SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies : a non-systematic literature review for surveillance purposes.
Date: 2023-07-20
Institutions: European Centre for Disease Prevention and Control
Subjects: activity report, coronavirus disease, health control, health risk, medicinal product, therapeutics

TECHNICAL REPORT 

SARS-CoV-2 variant mutations conferring reduced 
susceptibility to antiviral drugs and monoclonal 
antibodies: a non-systematic literature review for 
surveillance purposes 
July 2023 

Summary 

Antiviral drugs and monoclonal antibodies (mAbs), administered either separately or as combination therapy 
'cocktails’, have provided a valuable tool for fighting COVID-19. Surveillance data, coupled with data on antiviral 
treatment susceptibility, can guide clinical decisions on selecting the best therapy for the patient. 

The aim of this report is to provide a non-systematic literature review on the currently available data on SARS-
CoV-2 therapeutic mAbs and antiviral drugs authorised for use in the European Union/European Economic Area 
(EU/EEA). In total, 258 publications on the four approved mAbs and 23 publications on antiviral drugs were 
analysed. According to these studies, the ORF1ab mutations nsp5:S144A, nsp5:Q189K, nsp5:H172Y, nsp5:E166A, 
and nsp5:F140A conferred moderate to high reduction in susceptibility to Paxlovid (nirmatrelvir/ritonavir). The 
data indicated a highly reduced neutralisation capacity of Ronapreve (casirivimab/imdevimab) for all Omicron sub-
lineages included in this report. The sub-lineages BA.1, BA.2, and BA.5 showed high reduction in susceptibility to 
Regkirona (regdanvimab). Xevudy (sotrovimab) showed high neutralisation efficacy against most SARS-CoV-2 
variants, but moderate reduction in neutralisation activity for BA.2, BA.4, and BQ.1.1. Highly reduced 
neutralisation activity against the BQ.1 and BQ.1.1 sub-lineages was observed for Evusheld 
(tixagevimab/cilgavimab). 

Monitoring the resistance of circulating new variants to mAb-based antiviral treatments is important for making 
decisions on whether some of the developed mAbs should be discontinued or different combinations of mAbs 
should be used. Neutralising susceptibility data are quite variable, leading to discordant findings among 
investigations. Therefore, adopting a global external standard for calibration would improve concordance across 
various tests and results could be provided in global units. 

Introduction 

As of June 2023, the SARS-CoV-2 pandemic had resulted in more than 766 million confirmed cases of COVID-19 
and over 6.9 million deaths globally [1]. During the pandemic, non-pharmaceutical interventions such as stay-at-
home measures, contact tracing, and social distancing were implemented at different phases to contain the spread 
[2-4]. To mitigate the impact of the disease, vaccines, antiviral drugs, and monoclonal antibodies (mAbs) were also 
developed. The development and licensure of vaccines against COVID-19 became a global effort, pushed forward 
at an unprecedented speed. The successful implementation of vaccines against COVID-19 less than a year after 

Suggested citation: European Centre for Disease Prevention and Control. SARS-CoV-2 variant mutations conferring reduced 
susceptibility to antiviral drugs and monoclonal antibodies: a non-systematic literature review for surveillance purposes – July 
2023. Stockholm: ECDC; 2023. 

Stockholm, July 2023 

ISBN 978-92-9498-644-3 
doi: 10.2900/192733 
Catalogue number TQ-04-23-728-EN-N 

TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

the beginning of the pandemic significantly contributed to decreasing the burden of COVID-19, both in terms of 
disease severity and mortality. Medical treatment of COVID-19 is currently mostly supportive, including oxygen 
therapy for severely ill patients and patients at risk of developing severe disease, and ventilation for critically ill 
patients. Antiviral drugs and mAbs, administered either separately or as combination therapy ‘cocktails’, have been 
used as another tool for fighting COVID-19. Their administration should be considered in consultation with clinical 
specialists and based on clinical guidelines for the treatment of adults and adolescents at risk of developing severe 
disease. For example, they can be administered to moderately to severely immunocompromised patients who may 
have an inadequate immune response to COVID-19 vaccination. 

Antiviral drugs are used to disrupt the viral life cycle by preventing virus attachment to host cells, blocking 
proteolytic cleavage of the viral Spike (S) protein and suppressing or inhibiting viral replication [5]. Antiviral drugs 
currently authorised for use by the European Medicines Agency (EMA) include Paxlovid (PF-07321332/ritonavir) 
and Veklury (remdesivir). Paxlovid is a SARS-CoV-2 protease inhibitor containing nirmatrelvir (NTV), a main 
protease (Mpro) inhibitor specifically designed to block the activity of the SARS-CoV-2 Mpro enzyme and therewith 
inhibiting viral replication. It also contains low-dose ritonavir (RTV), a HIV-1 protease inhibitor and a strong 
cytochrome P450 (CYP) 3A inhibitor, acting as pharmacokinetic booster of NTV [6]. Remdesivir is a nucleoside 
analogue that inhibits RNA-dependent RNA polymerase (RdRp) with a broad-spectrum activity against multiple RNA 
viruses interrupting viral replication [7]. EMA has not recommended the marketing authorisation for Lagevrio 
(Molnupiravir) as its human medicines committee (CHMP) concluded that the clinical benefit of Lagevrio in the 
treatment of adults could not be demonstrated [8].  

Virus-targeting monoclonal antibodies are designed to decrease the severity of COVID-19 by binding to the SARS-
CoV-2 S protein and causing direct neutralisation, antibody-dependent cellular phagocytosis, antibody-dependent 
cell-mediated cytotoxicity and/or complement activation [9]. Monoclonal antibodies which are currently authorised 
for use by EMA include Evusheld (tixagevimab/cilgavimab), Regkirona (regdanvimab), Ronapreve 
(casirivimab/imdevimab) and Xevudy (sotrovimab). The emergence of new SARS-CoV-2 variants with specific 
amino acid substitutions that make the virus less sensitive to the existing therapies has put the efficacy of mAbs in 
question [10]. For instance, the observed reduced efficacy of Evusheld (tixagevimab/cilgavimab) against emerging 
resistant variants have limited its use [11]. 

In the first quarter of 2022, there were a series of outbreaks globally related to the emergence of the Omicron 
lineage, which included, among others, BA.4, BA.5, BA2.2.75 and XBB.1.5 [12,13]. Unfortunately, all the variants 
of concern (VOCs) mentioned above have demonstrated reduced sensitivity to neutralisation with existing mAb 
therapies in vitro [14,15].  

The risk of developing drug resistance is increased for immunocompromised patients, who are prone to prolonged 
infection due to their reduced ability to control virus replication. Prolonged use of antiviral treatment may lead to 
the emergence of SARS-CoV-2 variants with reduced susceptibility to drugs and may, in certain circumstances, 
result in viral resistance being the cause of failure of clinical treatment. 

Surveillance data, coupled with data on antiviral treatment susceptibility, can guide clinical decisions on selecting 
the best therapy for the patient. In addition, the use of appropriate antiviral therapy can reduce the development 
of drug resistance. Continuous monitoring of antiviral drug resistance of the different emerging SARS-CoV-2 
variants is therefore important. 

Numerous phenotypic and genotypic laboratory techniques have been developed to assess virus neutralisation 
capacities and susceptibility to antiviral drugs [16]. Examples include the plaque/focus reduction neutralisation 
tests (PRNT/FRNT), microneutralisation assay (MNA), and pseudovirus (PSV) neutralisation assays [17,18]. 
PRNT/FRNT or TCID50 (Median Tissue Culture Infectious Dose)-based and MNA assays typically use replication-
competent SARS-CoV-2 clinical isolates. While these assays permit assessment against the fully antigenic content 
and molecular complexity of VOCs, the disadvantage of these assays is the requirement of a biosafety level (BSL)-3 
laboratory and the associated labour-intensive requirements. PRNT have shown to be more sensitive compared to 
other approaches [19], while FRNT and MNA offer faster turn-around times than PRNT. Antiviral and therapeutic 
resistance can be assessed with Inhibitory Concentration (IC)50 assays, expressed as the concentration of drug 
that is required to inhibit the viral growth by 50%, also called ‘half maximal inhibitory concentration’. Genetic 
characterisation using Whole Genome Sequencing (WGS) allows for screening and identification of mutations in 
key areas of the viral genome that confer reduced susceptibility to antiviral drugs or mAbs.  

Below, we provide an overview of the currently available data on SARS-CoV-2 therapeutic monoclonal antibodies 
and antiviral drugs authorised for use in the EU/EEA. 

Methods 

We compiled an in-house database using several different data sources: the Stanford University coronavirus antiviral 
& resistance database [20], COG-UK mutation explorer [21], journal publications, European Medicines Agency (EMA) 
summaries of product characteristics and United States Food and Drug Administration (FDA) emergency use 
authorisation fact sheets. Publications included in the database were obtained and reviewed monthly from four 
literature sources: PubMed using the search terms ‘SARS-CoV-2 combined with monoclonal antibodies/antiviral drugs’, 
Science Direct using the search terms ‘SARS-CoV-2 combined with monoclonal antibodies/antiviral drugs’, LitCovid 

2 

 
 
 
 
 
 
TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

using the search terms ‘SARS-CoV-2 combined with monoclonal antibodies/antiviral drugs’ and BioRxiv/MedRxiv 
COVID-19 SARS-CoV-2 preprint servers. According to the inclusion criteria, only studies on antiviral drugs and 
monoclonal antibodies approved by the EMA were considered. The collection of data began in April 2022 and was 
continued until 1 December 2022. The database was updated regularly, and new virus variants and results were 
included. The following data were extracted: the assays used for antiviral resistance testing, the IC50 value of the 
used control, fold-reductions in neutralisation titre associated with variants and mutations and corresponding IC50 
values for the quantification of the observed reduction. Details on mutations in the open reading frame 1ab (ORF1ab) 
and spike genes were collected from in vitro and in vivo studies, as well as VOCs’ data for which the collection of spike 
and genomic mutations was known. Neutralisation data from replication-competent SARS-CoV-2 isolates and non-
replication-competent pseudotyped viruses using VSV (vesicular stomatitis virus), HIV (human immunodeficiency virus 
type 1), MLV (murine leukaemia virus), and a lentivirus containing a SARS-CoV-2 S protein with specific mutations 
were also included in the database. 

Results 

We analysed 258 publications on the four approved mAbs and 23 results on antiviral drugs (Table 1). These 
publications covered data on 28 individual S protein mutations and 25 ORF1ab protein mutations. They also 
described the effect of 6 combinations of S protein mutations associated with reduced susceptibility to mAbs and 
antiviral drugs (Annex 1). These combinations generally consisted of sets of two, three, 15, 16, or 20 mutations 
that were present within the genome of a VOC. Two thirds of the results for mAbs were obtained using pseudotype 
neutralisation assays, while one third was obtained using assays with replication-competent SARS-CoV-2 isolates. 

Table 1. Antiviral drugs and monoclonal antibodies approved by EMA and number of publications 
included in the database 

Antiviral drugs 

Number of 
publications 

Monoclonal antibodies 

Number of 
publications 

Paxlovid (PF-07321332/ritonavir) 

Veklury (remdesivir) 

10 

13 

Evusheld (tixagevimab/cilgavimab) 

Regkirona (regdanvimab) 

Ronapreve (casirivimab/imdevimab) 

Xevudy (sotrovimab) 

71 

34 

65 

88 

The results in the data showed that the mutations E337/K/R/L and E340K/V/I/A occurring in the Delta variant 
conferred ≥100-fold reduction in susceptibility to Xevudy (sotrovimab). However, their global and EU/EEA 
frequency was quite low (<0.01%). The combination of mutations K417N+E484K+N501Y in the Beta and Gamma 
variants demonstrated a highly and moderately reduced neutralisation efficacy for Regkirona (regdanvimab) 
(≥100-fold and 25-99-fold), respectively. These mutations had a high global and EU/EEA frequency when occurring 
in Beta (79.5 and 83%, respectively). The mutations K417N+L452R+T478K present in the Delta variant conferred 
25–99-fold reduction in susceptibility for Regkirona (regdanvimab). The set of mutations 
(G339D+S371L+S373P+S375F+K417N+ N440K+G446S+S477N+T478K+E484A+Q493R+G496S 
+Q489R+N501Y+Y505H) present in BA.1, BA.4, and BA.5 led to different fold-reductions in susceptibility to mAbs. 
When occurring in a BA.1 virus sub-lineage, these mutations conferred ≥100-fold reduction in susceptibility to 
Ronapreve, Sotrovimab, and Evusheld, with an EU/EEA frequency of 50%. On the other hand, the same set of 
mutations present in the virus sub-lineages BA.4 and BA.5 have led to moderately reduced neutralisation efficacy 
for Evusheld (tixagevimab/cilgavimab) (Table 2).  

3 

 
 
 
 
 
 
 
 
 
 
 
 
TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies

Table 2. Mutations and combinations of mutations in the S protein and their corresponding reductions 
in susceptibility to mAbs 

Mutation (S protein) 

Variant 

mAbs 

Global 
frequency** 

EU/EEA 
frequency** 

Ronapreve 
(casirivimab/ 
imdevimab) 

Xevudy 
(sotrovimab) 

Evusheld 
(tixagevimab/ 
cilgavimab) 

Regkirona 
(regdanvimab) 

P337K 
P337R 
P337L 
P337T 
P337H 
G339D 
E340K 
E340I 
E340V 
E340A 
E340Q 
E340G  
S371L 
S373P 
S375F 
K417N 
K417N 
N440K 
G446S 
L452R 
S477N 
T478K 
T478K 
E484A 
E484K 
E484K 
Q493R 
G496S 
Q498R 
N501Y 
N501Y 
N501Y 
N501Y 
Y505H 
N501Y+P681H 

Delta 
Delta 
Delta 
Delta 
Delta 
BA.1  
Delta 
Delta 
Delta 
Delta 
Delta 
Delta 
BA.1 
BA.1 
BA.1 
Beta 
BA.1 
BA.1 
BA.1 
Delta 
BA.1 
Delta 
BA.1 
BA.1 
Beta 
Gamma 
BA.1 
BA.1 
BA.1 
Alpha 
Beta 
Gamma 
BA.1 
BA.1 
Alpha 

K417N+E484K+N501Y 

Beta 

Gamma 
Delta 
Delta 

K417T+E484K+N501Y 
L452R+T478K 
K417N+L452R+T478K 
G339D+S371L+S373P
+S375F+K417N+N440
K+G446S+S477N+T47
8K+E484A+Q493R+G
496S+ 
Q489R+N501Y+ 
Y505H
G339D+S371L+S373P
+S375F+K417N+N440
K+G446S+S477N+T47
8K+E484A+Q493R+G
496S+ 
Q489R+N501Y+ 
Y505H
G339D+S371L+S373P
+S375F+K417N+N440
K+G446S+S477N+T47
8K+E484A+Q493R+G
496S+ 
Q489R+N501Y+ 
Y505H

G339D+S371L+S373P
+S375F+K417N+N440
K+G446S+S477N+T47
8K+E484A+Q493R+G
496S+ 

304 
192 
192 
10.62 
5.13 
2 
297 
190 
200 
100 
50 
18.2 
90.1 
4.9 
1.4 

1.7 

1.6 

2.3 
0.8 

1.3 
2.9 
0.8 

1.4 
1.4 
1.4 
1.2 

1.8 

2.8 
3 
0.8 
2.5 
2.5 
2.2 
3.3 
5.4 

1.9 

4.3 
1.8 
1.8 

1.5 

<2 

<2 
<2 
<2 

0.00 
0.00 
0.01 
0.00 
0.00 
93.04 
0.01 
0.00 
0.00 
0.00 
0.00 
0.00 
85.50 
86.22 
86.15 
93.24 
66.26 
69.14 
70.44 
96.53 
88.27 
96.67 
88.47 
88.26 
85.80 
94.62 
88.37 
85.78 
85.56 
97.34 
86.74 
94.85 
86.07 
85.99 
96.62 

79.46 

0.00 
95.95 
0.17 

0.00 
0.00 
0.01 
0.00 
0.00 
91.01 
0.01 
0.00 
0.00 
0.00 
0.00 
0.00 
81.03 
83.08 
83.75 
91.28 
72.04 
76.79 
78.85 
97.35 
84.95 
97.74 
85.26 
84.02 
91.81 
96.40 
82.35 
80.97 
80.03 
98.29 
92.16 
96.46 
81.91 
83.89 
97.28 

83.03 

0.01 
96.81 
0.04 

8.7 

5.5 

<5 

102 

99.6 

105.3 

5 

<5 

<5 
<5 

BA.1 

1013 

106.5 

106 

51.40 

47.98 

BA.2 

BA.4 

BA.5 

5.4 

65 

0.07 

0.01 

0.00 

0.00 

40.5 

0.00 

0.00 

4 

TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies

Mutation (S protein) 

Variant 

mAbs 

Global 
frequency** 

EU/EEA 
frequency** 

Ronapreve 
(casirivimab/ 
imdevimab) 

Xevudy 
(sotrovimab) 

Evusheld 
(tixagevimab/ 
cilgavimab) 

Regkirona 
(regdanvimab) 

Q489R+N501Y+ 
Y505H 

G339D+S371L+S373P
+S375F+K417N+N440
K+G446S+S477N+T47
8K+E484A+Q493R+G
496S+ 
Q489R+N501Y+ 
Y505H
G339D+S371F+S373P
+S375F+ 
T376A+D405N+ 
R408S+K417N+N440K
+ S477N+ 
T478K+E484A+ 
Q493R+ Q498R+ 
N501Y+Y505H+H655Y
+ N679K+ P681H+ 
N764K

BA.2.75 

15 

0.00 

0.00 

BA.2 

 <5 

68.68 

64.15 

*A red cell indicates ≥100-fold reduction in susceptibility; an orange cell indicates a 25-99-fold reduction in susceptibility; a 
yellow cell indicates 5-25-fold reduction in susceptibility and a green cell indicates <5 -fold reduction in susceptibility. An empty 
cell indicates no neutralisation data. 
** Global and EU/EEA frequency among sequenced isolates deployed to GISAID. 

The mutations found in ORF1ab, namely nsp5:S144A, nsp5:Q189K, nsp5:H172Y, nsp5:E166A, and nsp5:F140A 
conferred moderate to high reduction in susceptibility to Paxlovid (nirmatrelvir/ritonavir), while nsp12:S861G 
conferred 25–99-fold reduction in susceptibility to Veklury (remdesivir) (Table 3). 

Table 4 summarises the neutralisation efficacy of the four EMA approved mAbs against 11 SARS-CoV-2 variants. 
The median fold-reduction values extracted from the data indicated a highly reduced neutralisation capacity of 
Ronapreve (casirivimab/imdevimab) for all Omicron sub-lineages, especially for BA.1 and BA.2.75 (>1000 fold-
reduction). Similar results have been obtained for Regkirona (regdanvimab), to which the sub-lineages BA.1, 
BA.2, and BA.5 showed high reduction in susceptibility (>1 000-fold reduction). The extracted results have shown 
high neutralisation efficacy of Xevudy (sotrovimab) against most SARS-CoV-2 sub-lineages, but moderate 
reduction in neutralisation activity was noticed for BA.2, BA.4, and BQ.1.1. Evusheld (tixagevimab/cilgavimab) has 
been shown to have highly reduced neutralisation activity against the BQ.1 and BQ.1.1 sub-lineages (median 
value fold-reduction of 476). 

5 

TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

Table 3. Mutations in the ORF1ab protein and their corresponding reductions in susceptibility to 
antiviral drugs 

Mutation (ORF1ab protein) 

Antiviral drugs 

Veklury (remdesivir) 

Paxlovid (Nirmatrelvir/ritonavir) 

Global frequency** 

EU/EEA frequency** 

4.4 

23.6 

3.5 

39 

91.9 

6.4 

33.4 

233 

65.4 

3.7 

nsp5:G15S 

nsp5:Y54A 

nsp5:T135S 

nsp5:F140A 

nsp5:S144A 

nsp5:H164N 

nsp5:E166A 

nsp12:V166A 

nsp5:H172Y 

nsp5:Q189K 

nsp12:N198S 

nsp5:D248E 

nsp12:F480L 

nsp12:D484Y 

nsp12:V557L 

nsp12:V792I 

nsp12:E796G 

nsp12:C799F 

nsp12:C799R 

nsp12:E802D 

nsp12:E802A 

nsp12:S861G 

nsp12:S861A 

10.4 

10.4 

3.8 

3.1 

5.7 

8 

2.6 

11.5 

2.7 

7.3 

3.9 

29.7 

2.8 

0.2% 

0.0% 

0.0% 

0.0% 

0.0% 

0.03% 

0.0% 

0.0% 

0.0% 

0.0% 

0.01% 

0.01% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.13% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.01% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

0.0% 

*A red cell indicates ≥100-fold reduction in susceptibility; an orange cell indicates a 25–99-fold reduction in susceptibility; a 
yellow cell indicates 5–25-fold reduction in susceptibility and a green cell indicates <5-fold reduction in susceptibility. An empty 
cell indicates no neutralisation data. 

** Global and EU/EEA frequency among sequenced isolates deployed to GISAID. 

Table 4. Median fold-reduction values for neutralisation susceptibility of four mAbs to 11 variants 
and sub-lineages 

Ronapreve 
(casirivimab / 
imdevimab) 

Xevudy 
(sotrovimab) 

Evusheld 
(tixagevimab / 
cilgavimab) 

Regkirona 
(regdanvimab) 

Alpha 

Beta  

0.9 

1.6 

Gamma 

0.85 

Delta 

2.2 

BA.1 

BA.2 

BA.4 

BA.5 

>1 000 

164 

135 

432 

 BA.2.75 

>1 000 

BQ.1 

100 

 BQ.1.1  

100 

1.8 

1 

1.35 

1.5 

4.8 

29 

27 

19 

19 

14 

41 

0.8 

1.7 

0.75 

1.05 

81 

7.75 

6 

20 

19.5 

476 

476 

1.2 

39 

99.5 

8.6 

>1 000 

>1 000 

>1 000 

25 

A red cell indicates ≥100-fold reduction in susceptibility; an orange cell indicates a 25–99-fold reduction in susceptibility; a yellow 
cell indicates 5–25-fold reduction in susceptibility and a green cell indicates <5-fold reduction in susceptibility. An empty cell 
indicates no neutralisation data. 

6 

 
 
 
 
 
 
   
  
  
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

Discussion 

SARS-CoV-2 has infected millions of people worldwide since the beginning of the pandemic, and new variants are 
likely to continue to appear and have an impact on the regional and global epidemiological situation. Newly 
emerging variants, some of which have altered antigenic characteristics, may develop resistance to existing 
antiviral drugs and/or mAbs and may evade natural or vaccine-induced immunity. This could have clinical and 
public health implications, so efforts to detect new emerging virus variants and to develop effective drugs and 
treatment early should continue. Monitoring viral load and antiviral susceptibility, especially in 
immunocompromised patients, will continue to be important in order to quickly identify, assess, and counteract 
emerging resistance to available antiviral and/or therapeutic treatments. In particular, specimens from 
immunocompromised patients under treatment should be selected for antigenic characterisation, given the higher 
probability of acquiring mutations associated with resistance and antigenic drift due to prolonged viral shedding. 
The ‘fitness’ and the clinical and public health importance of any emerging virus variant should be swiftly evaluated 
for its resistance pattern using established methods and techniques. 

The mutations S144A, Q189K, H172Y, E166A, and F140A in ORF1ab lead to partial or complete resistance to 
Paxlovid (nirmatrelvir/ritonavir), causing concerns regarding the decreased effectiveness of this drug against SARS-
CoV-2 [22]. Ronapreve (casirivimab/imdevimab) showed complete loss of activity against all Omicron sub-lineages 
in vitro [23-25], while it effectively neutralised Alpha, Beta, and Delta variants [23,26,27]. Clinical studies have 
demonstrated statistically significant risk reduction (81%) in the development of symptomatic SARS-CoV-2 
infections with casirivimab and imdevimab treatment versus placebo [28,29]. Regkirona (regdanvimab) showed 
highly reduced neutralising activity against Omicron sub-lineages BA.1, BA.2, and BA.5, leading to complete 
resistance in in vitro conditions [30]. Clinical studies conducted before the emergence of the Omicron variant have 
shown that Regkirona (regdanvimab) significantly reduced the proportion of patients progressing to severe/critical 
COVID-19 condition and that it shortened the time to clinical recovery [31,32]. Xevudy (sotrovimab) maintained 
complete neutralising activity against most SARS-CoV-2 variants. However, it demonstrated partial loss of activity 
against Omicron sub-lineages BA.2, BA.4, and BQ.1.1 in cell culture neutralisation assays but not in hamsters 
[33,34]. This discrepancy needs further investigation and may require the development of alternative methods to 
those currently available. Evusheld (tixagevimab/cilgavimab) showed highly reduced neutralising activity against 
the BQ.1 and BQ.1.1 sub-lineages. The United States Food and Drug Administration (FDA) issued a statement of a 
potential risk of treatment failure due to the development of viral variants that are resistant to Evusheld [11]. 
Virus-like particles (VLPs) pseudotyped with the S protein of Omicron sub-lineages BQ.1 or BQ.1.1 showed >2 000-
fold reductions in neutralising activity [11]. However, it is not known how neutralisation data with pseudotyped 
VLPs or virus isolates correlate with clinical outcome in patients. Collection of clinical data (e.g. comorbidities, 
disease duration, clinical outcome) for patients under treatment, for which further genetic and/or antigenic virus 
characterisation is conducted, will enable the identification of amino acid substitutions associated with laboratory 
resistance that are clinically relevant. 

Monitoring the resistance of circulating new variants to mAb-based antiviral treatments is important for making decisions 
on whether some of the developed mAbs should be discontinued or different combinations of mAbs should be used. 
Neutralising susceptibility data appeared quite variable, leading to discordant findings among investigations [35,36]. This 
variability comes from the fact that there are various neutralising assays, including those carried out in cell culture using 
clinical isolates, chimeric, recombinant, and pseudotyped viruses. There may be the need to develop new tools for drug 
and therapeutic assessment if traditional assays do not have the scope to evaluate changes that are outside of the spike 
region and/or require Fc mediated or cellular immunity elements to be present for full therapeutic effect to be modelled. 
Due to variations in the quantity of the virus inoculum and the cells used for culture, results for the same specimen 
against a given virus variant might vary even among laboratories employing the same type of assay [35,36]. It is 
anticipated that reproducibility between studies will increase as neutralising assays become more standardised, and as 
external controls like those offered by the WHO [37] are utilised more frequently. 

The available information on mAbs and antivirals neutralising efficacies against SARS-CoV-2 is constantly changing 
[38,39]. As a result, the data will need to be updated frequently when new assays and results are published, as well 
as when new variants emerge. Genotypic and phenotypic testing need to be implemented in the laboratories to 
monitor the emergence and spread of resistant virus strains. Neutralisation assays can be used to examine the 
neutralising capacity of therapeutic antibodies, while WGS data can be used in combination to assess the association 
of the different amino acid substitutions with resistance [16]. Adopting a global external standard for calibration would 
improve concordance across various tests and results would be provided in global units rather than IC50 values (for 
mAbs) or plasma dilution values [37,40]. Following the example of the existing influenza antiviral resistance 
surveillance system, establishment of a global surveillance system, criteria for evaluation of antiviral susceptibility and 
collection of clinical data to correlate with in vitro data for COVID-19 therapeutics could be considered. 

Contributors 

Contributing ECDC experts (alphabetical order): Eeva Broberg, Annette Kraus, Angeliki Melidou, Priyanka 
Nannapaneni, Maja Vukovikj. 

Acknowledgements: Simon Funnell, UK Health Security Agency, United Kingdom. 

7 

 
 
 
 
 
 
TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

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TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

Annex 1 

Individual and combination of SARS-CoV-2 spike mutations for which data were available. 

Gene 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

ORF1ab 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

Mutation 

Number of publications  

G15S 

Y54A 

T135S 

F140A 

S144A 

H164N 

E166A 

V166A 

H172Y 

Q189K 

N198S 

D248E 

F480L 

D484Y 

V557L 

S759A 

V792I 

E796G 

C799F 

C799R 

E802A 

E802D 

S861A 

S861G 

P337H 

P337K 

P337L 

P337R 

P337T 

G339D 

E340Q 

E340V 

E340A 

E340G  

E340I 

E340K 

S371L 

S373P 

S375F 

K417N 

N440K 

L452R 

S477N 

T478K 

T478K 

E484A 

E484K 

Q493R 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

2 

2 

2 

1 

1 

1 

1 

1 

2 

2 

1 

1 

1 

1 

1 

1 

1 

2 

1 

1 

1 

1 

1 

1 

2 

2 

2 

3 

2 

1 

1 

1 

1 

2 

5 

1 

10 

 
 
 
 
 
 
TECHNICAL REPORT  SARS-CoV-2 variant mutations conferring reduced susceptibility to antiviral drugs and monoclonal antibodies 

Gene 

Mutation 

Number of publications  

S 

S 

S 

S 

S 

S 

S 

S 

S 

S 

G496S 

Q498R 

N501Y 

Y505H 

L452R+T478K 

K417N+E484K+N501Y 

N501Y+P681H 

G339D+S371F+S373P+ 
S375F+T376A+D405N+ 
R408S+K417N+N440K+ 
S477N+T478K+E484A+ 
Q493R+Q498R+N501Y+ Y505H 

G339D+S371F+S373P+S375F+ 
T376A+D405N+R408S+K417N+ 
N440K+S477N+T478K+E484A+ 
Q493R+Q498R+N501Y+Y505H+ H655Y+ 
N679K+ P681H+ N764K 

G339D+S371L+S373P+ 
S375F+K417N+N440K+ 
G446S+S477N+T478K+ 
E484A+Q493R+G496S+ 
Q489R+N501Y+Y505H 

2 

1 

8 

1 

5 

14 

2 

6 

2 

5 

11