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Our Top Viral Surveillance Insights in Early August

Viral Surveillance Insights

A few notable COVID insights on the latest (sub)variants and reinfections from our viral surveillance efforts. Our top 3 takeaways:

  1. Cases are coming down across the country: While positive cases had been fluctuating the last few weeks, they are now officially down across the country, with both BA.4 and BA.5 likely having peaked. As of last week, BA.5 was 87% of cases which closely aligns with our prediction that it would reach its max penetration the first week of August.

    Exhibit 1: Shows a model of how each variant contributes to the national case trajectory. Shaded region represents our confidence intervals, while the dotted line is Helix’s forecast. Other gray lines represent BA.1.1, BA.2 and BA.2.12.1 
  2. New data reinforces our earlier conclusion that while reinfections are rising rapidly, ones that occur within 90 days of the original infection are rare: About 98% of reinfections are happening in people who were previously infected more than 90 days ago, suggesting that waning immunity is driving the uptick in reinfections, rather than a super fit variant.

    Exhibit 2: Shows reinfections across time are rising rapidly, likely due to waning immunity
     


    Exhibit 3: Shows the % of reinfections that happened within 90 days of an individual’s original COVID infection and how they only make up ~2% of the total
     

  3. Subvariants of concern are still <10% of positives: The two subvariants that have recently sparked scientific interest include BA.4.6, which is predicted to have a mutation that can escape neutralizing antibodies, and BA.2.75, which has made headlines in India. But both of these are only 6% and <1% of positive cases in the U.S., respectively, and seem to be growing at a moderate rate for now.

Our hypotheses around why cases are coming down now include: 1) at the population level, immunity is sufficiently high that current variants are less successful in fully escaping previous COVID immunities, 2) we are observing a seasonal trend with schools out and less indoor mixing. Our data shows the rate of positive cases from those < 18 years old has been significantly lower in recent months.

It will be interesting to see what happens given the latest CDC guidance change that drops quarantine and social distancing requirements, as well as, when we enter autumn and schools reopen. We’ll be watching flu positivity rates as well, since flu may have a greater advantage with greater COVID immunity, and with communities more open than they have been in several years. As always, we’ll also continue to keep a lookout for antibody-evading variants.

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Helix
Helix is the leading population genomics and viral surveillance company operating at the intersection of clinical care, research, and data analytics.