–48) and B.1.617.2 at 97% (95% CI: 76–117) (Figure 1).
Of the six variants currently designated as VOI, five were considered in our analysis and among these, only B.1.617.1 and B.1.525 demonstrated a statistically significant increase in the effective reproduction number of 48% (95% CI: 28–69) and 29% (95% CI: 23–35), respectively. In line with these estimates, our results showed rapid replacement of previously circulating variants by VOC/VOI in nearly all countries; of the 64 countries considered in this analysis, we estimate VOC/VOI to be the most frequently circulating lineage on the last day of available data in 52 countries, the most common variants being B.1.1.7 (40 countries) and B.1.617.2 (India, Singapore, United Kingdom and Australia) (Figure 2, Supplementary Figures S1 and S2).
(SNIP)
Discussion
In this analysis we have highlighted the global spread of SARS-CoV-2 variants and estimated their relative transmission rates. Given our estimates and all other factors remaining constant, B.1.617.2 is expected to rapidly outcompete other variants and become the dominant circulating lineage over the coming months.
(SNIP)
The more rapid growth and widespread prevalence of VOC pose challenges to the control of SARS-CoV-2 worldwide, especially with the recent emergence of B.1.617.2. Despite the emergence and rapid replacement by more transmissible VOC, several countries have successfully reduced SARS-CoV-2 transmission with the use of available and proven public health and social measures (PHSM).
Evidence has shown that the higher transmissibility of VOC has required increases in the duration or stringency of PHSM (as elaborated in the WHO interim guidance [8]) in order to achieve the same levels of reduction as before VOC circulation [9]. The increased transmissibility of VOC will probably also lead to a higher community immunity threshold, which may additionally mean that PHSM may need to be maintained for longer periods of time as vaccines are being rolled out.
As the virus continues to evolve, the degree of protection offered by the different vaccines against future VOC/VOI remains unclear; vaccination coverage targets themselves may need to be revised [10]. Lastly, given that higher transmissibility has increased case numbers in countries where VOC are circulating and the fact that some VOC are suggested to be associated with higher rates of hospitalisation and mortality [11], the burden on healthcare systems per coronavirus disease (COVID-19) case is likely to increase, although this effect will depend on vaccination coverage and efficacy.
The convergent evolution of mutations thought to be associated with higher transmissibility or immune escape in VOC (e.g. N501Y, E484K) highlights the fact that variants will probably continue to emerge under selective pressures such as PHSM and population immunity [7].
The emergence of new variants threatens the effectiveness of vaccines and requires constant evaluation of available diagnostic, therapeutic, PHSM and vaccination strategies as the COVID-19 pandemic continues. The WHO has established a SARS-CoV-2 Virus Evolution Working group to critically evaluate variants and a Global Risk Assessment and Monitoring Framework for SARS-CoV-2 variants to harmonise the decision-making processes for assessing the impact of VOC on public health and medical interventions [12].
(Continue . . . )
While the world is weary of COVID, and desperately wants to move on, the pandemic may not be so accommodating. As `herd immunity' - either from natural infection or vaccination - increases, the virus will be under pressure to evolve to evade that immunity.
Over the past 18 months, SARS-CoV-2 has repeatedly demonstrated its ability to reinvent itself in order to survive. So far, we've seen nothing to suggest that evolutionary cycle is slowing down.
All of which means the current pullback of the pandemic much of the world is enjoying may not last, and we need to be prepared to pivot if the virus throws another surprise in our direction.
