slow page loading – update query on wp_options

Hello All,
running last version of wordpress. 2 sites running on an EC2 instance. All installed myself.
Same local db (not RDS). Different plugins and themes.

Both sites suffer from the same problem. Some pages are lightning fast, and then, randomly (like, once every 20 something requests), one takes 10 seconds to load.
not 9 seconds, not 11 seconds, not 20 seconds… 10 seconds. EVERYTIME.
I activated general query log on mysql and the request duration on apache.
Everytime this next query runs, the page request is slow and it takes 10 seconds.
2017-07-17T01:29:58.546814Z 118 Query UPDATE wp_options SET option_value = ‘1500254998.5463140010833740234375’ WHERE option_name = ‘_transient_doing_cron’

it doesn’t run everytime I try to get a post.
The table is just 148 long, and the option_name column is indexed.
if I run that update directly on the shell, it is super fast everytime.

here are the apache logs (the last number is the time the request took in seconds, with some 10s):
x.y.z.a – – [17/Jul/2017:01:28:40 +0000] “GET /site2/?p=11 HTTP/1.1” 200 14375 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:28:41 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:28:42 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:28:44 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:28:58 +0000] “GET /site2/?p=7 HTTP/1.1” 200 14495 “-” “curl/7.38.0” 10
x.y.z.a – – [17/Jul/2017:01:29:17 +0000] “GET /site2/?p=11 HTTP/1.1” 200 14375 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:21 +0000] “GET /site2/?p=12 HTTP/1.1” 301 – “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:29 +0000] “GET /site2/?p=1 HTTP/1.1” 200 15478 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:34 +0000] “GET /site2/?p=111 HTTP/1.1” 404 10556 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:41 +0000] “GET /site2/?p=7 HTTP/1.1” 200 14495 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:44 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:55 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 0
x.y.z.a – – [17/Jul/2017:01:29:58 +0000] “GET /site2/?p=27 HTTP/1.1” 200 14168 “-” “curl/7.38.0” 10

anybody has any idea what might be the problem?
Thank you everyone.
jp