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Comparable neutralization of SARS-CoV-2 Delta AY.1 and Delta with individuals sera
vaccinated with BBV152
1*Pragya D. Yadav, Ph.D, 1Rima R Sahay, MD, 1Gajanan Sapkal, Ph.D, 1Dimpal Nyayanit, Ph.D,
1Anita M. Shete, Ph.D, 1Gururaj Deshpande, Ph.D, 1Deepak Y. Patil, Ph.D, 2Nivedita Gupta,
Ph.D, 3Sanjay Kumar, M.Ch, 1Priya Abraham, Ph.D, 2Samiran Panda, Ph.D, 2Balram Bhargava,
1Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra,
2Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911,
Ansari Nagar, New Delhi, India Pin-110029
3Department of Neurosurgery, Command Hospital (Southern Command), Armed Forces
Medical College, Pune, Maharashtra, India - 411040.
© International Society of Travel Medicine 2021. Published by Oxford University Press. All
rights reserved. For Permissions, please e-mail: firstname.lastname@example.org
Dr. Pragya D. Yadav,
Scientist ‘E’ and Group Leader,
Maximum Containment Facility,
Indian Council of Medical Research-National Institute of Virology,
Sus Road, Pashan, Pune, Maharashtra, India Pin-411021.
Phone: +9120-26006111, Fax No. 91-20-26122669
Keywords: SARS-CoV-2; Variant of concern; Delta; Delta AY.1; Neutralization; BBV152
Sera of COVID-19 naive vaccinees, COVID-19 recovered cases with vaccination and
breakthrough cases demonstrated 1.3, 2.5 and 1.9-fold reduction in neutralization titers
against Delta and 1.5, 3.5, 2.8-fold against Delta AY.1 compared to B.1 respectively.
However, high neutralization titers would still effectively protect against Delta, Delta AY.1
and B.1.617.3 variants.
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Delta variant
(B.1.617.2), a variant of concern (VOC), was associated with the second wave of pandemic
in India during March-May 2021. Delta variant has outpaced the other two sub-lineages
Kappa (B.1.617.1) and B.1.617.3 and was responsible for 90% of the cases reported in
India.1 It has spread across 112 countries and found to be more infectious than the Alpha,
Beta and Gamma variants. Reduced neutralization has been reported with the sera of
individuals vaccinated with BNT162b2, BBV152/Covaxin and chAdOx1-s against Delta
variant in recent reports.2,3 Delta variant has also been identified as the leading cause of
breakthrough infections globally among vaccinated individuals.4
Delta variant with its characteristic spike protein mutations (L452R, T478K, D614G
and P681R) has mutated further into four sub-lineages with additional mutations which
are associated with higher transmission and probable immune escape.1 Recently, Delta
variant has mutated to Delta AY.1, AY.2 and AY.3. Of these, apparently highly infectious
Delta AY.1 variant was first detected in India in April 2021 and subsequently from twenty
seven other countries as well.1 Cases of Delta AY.1 have also been reported from Europe,
Asia and America with the highest prevalence observed in United States of America,
Portugal, Japan, United Kingdom and Switzerland.5 The variant has characteristic
mutations in the genome at ORF1a (A1306S, P2046L, P2287S, V2930L, T3255I, T3646A),
ORF1b (P314L, G662S, P1000L, A1918V), S (T19R, L452R, T478K, D614G, P681R), ORF3a
(S26L), M (I82T), ORF7a (V82A, T120I), ORF7b (T40I), ORF8 (del119/120) and N (D63G,
R203M, G215C, D377Y) which probably enhances the ability to escape immune response
and becomes a major concern for the ongoing vaccination programs.5 Moreover, this
variant contains an additional K417N mutation in the spike protein and emerging evidence
suggests that this mutation could lead to resistance against monoclonal antibodies i.e.,
Casirivimab and Imdevimab.6 However, it is uncertain whether Delta AY.1 is capable of
causing higher transmissibility, severe disease and evasion of immune response compared
to Delta variant. The prevalence of Delta AY.1 is found to be low in India and the rest of the
world. As of now no information is available on the efficacy of currently available vaccines
against Delta AY.1 variant.
The clinical efficacy against COVID-19 infection of BBV152, a whole-virion
inactivated SARS-CoV-2 vaccine was assessed in a double-blind, randomized, multicentre,
phase 3 clinical trial on 25,798 participants to evaluate the efficacy, safety, and
immunological lot consistency of BBV152. Overall efficacy against symptomatic COVID-19
disease was 77.8% and 65.2% protection against Delta variant has been reported with
The second wave of the SARS-CoV-2 pandemic was devastating for public health
system of India and breakthrough cases were reported during this period. Besides this, the
association of Delta variant in the breakthrough cases created serious concerns among the
public health experts regarding the effectiveness of the available COVID-19 vaccines.
Considering this, we conducted this study to determine the neutralization potential in sera
of the BBV152 vaccinated individuals against Delta and Delta AY.1 variant.
Here, we present the data from a cross-sectional study, where the sera of the fully
vaccinated study participants with two doses of BBV152 vaccine were evaluated for
neutralizing antibodies. The participants were divided in three separate groups viz. COVID-
19 naïve vaccinees (CNV), COVID-19 recovered cases (real time RT-PCR positive) and
vaccinated (CRV) and breakthrough infections post vaccination (BTI). The data of the
variants responsible for SARS-CoV-2 infection in CRV and BTI groups was not available.
However, the participants of CRV group were infected before the emergence of Delta
variant in India when the predominant circulating SARS-CoV-2 strain was B.1. The BTI
occurred mainly during the second wave of pandemic in India when the commonly
circulating variant in the country was Delta in March-May 2021.8-9
The sera of individuals of CNV group [n=42; Female (n=24; median age: 43.5yrs);
Male (n=18; median age: 46 yrs)] was collected between 2.5 to 22 weeks [median: 16
weeks] after second dose, CRV group [n=14; female (n=8; median age: 44.5yrs); male (n=6;
median age: 42 yrs)] 14-70 weeks [median: 38 weeks] after second dose and BTI group
[n=30; female (n=17; median age: 45 yrs); male (n=13; median age: 39 yrs)] collected
between 2-18 weeks (median: 9 weeks). The neutralizing potential of the individuals was
determined against Delta, Delta AY.1, B.1.617.3 compared to B.1 variant. Neutralizing
antibody titers of the serum samples against all the variants were determined using 50%
plaque reduction neutralization test. IgG response was also assessed using whole
inactivated SARS-CoV-2 antigen, nucleocapsid and S1-RBD protein IgG ELISA.
The sera of individuals of CNV group showed a geometric mean titer (GMT) of NAb
to be 310.6 (95% confidence interval (CI): 222-434.6); 241.6 (95% CI: 167.8-347.7); 209.1
(95% CI: 146.5-298.3); 165.3 (95% CI: 115.6-236.5) against B.1, Delta, Delta AY.1 and
B.1.617.3 respectively. The sera of the individuals of CRV showed uniformly increased NAb
titer with GMT of 820.1 (95% CI: 469-1434)’ 328.6 (95% CI: 186.9-577.9)’ 234.5 (95% CI:
138.7-396.4) and 217.8 (95% CI: 136.7-347.1) against B.1, Delta, Delta AY.1 and B.1.617.3
respectively. Sera of individuals of BTI group had higher NAb titer compared to the CNV
and CRV groups. The GMT titers were 896.6 (95% CI: 550.3-1461), 465.6 (95% CI: 213.2-
1016), 317.2 (95% CI: 125.5-801.4), 259.7 (95% CI: 157.1-429.4) against B.1, Delta, Delta
AY.1 and B.1.617.3 respectively (Figure 1a-d).
The sera of individuals of CNV group showed moderate fold-reduction in the NAb
titer against Delta, Delta AY.1 and B.1.617.3 [1.29 (p-value: < 0.0001); 1.49 (p-value :
<0.0001); 1.88 (p-value: <0.0001)] compared to B.1 (Figure 1e). However, the sera of
individuals of CRV and BTI groups had higher fold-reductions in the NAb titer [2.5 (p-value:
0.0011); 3.5 (p-value: 0.0007); 3.77 (p-value: 0.0007)] and [1.93 (p-value: <0.0001); 2.83
(p-value: <0.0001); 3.45 (p-value: <0.0001)] against Delta, Delta AY.1 and B.1.617.3
variants respectively compared to the B.1 strain (Figure 1f-g). However, NAb titer of sera of
CRV and BTI groups were significantly higher compared to CNV group.
Sera of individuals of CNV and BTI groups had 3.04 fold (p-value: 0.0019), 3.56 fold
(p-value: <0.0001) and 4.42 fold (p-value: <0.0001) higher antibodies than sera of CRV
group for inactivated SARS-CoV-2, S1-RBD protein and N protein based anti-SARS-CoV-2
ELISA respectively (Figure 1h-j).
A significant increase in the NAb titer against B.1, Delta, Delta AY.1 and B.1.617.3
variants in CRV and BTI groups was observed compared to the CNV group individuals. This
demonstrates the possible role of memory cells in immune boosting with post-infection or
infection after immunization. The NAb titre in sera of the individuals from CRV and BTI
groups were higher due to boosting effect of vaccination and natural infection or vice versa
than individuals from CNV group. In a recent studies by Gupta et al., has shown that two
dose vaccinated individuals though got infected with COVID-19 with Delta variant; but
severity, admission to ICU and mortality was negligible during second wave of Pandemic in
India.9 The comparative analysis of three different cohorts revealed that B.1.617.3 variant
showed reduced neutralization followed by Delta AY.1 and Delta variants when compared
to B.1 (Figure 1a-g). A recent study demonstrated a reduction in neutralization by 4 fold
and 11 fold against Delta variant with the sera of healthy individuals vaccinated with two
doses of ChAdOx1 and BNT162b2 vaccine respectively.2 Our earlier studies with
BBV152/Covaxin™ and Covishield™ have shown 2.7- and 3.2-fold reduction in NAb titer
against Delta variant compared to B.1.3,10 The present study revealed 1.5, 3.5, 2.8-fold
reduction in NAb titer for Delta AY.1, 1.3, 2.5 and 1.9-fold reduction against Delta variant
compared to B.1 variant in sera of CNV, CRV and BTI respectively.
The primary objective of this study was to determine the neutralization efficacy of
BBV152 vaccine against Delta variants in real time scenario as oppose to the controlled
clinical trial scenario. The time interval for collection of the serum samples is a limitation of
this study. However, the results demonstrated reduction in the neutralization titer in the
individual cohorts against the Delta, Delta AY.1 and B.1.617.3 variants compared to B.1
strain. In conclusion, reduction in the NAb titer was observed in the sera of COVID-19 naïve
vaccinated individuals, COVID-19 recovered followed by vaccination and breakthrough
cases post two doses of BBV152. The sera of individuals belonging to three different
cohorts had high NAb titer. This suggests that BBV152 would still be able to protect
vaccinated individuals with severe disease from Delta, Delta AY.1 and B.1.617.3 variants.
The study was approved by the Institutional Human Ethics Committee of ICMR-NIV, Pune,
India under the project ‘Assessment of immunological responses in breakthrough cases of
SARS-CoV-2 in post-COVID-19 vaccinated group’.
PDY contributed to study design, data analysis, interpretation and writing. RRS, GS, GRD,
DAN, AMS, DYP and SK contributed to data collection, data analysis, interpretation and
writing. PA, NG, SP, and BB contributed to the critical review and finalization of the paper.
Conflicts of Interest
Authors do not have a conflict of interest among themselves.
Financial support & sponsorship
The grant was provided from Indian Council of Medical Research (ICMR), New Delhi under
intramural funding ‘COVID-19 to ICMR-National Institute of Virology, Pune for conducting
We sincerely acknowledge the excellent support of Mr. Prasad Sarkale, Mr. Shreekant
Baradkar, Dr. Rajlaxmi Jain, Ms. Aasha Salunkhe, Mr. Chetan Patil, Mrs. Triparna Majumdar
and Mrs. Savita Patil during the study.
1. PANGO lineages. https://cov-lineages.org/lineage.html?lineage=B.1.617.2. Accessed
on 29 July 2021.
2. Lopez Bernal J, Andrews N, Gower C, et al. Effectiveness of Covid-19 Vaccines
against the B.1.617.2 (Delta) Variant. N Engl J Med. 2021 ;385(7):585-594.
3. Yadav PD, Sapkal GN, Ella R, et al. Neutralization of Beta and Delta variant with sera
of COVID-19 recovered cases and vaccinees of inactivated COVID-19 vaccine
BBV152/Covaxin. J Travel Med. 2021, taab104.
4. Hacisuleyman E, Hale C, Saito Y, et al. Vaccine Breakthrough Infections with SARS-
CoV-2 Variants. N Engl J Med. 2021;384(23):2212-2218.
5. PANGO lineages. https://cov-lineages.org/lineage.html?lineage=AY.1. Accessed on
29 July 2021.
6. Latif AA, Mullen JL, Alkuzweny M, et al. outbreak.info.
https://outbreak.info/situation-reports?pango=AY.1). Accessed 29 July 2021.
7. Ella R, Reddy S, Jogdand H, et al. Safety and immunogenicity of an inactivated SARS-
CoV-2 vaccine, BBV152: interim results from a double-blind, randomised,
multicentre, phase 2 trial, and 3-month follow-up of a double-blind, randomised
phase 1 trial. Lancet Infect Dis. 2021 Jul;21(7):950-961. doi: 10.1016/S1473-
3099(21)00070-0. Epub 2021 Mar 8. PMID: 33705727; PMCID: PMC8221739.
8. Thangaraj JWV, Yadav P, Kumar CG, et al. Predominance of delta variant among the
COVID-19 vaccinated and unvaccinated individuals, India, May 2021 [published
online ahead of print, 2021 Aug 6]. J Infect. 2021;S0163-4453(21)00387-X.
9. Gupta N, Kaur H, Yadav PD, et al. Clinical Characterization and Genomic Analysis of
Samples from COVID-19 Breakthrough Infections during the Second Wave among
the Various States of India. Viruses, 2021, 13: 1782.
10. Sapkal GN, Yadav PD, Sahay RR, et al. Neutralization of Delta variant with sera of
Covishield™ vaccinees and COVID-19-recovered vaccinated individuals. J Travel
Med. 2021, taab119.
Legend of Figures:
Figure 1: Neutralization of individual sera vaccinated with BBV152 vaccines from
different scenarios against B.1, Delta, Delta AY.1 and B.1.617.3 strains and ELISA titer
of individual sera vaccinated from different scenarios: Neutralization titer comparison
of individual cases sera immunized with two dose vaccine BBV152, recovered case sera
immunized with two dose vaccine BBV152 and breakthrough cases; B.1 (GISAID identifier:
EPL_ISL_825088). Dotted lines represents the cut-off value of the assay (20) (a), Delta
(GISAID accession number: EPI_ISL_2400521) (b), Delta AY1 (GISAID accession number
EPI_ISL_2671901) (c), and B.1.617.3 (GISAID accession number: EPL_ISL_2497905) (d).
The statistical significance was assessed using a two-tailed Kruskal Wallis test with Dunn’s
test of multiple comparisons was performed to analyze the statistical significance. NAb titer
of individual sera vaccinated with two doses of BBV152 (e), recovered cases administered
with two doses of BBV152 (f) and breakthrough cases (g). A matched pair two-tailed pair-
wise comparison was performed using the Wilcoxon signed-rank test to analyze the
statistical significance. Anti-SARS-CoV-2 IgG titers of vaccinated individual’s sera for
inactivated SARS-CoV-2, dotted lines represents the cut-off value of the assay (100) (h), S1-
RBD protein, dotted lines represents the cut-off value of the assay (50) (i) and N protein,
dotted lines represents the cut-off value of the assay (50) (j). The statistical significance
was assessed using a two-tailed Kruskal-Wallis test with Dunn’s test of multiple
comparisons. P-value less than 0.05 were considered to be statistically significant for the
tests applied. The dotted line on the figures indicates the limit of detection of the assay.
Data are presented as mean values +/− standard deviation (SD).