Table 2.

ΦX174 Genotypic Evolution

Nucleotide	Gene	Change	Gene Function	ΦX174C	ΦX174C#2	ΦX174ΔslyD	ΦX174slyDlow
756† ‡	D	T- > C F123L	External scaffolding protein	+
756† ‡	E	T- > C R63R	Lysis	+
873† ‡	J	G- > C G9A	DNA Packaging	+
930‡	J	C- > T A28V	DNA Packaging	+
1033†	F	G- > C A11P	Major coat protein	+
1648†	F	C- > T P216S	Major coat protein	+
3800	H	T- > C C868R	Minor spike protein	+
4706†	A	G- > A S726S	DNA replication
4706†	A*	G- > T208A	Nonessential
1735	F	A- > G A245A	Major coat protein		+
3339	H	G- > D137N	Minor spike protein		+
575§	D	G- > A T62T	External scaffolding protein			+
575§	E	G- > A R3H	Lysis			+
576	D	C- > T L63L	External scaffolding protein			+	+
576	E	C- > T R3R	Lysis			+	+
624§	D	G- > T A79S	External scaffolding protein			+	+
624§	E	G- > T L19F	Lysis			+	+

All changes were identical between two sequenced ΦX174_C isolates

^†indicates mutation present in ΦX174 Af [42], one of the adapted lines used to start the adaptation

^‡indicates mutation present in ΦX174_pif- [43], the other adapted line with mutations available at the start of adaptation. All mutations in ΦX174_C not present in ΦX174⁺ were sequenced in ΦX174_pif-

^£Also silent in context of change at 575

^§Mutations previously found to compensate for slyD hosts [40]