Table 2.

MERS-CoV genome variation in support of human transmission pairs

	Δ time (days)	Recorded substitutions	Expected substitutions	p value*(X≥observation)
ASR vs B	34	0	1·869	1
ASR vs F	28	3	0·714	3·58 × 10−2
ASR vs G	30	2	1·494	4·40 × 10−1
ASR vs H	28	1	1·436	7·62 × 10−1
ASR vs I	19	0	1·045	1
ASR vs J	18	1	0·985	6·26 × 10−1
F vs K	0	3	0	NA†
G vs X	6	7	0·139	1·76 × 10−10‡
G vs M	1	4	0·018	4·55 × 10−9‡
J vs Q	16	8	0·332	2·74 × 10−9‡
K vs V	8	0	0·422	1
Q vs T	5	9	0·106	4·00 × 10−15‡
X vs Y	2	7	0·057	3·50 × 10−13‡

MERS-CoV=Middle East respiratory syndrome coronavirus. ASR=likelihood-based ancestral state reconstruction of the root of the Al-Hasa clade.

^*p values for accepting or rejecting the null hypothesis are significant at the 0·05 level, after using the Bonferroni correction to adjust the p value for each hypothesis to 3·85 × 10⁻³.

^†The samples from F and K were collected on the same day resulting in an expected substitution value of 0. Therefore no conclusions could be made for this pair.

^‡Transmission pair not statistically supported.