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The more transmissible Delta variant of Covid-19 is taking hold in Missouri and Colorado, putting them among US states that are experiencing the highest rates of infection in the country.

The Delta variant, which was first identified in India, made up 29.1 per cent of genomically sequenced samples in Missouri in the four weeks to June 5, the most recent data on the Centers for Disease Control and Prevention web site revealed on Wednesday.

That is the highest proportion in the US, and ahead of second-ranked Colorado, with 10.9 per cent. New Jersey, Arizona and Texas round out the top five, with the Delta variant making up 7.4 per cent, 7.1 per cent and 6.5 per cent of samples over that period.

Those figures may underestimate the current spread of the Delta variant in the US, though. Anthony Fauci, chief medical adviser to President Joe Biden, told a press conference on Tuesday this new strain made up 20.6 per cent of sequenced samples in the weeks ended June 19, up from 9.9 per cent in the fortnight ended June 5.

Missouri, a state of about 6.1m residents, reported almost 4,800 cases in the week ended June 22, according to CDC data. That is the fourth-highest volume of cases in the US, ranking behind Florida, Texas and California, which rank third, second and first in the US by population.

Adjusted for population, Missouri has reported about 11.2 new infections per 100,000 people a day over the past seven days. That is the highest rate in the country, and compares with a national average of about 3.4 a day. Colorado, the other Delta variant hotspot, ranks seventh in the US in terms of overall per capita infections, and averaged about 6.9 new cases a day per 100,000 people over the past week.

Most of the 10 states with the highest per capita rates of new cases are geographically close to either Missouri or Colorado, making these regions the country’s coronavirus hotspots — although daily infections remain well below peak levels in the autumn and winter.

Louisiana, Arkansas and Missouri, whose eastern borders front the Mississippi River, are among those hotspot states and also have some of the lowest first-dose vaccination proportions in the US. Wyoming, another infection hotspot, borders Colorado and has one of the lowest proportions of vaccinated residents in the country.

An additional challenge in evaluating the spread of the Delta variant in the US is that the CDC data are only displaying figures from states that have reported at least 300 sequences. That may explain the absence of Louisiana, Arkansas, Wyoming and Utah, which is also experiencing elevated infection rates, from the CDC’s data set.