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Table 1 Details of patients starting treatment at our hospital (Nos. 1–11) and patients who were transferred after treatment at other hospitals (Nos. 12–17)

From: Clinical experience of treatment of immunocompromised individuals with persistent SARS-CoV-2 infection based on drug resistance mutations determined by genomic analysis: a descriptive study

   

Mutations before the treatment for COVID-19

 

Mutations after the treatment for COVID-19

 

No

PANGOLIN

GISAID count

NSP5 (number of registrations) [% of mutation]

NSP12 (number of registrations) [% of mutation]

RBD (number of registrations) [% of mutation]

Drugs administered prior to subsequent GA

NSP5 (number of registrations) [% of mutation]

NSP12 (number of registrations) [% of mutation]

RBD (number of registrations) [% of mutation]

Outcome

1

BA.1.1

1047522

–

–

–

Rem, Nir/Rit

Sot

–

A625V(11)[50%]

*P337S(71)[54%]

*E340K(228)[100%]

F374L(11)[39%]

Ended isolation

2

BA.1.1

1047522

–

–

–

Rem

Sot

–

–

*S371F(1817)[78%]

Ended isolation

3

BA.1.1.2

62165

–

–

–

Rem

Sot

–

*C799F(3)[72%]

–

Ended isolation

4

BA.2.29

8463

–

–

–

Mol

Cas/Imd

–

–

–

Ended isolation

5

BA.5.1

254400

–

–

–

Rem, Mol

Nir/Rit

Cas/Imd

Q273R(2)[45%]

R457C(12)[44%]

*K444R(638)[46%]

*G446S(183)[23%]

Ended isolation

6

BA.5.1

254,400

–

–

–

Mol

Cas/Imd

–

I145V(5)[57%]

D164N(0)[55%]

*G446S(183)[20%]

*G446D(114)[34%]

P499S(6)[59%]

Ended isolation

7

BA.5.2.1

302404

–

–

–

Mol

Cas/Imd

–

D260N(6)[99%]

V445A(1309)[91%]

Ended isolation

8

BA.5.2.1

302404

–

–

–

Rem, Ens

Tix/Cil (before onset)

*M49L(0)[100%]

A529V(1808)[100%]

G671S(708)[35%]

E796D(7)[64%]

*R346S(220)[33%]

*N450D(994)[62%]

Ended isolation

9

BA.5.2.6

12935

–

–

–

Mol, Rem

Tix/Cil

–

–

–

Ended isolation

10

BA.5.2.46

155

–

–

–

Ens, Mol

–

–

–

Ended isolation

11

BF.5

85649

–

–

–

Mol

Sot

–

–

–

Ended isolation

12

BA.1.1.1

66698

   

Sot

–

P227S(8)[100%]

*P337H(9)[99%]

*S371F(272)[99%]

Y508H(1)[100%]

Ended isolation

13

BA.5.2.1

302404

   

Rem, Mol

–

–

–

Ended isolation

14

BA.5.1

254400

   

Rem, Nir/Rit

Tix/Cil

K90R(1127)[96%]

T246I(749)[99%]

*C799Y(6)[96%]

–

Ended isolation

15

BA.5.2.1

302404

   

Rem

Cas/Imd

Q273R(1)[24%]

*V166A(8)[34%]

E796K(5)[29%]

L368I(23)[24%]

K417H(1)[19%]

*G446S(227)[25%]

Ended isolation

16

BA.5.2.1

302404

   

Rem

Tix/Cil

K236R(40)[99%]

V233I(36)[100%]

G671S(708)[100%]

P918L(143)[99%]

L335S(3)[98%]

G339Y(46)[58%]

*K444R(726)[96%]

Ended isolation

17

BF.5

85649

   

Rem

–

E876D(0)[27%]

Y369H(0)[33%]

V503F(0)[28%]

Death

  1. PANGOLIN Phylogenetic Assignment of Named Global Outbreak Lineages, GISAID Global Initiative on Sharing All Influenza Data, NSP Non-structural protein, RBD Receptor-binding domain, GA Genomic analysis, Rem Remdesivir, Nir/Rit nirmatrelvir/ritonavir, Sot Sotrovimab, Mol molnupiravir, Cas/Imd casirivimab/imdevimab, Tix/Cil Tixagevimab/cilgavimab, Ens Ensitrelvir
  2. *Asterisk (*) indicates a drug-resistant mutation noted in a paper or manufacturer's fact sheet