The Compelling Evidence that Variants Drive Covid Surges

Recently, Anthony Brookes, a Professor of Genomics and Health Data Science at the University of Leicester, wrote a piece for the Daily Sceptic arguing that central to the virus’s surge-and-decline behaviour is the emergence of new variants, which are “able to infect (or re-infect) some fraction of individuals”.

He writes:

A series of SARS-CoV-2 variants have arisen, many of which possessed a transient selective advantage that led to a wave of infection that peaked some three-to-four months later. Several such variants have spread globally, though different successful variants have arisen simultaneously in a number of countries. The result is a three-to-four month wave pattern per country, which is also apparent globally.

The global wave pattern is shown below. It features an extended autumn and winter wave, a spring wave and a summer wave (seasons here for the northern hemisphere, of course). Note that this graph is raw positive test numbers so does not allow for increased testing.

To illustrate how this global pattern is reflected in different countries and how it relates to the emergence of new variants, I have superimposed the graph of variant proportions over time from the CoVariants website onto the positivity rate curves (the proportion of tests that come back positive, which takes into account changes in the amount of testing) from Our World in Data. I’ve done this for the 12 countries which have done the most sequencing of virus samples (according to CoVariants), plus Israel and South Africa.

Note that the sequencing data is not necessarily representative, though the more sequencing that is done the more likely it is to be representative. Jagged lines in early data indicate small samples that are unlikely to be representative. Grey areas are unidentified variants.

My apologies that it is difficult to read the dates along the bottom of these composite images but hopefully you can see enough to figure out what is what.

U.K.

The three peaks in the U.K. are associated with the three dominant variants: the ‘Spanish’ variant (20A.EU1) in orange in autumn 2020, Alpha in red in the winter and Delta in green in the summer. The Alpha surge was large, presumably due to it occurring in the winter. Note the lack of a spring 2021 surge, which in other countries was associated with Alpha.

U.S.A.

There is evidence in the U.S. of a small spring surge associated with Alpha and a larger summer one associated with Delta. There is no data here on the variant(s) associated with the large winter wave or the smaller summer 2020 surge.

Germany

The Spanish variant is significant in the large winter surge in Germany, but is not dominant on this data. The spring surge associated with Alpha and the summer surge associated with Delta are present again.

Denmark

The large winter wave in Denmark is associated with the Spanish variant, though again it is not entirely dominant on this data. The spring bump associated with Alpha is there but very small, while the summer surge associated with Delta is more pronounced.

Sweden

Sweden’s large winter wave was mixed variant-wise, though data at this point was sparse (indicated by the jagged lines). Alpha is associated with a slowing of the drop-off from winter and a second peak. Delta so far in the summer is associated with only a small ripple.

France

France’s large autumn surge was mainly associated with the ‘French’ variant (20A.EU2) in light blue, though again it was not entirely dominant. The subsequent winter peak was very muted, though a spring surge associated with Alpha and a smaller summer ripple associated with Delta are present.

Japan

Variant data was sparse before spring 2021 in Japan, but the two most recent surges are associated with Alpha in the spring and Delta in the summer.

Netherlands

The Netherlands’ positivity curve is bumpier than most, but there appears to be a large winter wave associated with (though not dominated by) the Spanish variant, a spring resurgence associated with Alpha and a summer surge associated with Delta.

Spain

Spain’s autumn surge is dominated by the Spanish variant, but its winter wave seems to be a mixture of Alpha and the Spanish variant, while there is also a spring bump associated with Alpha. A summer surge associated with Delta is clear. Spain is unusual in having four peaks but three dominant variants, perhaps a result of the winter wave occurring just as Alpha was taking over from the Spanish variant.

Canada

Canada had little data till recently. While a summer surge associated with Delta is clear, the spring surge is associated with both Alpha and other variants, including Gamma (in pink).

Switzerland

Switzerland’s autumn and winter wave featured a mix of variants, especially the French and Spanish. Alpha is associated with a spring bump and Delta with a moderate summer surge.

Italy

A large and extended autumn and winter wave associated with the Spanish variant is evident in Italy, and is similar to Spain in that Alpha takes over from the Spanish variant during the winter. There is then also a spring bump associated with Alpha and a small summer ripple associated with Delta.

South Africa

South Africa has not sequenced so many samples as the countries above, but a summer wave associated with Beta (light red) is evident, as is a winter wave (in this case) associated with Delta. South Africa is the only one of these countries where Alpha never became dominant, apparently being squeezed out by Delta.

Israel

Sequencing in Israel has also been quite sparse, but there is some evidence of a winter wave associated with Alpha and a summer surge associated with Delta. The lack of spring bump may be, as in the U.K., because the Alpha wave occurred over winter.

These 14 graphs illustrate how variants are associated with surges in different countries. Importantly, almost every time there is a surge and a peak it is associated with one of the highly successful variants (Delta, Alpha, Spanish, French). The main exception is in winter, when there is a peak anyway, though even then it is usually associated with these variants in some way.

Importantly, by way of control, the U.K. and Israel show that when Alpha was the dominant winter variant, the spring peak, typically associated with Alpha, was absent.

This is to my mind compelling evidence that variants play a key role in driving new surges of coronavirus. It suggests that herd immunity is to some extent variant-specific, and that a new variant temporarily disturbs the herd immunity until the latest wave of infections tops it up again.

There is no sign yet of the emergence of a new successful variant that will take over from Delta. This holds out the hope that Delta may be some kind of evolutionary endpoint or optimum for the virus, and thus that the autumn and winter may be mild from a Covid point of view – though other viruses like flu may take the opportunity to make a comeback.

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