A July BA Update

 I haven't been following the local case data because I think the numbers are flawed. With home tests and everyone pretending that the COVID-19 pandemic is over, the reported numbers are lower than what I suspect are the actual case levels are.

Hospitalization are likely counted somewhat more accurately. Here's the latest five county hospitalization averages. The data comes from health.data.ny.gov.

Hospitalizations are down from their Spring peak and except for Albany county the levels of hospitalization are low. That seems good. The data for the plot is available on GitHub.

BA variants

I downloaded 11,863,817 meta records from GISAID on July 15, 2022. BA.4 and BA.5 continue to advance throughout the US, UK, and the world.

The overall counts are still dominated by BA1 and BA.2, but recent data has large numbers of BA.4 and BA.5.

meta_data <- read_tsv('data/metadata.tsv')
df_BA_usa <- count_BA(meta_data, log = TRUE, title = 'USA BA variants')
df_BA_usa %>% group_by(Pango_lineage) %>% summarise(Total = sum(Count))

# A tibble: 5 × 2
  Pango_lineage  Total
  <chr>          <int>
1 BA.1          855838
2 BA.2          400423
3 BA.3              76
4 BA.4           15615
5 BA.5           32672
> 

In the UK,

df_BA_uk <- count_BA(meta_data, country = 'United Kingdom', log = TRUE, title = 'UK BA variants')
df_BA_uk %>% group_by(Pango_lineage) %>% summarise(Total = sum(Count))

# A tibble: 5 × 2
  Pango_lineage  Total
  <chr>          <int>
1 BA.1          654948
2 BA.2          473598
3 BA.3              52
4 BA.4            8166
5 BA.5           18784
> 

Results for the world are similar.

df_BA_world <- count_BA(meta_data, country = NULL, log = TRUE, title = 'World BA variants')
df_BA_world %>% group_by(Pango_lineage) %>% summarise(Total = sum(Count))
# A tibble: 5 × 2
  Pango_lineage   Total
  <chr>           <int>
1 BA.1          2369944
2 BA.2          1913697
3 BA.3             1115
4 BA.4            42368
5 BA.5           117946
> 

The code for plots is available here.

BA County Variants.

BA.4 and BA.5 haven't shown up in significant numbers locally.

BA.4 and BA.5 are around, but they haven't shown up in the data yet.

Code for this plot is available here.