Introduction
One
of the most economically significant diseases of poultry is infectious
bronchitis virus (Uddin et al. 2016).
This virus is a continuously evolving with an envelope that carries a
positive-sense, single-stranded RNA genome. It is classified within the Gamma
coronavirus genus of the Coronaviridae family. The poultry industry worldwide
has faced remarkable economic losses due to IBV-accompanying conditions such as
tracheitis, proventriculitis, nephritis, salpingitis and significant decrease in
egg production (Zhang et al. 2020).
The important structural proteins are encoded by the IBV genome which are N
protein (nucleocapsid), M (membrane-protein), S (spike-glycoprotein) and E
(small membrane-protein). IBV can cause harm to the host's kidneys,
reproductive system, and respiratory tract by replicating within the epithelium
of numerous organs (Wit et al. 2019).
IBV strains are categorized into 35 lineages having seven genotypes using a
novel classification technique (GI to GVII) (Valastro
et al. 2016; Chen et al. 2017; Jiang et al. 2017; Ma et
al. 2019). It is typical to see the disease in vaccinated chickens
also, which has a significant negative economic impact globally (Sumi et al. 2012). Respiratory diseases
such as tracheal rales, coughing, and sneezing, as well as excessive mucus
formation and accumulation in the bronchi, decreased broiler growth, nephritis,
urolithiasis, and permanent oviduct damage, which results in high mortality
rates and abnormal egg production (Worthington
et al. 2008; Bickerton et al. 2018). The size of IBV viral
genome is approximately 27.6 kb having 5 prime and 3 prime non-coding regions (Abro et al. 2012a). It contains three
most important structural proteins that are encoded by the virus, one of which
is the highly variable spike (S) glycoprotein, which is interpreted as a
pre-protein or protein prior to being fragmented into the N-terminal (S1) and
the C-terminal (S2) glycol-polypeptides (Farsang
et al. 2002). The portion of
surface protein (S1) of IBV virus is involved in hem-agglutination and
pathogenicity due to the presence of virus neutralizing epitopes (Abro et al. 2012b). The S1
protein's antigenic determinants alter, resulting in the creation of novel
strains and genotypes (Promkuntod et al. 2015).
IBV serotypes differ in their S1 glycoprotein by around 20 to 25%. On the other
hand, variations of up to 50% have been noted, which has an impact on
cross-protection against virus strains that are developing or reoccurring (Ennaji et al. 2020). The S1 gene of IBV
is most frequently addressed in molecular epidemiological investigations to
describe (e.g., genotyping) and
comprehend the spread of the virus because of its genetic diversity (Bande et al. 2017). It is possible to determine
the path of the virus distribution and identify the strains of the virus that
are most common in a given location by using sequencing and phylo-genomics (Zulperi et al. 2009). However, because
IBV is an extremely fluctuating coronavirus, the current occurrence of novel
strains significantly reduces the efficacy of IBV vaccines (Fan et al. 2018). The vaccines' low
cross-protection rates unavoidably impede the disease's prevention and control (Jordan 2017). IBV can take many different
forms that are difficult to manage. Their vaccines sometimes do have the
ability of cross protection. Attenuated live vaccines are given to broilers and
pullets, and killed vaccines are typically given to layers and breeders.
Effective control requires the identification of the virus that causes the
disease and the subsequent administration of an appropriate vaccine against it (Cavanagh and Naqi 2003). The emergence of new
serotypes as a result of some changes in amino acid sequence is due to the
immunological stress triggered by extensive use of vaccines. The other filed
strains emerge due to the consequence of mixed infection or decline of most
prevailing serotype (Liu et al. 2006).
Numerous IBV serotypes have been identified globally, and there is minute to no
cross-immunity between the various antigenic variants (Cavanagh 2007). This results in an increasing number of
immunological failures and large financial losses for the chicken sector Chen et al. 2017).
Molecular characterization of BV in India
A study was conducted in India to identify and
characterize two strains of the infectious bronchitis virus (IBV) from field
occurrences in broiler chickens in 2008 and 2010 which were
India/LKW/56/IVRI/08 and India/NMK/72/IVRI/10, respectively. The two Indian IBV
isolates presented 73% similarity among them according to nucleotide sequencing
analysis, while India/LKW/56 and India/NMK/72 were 99% similar with the 4/91
(it is pathogenic strain in the UK), JP/Wakayama/2/2004 (Japan), and TA03 (China).
The presence of 4/91 (793/B) IBV nephron-pathogenic variant existing in India
was confirmed for the very first time. Phylogenetic Analysis revealed that the
isolate India/LKW/56/IVRI/08 formed a group with THA280252 (Thailand), and the
isolated strain, India/NMK/72/IVRI/10 formed a separate group with 4/91
pathogenic (UK) (Sumi et al. 2012).
The furthermost prevalent IBV variants identified in India since 1991 were the
(India/Mass/16-V-AD/07) in Mass genotype and 793B strain (Elankumaran et al. 1999).
The strain India/PDRC/Pune/9/99 and various
nephro-pathogenic variants or strains of Infectious Bronchitis were recognized
in 1991 (Bayry et al. 2005). The
five IBV strains were identified and described as Anand isolates. These
isolates were isolates in Gujrat, India and were compared with already isolated
field strains of IBV in Gujrat (Patel et al.
2015). These isolates with other strains are given in Table 1. Another study found that 20 field strains of IBV were
examined in India between 2003 and 2011 using RT-PCR and sequencing of the S1
gene's HVR I and HVR II. The three isolates (I. IND-TN-168-06, II.
IND-TN-280-10, III. IND-TN-290-11) out of 20 were totally new variants which
matched with GI-24 lineage. The Fourteen isolates (a. IND-113-03, b.
IND-114-03, c. IND-TN-04-03, d. IND-TN-20-03, e. IND-TN-92-03, f. IND-TN-95-03,
g. IND-TN-97-03, h. IND-TN-98-03, i. IND-AP-151-05, j. IND-KA-152-05, k.
IND-TN-162-06, l. IND-TN-163-06, m. IND-TN-270-09, n. IND-TN-183-09) were
grouped in GI-1 lineage. The further two (02) field isolates (I. IND-TN-174-07,
II. IND-TN-175-07) grouped into the GI-13 genetic lineage (Raja et al. 2020). Some published IBV
isolates of India with accession numbers are given in Table 1.
Molecular characterization of IBV in China
Table 1: Prevalence
of different isolates of infectious bronchitis virus in India. The given
isolates of IBV have different levels of similarity index of S1 gene sequence.
This table contains the already published Indian IBV isolates with different Antigenic
variations
|
Country |
Strain |
Type |
Gene Bank No# |
Reference |
|
India |
India/ LKW/56/IVRI/08 |
Mass |
HM163471 |
Sumi et
al. (2012) |
|
India/Mass/16-V-AD/07 |
Mass |
HM179146 |
Elankumaran et al. (1999) |
|
|
India/NMK/72/ IVRI/10 |
4/91 |
HM748585 |
Sumi et
al. (2012) |
|
|
India/PDRC/Pune/9/99 |
(Unique) |
AY091551 |
Bayry et al. (2005) |
|
|
ANAND/GUJ/IBV1/2013 |
Cluster I |
KJ577258 |
Patel et al. (2015) |
|
|
ANAND/GUJ/IBV2/2013 |
KJ577259 |
|||
|
ANAND/GUJ/IBV3/2013 |
KJ577260 |
|||
|
ANAND/GUJ/IBV4/2013 |
KJ577261 |
|||
|
ANAND/GUJ/IBV5/2013 |
KJ577262 |
|||
|
IND-TN-168-06 IND-TN-290-11 |
Variant IBV (GI-24) |
JX966396 JX966403 |
Raja et al.
(2020) |
|
|
ND-113-03 IND-114-03 IND-TN-04-03 IND-TN-20-03 IND-TN-92-03 IND-TN-95-03 IND-TN-97-03 IND-TN-98-03 IND-AP-151-05 IND-KA-152-05 IND-TN-162-06 IND-TN-163-06 IND-TN-270-09 IND-TN-183-09 |
(Mass 41 IBV) GI-1 |
JX966392 EF165593 EF165596 EF165597 EF165598 EF165599 EF165600 EF165601 JX966393 EF165595 JX966394 JX966395 JX966400 JX966399 |
||
|
IND-TN-174-07 IND-TN-175-07 |
UK 4/91 IBV (GI-13) |
JX966397 JX966398 |
||
|
IND-284-10 |
Indian nephron-pathogenic IBV |
JX966402 |
In 2019, HeN-1/China/2019, HeN-2/China/2019, and
HeN-101/China/2019 were shown to be three extremely aggressive IBV strains in
China. The recently found IBV strain was closely linked to the
ck/China/I0529/17 strain and classified into the GI-19 genotype clade on the
basis of genetic sequence and phylogenetic study of the full S1 gene, despite
the fact that the gross pathological demonstration of two IB outbreaks was
divergent. This work shed light on recently occurring IBV epidemics in poultry
with IBV vaccinations and identified the genetic traits of three virulent GI-19
IBV strains, demonstrating the necessity of implementing appropriate
preventative measures and management tactics.
After Molecular detection, four IBV strains were isolated comprising
HeN-101/China/2019, and HeN-102/China/2019, HeN-1/China/2019, HeN-2/China/2019.
After complete sequencing the complete S1 gene Hen-1 and Hen-2 strains showed
99.9% similarity, while Hen-101 and Hen-102 showed 100 similarities exploring
the fact that these two outbreaks were triggered by single IBV strain (Zhang et al. 2020). In 2018, ck/CH/LDL/150434–I
(LDL/150434–I), ck/CH/LDL/150434–II (LDL/150434–II), and ck/CH/LDL/150434–III
(LDL/150434–III) are the three distinct IBV genotypes/serotypes that were
identified in chicken (Han et al. 2018).
The Novel IBV strain, ck/CH/LGX/111119 was identified in 2017 and grouped in
GI-28 lineage. This new novel strain may be the result of the recombination of
IBVs in LX4 genotype and non-identifies IBV strain, or S1 gene of unidentified
IBV or mutations in S1 gene of IBVs of LX4 genotype (Chen et al. 2017). Nine distinct genetic families,
including Mass- and 793B-type viruses, reported in China: LX4, LDT3, LHLJ, BJ,
LDL, N1/62, and LSC (Han et al. 2011).
The wider distribution and high pathogenicity make the IBVs of LX4 and LDL
groups more significant among all the identified genetic groups.
The different strains were published with Gene Bank No. as
China/LX4/QX/99 (AF193423), China/LDT3/03 (AY702975), China/LHLJ/95I
(DQ167141), China/BJ/97 with (AY31965), China/LDL/Q1/98 (AF286302),
China/N1/62/JAAS/04 (AY839140), China/LSC/99I (DQ167147), China/793B/Sichuan/06
(GQ844991), China/Mass-H120/ SDLY0612/06 (EU857816) and Taiwan/LDL/Q1-3374/05
(DQ402364) (Jackwood
2012). In 2019 and 2020, two isolates of IBV, designated CK/CH/TJ1904
and CK/CH/NP2011, from many poultry farms in the provinces of Tianjin and
Fujian were recovered, respectively. The
CK/CH/TJ1904 and CK/CH/NP2011 strains whole genome sequences have been added to
Gene Bank under the accession numbers MW815494 and MW815495 (Sun et al. 2021). For the previous 20 years, the QX (GI-19) genotype has
dominated the Chinese population. It was initially identified in Qingdao,
China, in 1996 (Xu et al. 2018)
(Zhao et al. 2016). China's
Guangxi province reported the first isolation of a GVI-1 strain in 2007. The
strain, dubbed TC07-2, differed significantly from six other key genotypes in
terms of evolution (Li et al. 2010).
The respiratory tract tropism observed in GVI-1 strains may be caused by
extensive gene 3 and S recombination (Ren et
al. 2019). The S1 glycoprotein gene nucleotide sequences of the
avian infectious bronchitis virus (IBV) strains Gray and JMK were identified
and cross-referenced with previously published IBV sequences (Kwon and Jackwood 1995). The new IBV GDTS13 strain was evaluated for vaccine
production, which was common and most prevalent in 2016-2017 in southern
China, GVI-1 is now the most common IBV genotype. Some
published IBV isolates of China with accession numbers are given in Table 2. The
Phylogenetic study was conducted on the basis of whole S1 gene sequences among
16 strains and 156 reference strains. In this experiment, GI-1 includes the mentioned
strains as reference like Mass 41 and H120 having accession numbers AY561711,
FJ888351, respectively (Chen et
al. 2021).
Molecular characterization of IBV in Pakistan
Table 2: Prevalence
of different isolates of infectious bronchitis virus in China. The given
isolates of IBV have different levels of similarity index of S1 gene sequence.
This table contains the already published Chinese IBV isolates with different
Antigenic variations
|
Country |
Strain |
Type |
Gene Bank No# |
Reference |
|
China |
China/LX4/QX/99 China/LDT3/03 China/LHLJ/95I China/BJ/97 China/LDL/Q1/98 China/N1/62/JAAS/04 China/LSC/99I China/793B/Sichuan/06 China/Mass-H120/ SDLY0612/06 Taiwan/LDL/Q1-3374/05 |
LX4 LDT3 LHLJ BJ LDL Subgroup 1 LSC 793B Mass N1/62 |
AF193423 AY702975 DQ167141 AY319651 AF286302 AY839140 DQ167147 GQ844991 EU857816 DQ402364 |
Jackwood
(2012) |
CK/CH/GD/GDJM1206
CK/CH/GD/GDSB1214
CK/CH/GD/BJSN17
|
GVI-1 GVI-1 GVI-1 |
MN193597
MN193599
MN193588
|
Chen et al.
(2021) |
|
|
HeN-1/China/2019 |
G-19 |
MN055627 |
Zhang et al. (2020) |
|
|
HeN-2/China/2019 |
G-19 |
MN055628 |
||
|
HeN-101/China/2019 |
G-19 |
MN635798 |
||
|
ck/CH/LDL/150434–I |
Mass |
Han et al. (2018) |
||
|
ck/CH/LDL/150434–II |
LDT3 |
|||
|
ck/CH/LDL/150434–III |
TWI like |
|||
|
ck/CH/LGX/111119 |
GI-28 |
KX640829 |
Chen et al. (2017) |
|
CK/CH/TJ1904
|
GV1 |
MW815494 |
Sun et al. (2021) |
|
CK/CH/NP2011
|
GV1 |
MW815495 |
||
DY07
MN07
DY05
ZX07
LZ07
NN04
HY06
CQ04-2
TC07-2
|
Genotype -I
Genotype--I
Genotype -I
Genotype--I
Genotype II
Genotype-II
Genotype
-III
Genotype--III
Genotype
-VI
|
GQ265927
GQ265946
GQ265928
GQ265949
GQ265944
GQ265951
GQ265941
GQ265953
GQ265948
|
Li et al. (2010) |
|
|
|
Ck/CH/LSD/091003
Ck/CH/LDL/091022
Ck/CH/LJL/090330
CK/CH/GD/GDJM502
CK/CH/GD/GDSB1220
|
QX like QX like QX Like GI-19 lineage GI-19 lineage |
HM194708
HM194640
HM194674
MN193595
MN193600
|
Ren et al. (2019) |
A trail was conducted to examine clinical samples
of IBV in Pakistan, 358 out of 905 samples were found to be positive, with
serotype distributions of Mass strain (43%), 4/91strain (51%), and various IBV
variants (5%), respectively. A variant Pak-973 was recovered from Broiler
Breeder flock through molecular characterization. IBV isolate was given name as
KX013102_NARC/973_Pakistan_2015. The phylogenetic study presented 93% resemblance
with KF360983_23/B/2008_India. After sequencing the Pak-973 isolate, a
difference of almost 7% was noticed with the rest of the variants and
serotypes. The 13 Amino acid substitutions also made pak-973 different from
rest of the isolates. The amino acid mutations were found on the hyper variable
region 1 and hyper variable region 2s, which made the Pak-973 as new IBV
strain. This study focused on the point that vaccine matching should be done
before the selection of vaccine to control IB in commercial poultry (Rafique et al. 2018a). The majority of IBV isolates in Pakistan was grouped
into GI-24 lineage and some were classified in GI-13. One isolate UAF-8 was
placed in GI-1 lineage. This study evaluated the criteria using the 9 novel
sequences for all Pakistani isolates of IBV that are currently available. The 8
sequences of IBV isolates out of 9 were grouped in GI-13 and one was placed in
GI-24 lineage. The isolates from the liver, kidney, and respiratory tract are
included in the GI-24 lineage and strains of GI-13 lineage are mostly linked to
samples isolated from the reproductive and respiratory system (Saleem et al. 2024). The Pakistani IBV
isolates from different areas are given in Table 1. Another study which
was conducted in Pakistan revealed the unique IBV strain named as Pak-786. It
showed link with GI-13 lineage that comprise the vaccine as well as highly
pathogenic field strains. The study backs up the idea that a range of variants
arise via random accidental mutation and genetic recombination, which may cause
genetic drift, as a result of the widespread use of live IBV vaccination strains
with different origins. The study's emerging strain of IBV highlights the
necessity of including these variants in killed vaccine form into the affected
region's immunization program (Rafique et al.
2018b). The most common strain of the
infectious bronchitis virus was determined to be M-41, which was detected in
100% of layer flocks and roughly 67% of broiler flocks, with a total combined
incidence of 88% in all flocks examined (Ahmed et
al. 2007). Some published IBV isolates of Pakistan with accession
numbers are given in Table 3.
Molecular characterization of IBV in Iran
Table 3: Prevalence
of different isolates of infectious bronchitis virus in Pakistan. The given
isolates of IBV have different levels of similarity index of S1 gene sequence.
This table contains the already published Pakistani IBV isolates with different
Antigenic variations
|
Country |
Strain |
Type |
Gene bank No. |
Reference |
|
Pakistan |
NARC/973_Pakistan_2015 IBV17/QAU/Pakistan/Talagang/2017 lung/trachea IBV/Ahad51 2018 Pakistan liver IBV/Ahad559 2019 Pakistan liver CK/PAK/UDL/MS-05/LHR/2020 Pakistan lung trachea kidney CK/PAK/UDL/MS-02/RWPD/2020 Pakistan lung trachea kidney CK/PAK/UDL/MS-03/MULT/2020 Pakistan lung trachea kidney CK/PAK/UDL/MS-06/LHR/2020 Pakistan lung trachea kidney CK/PAK/UDL/MS-04/MULT/2020 Pakistan lung trachea kidney CK/PAK/UDL/MS-01/ABTD/2020 Pakistan lung trachea kidney UAF-10 2020 Pakistan kidney UAF-9_2018 Pakistan lung IBV/Ahad 196 2018 Pakistan liver IBV/Ahad13 2018 Pakistan liver CK/PK/UVAS-GM-026-Lalamusa/2019
Pakistan IBV/Ahad4 2018 Pakistan liver IBV/Ahad3 2018 Pakistan liver IBV19/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBV20/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBV21/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBV18/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBVQ2/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBVQ1/QAU/Pakistan/Rawalpindi/2017 Pakistan lung IBV4/QAU/Pakistan/Rawalpindi/2017 Pakistan lung chicken/Pakistan/PATH-IX 2019 Pakistan tissue homogenate UAF-8 2020 Pakistan Liver NARC/786_Pakistan_2013 |
(GI-24) (GI-13) (GI-1) (GI-13) |
KX013102 MH703657 MW464186 MW464189 OL763345 OL763342 OL763343 OL763346 OL763344 OL763341 MW525215 MW525214 MW464188 MW464185 MK689242 MW464184 MW464183 MH703659 MH703661 MH703660 MH703858 MH703663 MH703662 MH703655 MW856023 MW525216 KU145467 |
Rafique et al. (2018a) Saleem et al. (2024) Rafique et al. (2018b) |
A unique study demonstrated that samples were collected from (40) forty IB infected
flocks from 4 different provinces of Iran. The samples were inoculated in to 9–11
days old chicken eggs (embryonated). After collection of fluid and RT-PCR,
results showed that Four (04) isolates (IBV-83, IBV-29, IBV-80, and IBV-56) had
high similarity (98.56 to 99.59%) to 4/91 serotype which belongs to (Pakistani
strain) GI-13 lineage. Following phylogenetic analysis (on comparison of
Nucleotide sequence), three isolates (IBV-80, IBV-16, and IBV-17) were
classified as belonging to the GI-19 lineage (QX-like viruses), as they had 98
to 99% of the similarities to Iran and Iraq origin QX-like viruses. Two
isolates IBV-34 and IBV-106, which belong to the GI-23 lineage (variant-2)
share a 95–97% resemblance with Iranian variants of the GI-23 lineage. In this
Current research, IBV was identified from 30% of the 40 flocks situated in
diverse areas of Iran. Among these isolates, the 793/B serotype emerged as the
most prevalent, with QX-like, variant-2 and Massachusetts isolates following in
respective order of occurrence. It's noteworthy that all four lineages were
identified to be actively circulating within these 40 flocks.
The dominant IBV genotypes identified in specific regions of Iran
include the GI-13, GI-19, and GI-23 lineages (Ghorbiani
et al. 2020). In 1994,
there was a report on the initial isolation of the IBV in Iranian chicken
flocks. A study revealed that IBV isolates in
Iran showed linkages to six different genetic groups. Group I had 40 field
isolates (34%) that were most similar to Var2 (IS/1494/06 strain), Group II
with 793/B serotype, Group III with QX like strain, Group IV with ISl720
strain, group V with Mass strain and Group VI showed similarity with IR1
genetic group (Najafi et al.
2016). Another molecular level study was conducted on infectious bronchitis
virus in Iran to investigate the prevailing strains. This study documented
Iran’s first–ever identification of Q1 infectious bronchitis virus genotype
which was originated from China from the proventriculus part of layers
chickens. The newly identified strains were Iran/Q1/UT-PCR-N1/ 2019 and
Iran/Q1/UT-PCR-N2/ 2019 linked to Q1 genotype. After sequencing both positive
samples, the sequences were given the accession codes MN841015 and MN841016 for
Iran/Q1/UT-PCR-N1/2019 and Iran/Q1/UT-PCR-N2/2019, respectively (Ghalyanchilangeroudi et al. 2020). Some published IBV isolates of Iran with accession
numbers are given in Table 4.
Molecular characterization of IBV in Bangladesh
In
this study, total 371 organ samples—the lungs, kidney, and trachea—were obtained
from breeder, broiler, and layer chickens and placed in sterile zipper-lock
bags., and Sonali breed (local) chickens that were exhibiting clinical
respiratory signs from 9 sampling areas. After processing of swab solution
(Homogenization, Suspension, Centrifugation and RNA Extraction), the next step
was undergone RT-PCR. The S1 gene specified primer and probe were used in
RT-PCR according to OIE guidelines as given in Anonymous (2004). Samples found
to be highly positive for IBV using RT-PCR were Table 4: Prevalence of different isolates of infectious
bronchitis virus in Iran. The given isolates of IBV have different levels of
similarity index of S1 gene sequence. This table contains the already published
Iranian IBV isolates with different Antigenic variations
|
Country |
Strain |
Type |
Genebank No. |
Reference |
|
Iran |
IBV-34 1BV-106 1BV-80 1BV-83 1BV-29 1BV-56 1BV-8 1BV-17 1BV-16 1BV-35 IS-1494/UTIVO-27/2014 IS-1494/UTIVO-66/2014
IS-1494/UTIVO-99/2014 IS-1494/UTIVO-90/2014 IS-1494/UTIVO-97/2014
IS-1494/UTIVO-93/2014 Iran/Variant
2/H840/14 IS-720/UTIVO-15/2014 IS-720/UTIVO-114/2014 IS-720/UTIVO-113/2014 IR-Razi-HKM3-2010 IR-Razi-HKM2-2010 IR-I/H600/13 IR-1/UTIVO-41/2015 IR-1/UTIVO-117/2015 Iran/793B/UTIVO-1/2014 Iran/793B/UTIVO-86/2014 Iran/793B/UTIVO-48/2014 Iran/793B/UTIVO-18/2014 Iran/793B/UTIVO-108/2014 IR-1062-GA IR-Razi-HKM4-2010 Iran/QX/UTIVO-103/2015 Iran/QX/UTIVO-6/2015 Iran/QX/UTIVO-2/2015 PCRLab/06/2012 Iran/Mass/UTIVO-111/2015 Iran/Mass/UTIVO-22/2015 Iran/Mass/UTIVO-46/2015 Iran/Mass/H650/13 Iran/Q1/UT-PCR-N1/ 2019 Iran/Q1/UT-PCR-N2/ 2019 |
GI-23 GI-23 GI-13 GI-13 GI-13 GI-13 GI-19 GI-19 GI-19 GI-1 IS/1494/06 like (Variant2 like) IS720 like IR-1 like (Iran- strains cluster) 4/91 like 793B like QX like Mass like Q1 Genetype Q1 Genotype |
MK850426 MK850429 MK850432 MK850428 MK850425 MK850431 MK850423 MK850424 MK850430 MK850427 KT583593 KT583597 KT583598 KT583599 KT583600 KT5835601 KP310028 KT583583 KT283585 KT583584 JN600612 JN600611 KP310035 KT583580 KT583581 KT583572 KT583577 KT583576 KT583573 KT583579 AY544777 JN600613 KT583571 KT583568 KT583567 JX477827 KT583566 KT583564 KT583565 KP310053 MN841015 MN841016 |
Ghorbiani et al. (2020)(Najfi et al. 2016)Ghalyanchilangeroudi et al. (2020) |
inoculated
into 9-day Specific pathogen free (SPF) chicken egg embryos according to OIE
guideline and observed for dwarfing and curling. The next step was harvesting
fluid, S1 gene sequence and phylogenetic analysis. Out of 371 samples, 65
(almost 17.5%) samples were positive for IBV in different areas of Bangladesh.
The commercial layer was highly prevalent (42.2%) and broiler chicken showed
lowest positive samples that were 16 out of 134 (11.9%). The prevalence of
local breed Sonali and broiler breeder chicken was 17 and 14.9%, respectively.
The results showed that Isolates of IBV were similar with a QX-like and Indian
isolates (Bhuiyan et al. 2019).
The total 5 isolates of IBV were found in Bangladesh which showed different
level of similarity with each other and hence these isolates were grouped after
phylogenetic analysis. The two isolates of IBV were grouped in 4/91 type and
two more isolates were grouped in Mass genotype. The remaining one was grouped
in QX like genotype (Parvin et al. 2021).
The IBV isolates are given with some other Bangladesh isolates in Table 5.
Molecular characterization of IBV in Afghanistan
According to first report on IBV in Afghanistan, between
2016 and 2017, IBV strains were found to be clustered into two different
genotypes, LX4 (GI-19) and IS-1494 similar (GI-23) (34/45), according to
phylogenetic analysis of all positive samples. The LX4 IBV (Afghan) is
different from Iranian QX IBV. The Iraqi IBV (QX) showed almost 98.9%
similarity with China QX like IBV stains. Regarding similarity to circulating
strains in Iran and Iraq, IS-1494 had a 20% spread. It should be noted that
frequent strains found in the area, such as Massachusetts and 793/B, were not
found in this investigation. The study aimed to evaluate the percentage homology
of partial sequences of nucleotide of the S1 genes of certain Afghan IBVs. The
obtained nucleotide and sequences of amino acids can be found in the Gene Bank
with accession numbers MF322853-MF322867 (Sadri et
al. 2019). It is evident that there are many different IBV
variations on the globe today. The challenges lie in Table 5: Prevalence of different isolates of infectious bronchitis
virus in Bangladesh. The given isolates of IBV have different levels of
similarity index of S1 gene sequence. This table contains the already published
Bangladeshi IBV isolates with different Antigenic variations
|
Country |
Strain |
Type |
Gene Bank No# |
Reference |
|
Bangladesh |
CK/ BD/IBV/NPHL1 CK/BD/IBV/NPHL2 CK/ BD/IBV/NPHL3 IBV_CK/Bangladesh/LBM1/2020-HVR1-2 S1
IBV_CK/Bangladesh/LBM5/2020-HVR1-2 S1 IBV_CK/Bangladesh/LT46/2020-HVR1-2 S1
IBV_CK/Bangladesh/LT1/2020-HVR1-2 S1 IBV_CK/Bangladesh/LT57/2020-HVR1-2 S1 |
QX like 4/91 like 4/914/91 like 4/91 like Mass like Mass like QX like |
MH631011.1 MH688060.1 MH685740.1 MW971986.1MW971987.1 MW971994.1 MW971988.1 MW971990.1 |
Bhuiyan et al. (2019) Parvin et al. (2021) |
Table 6: Prevalence
of different isolates of infectious bronchitis virus in Afghanistan. The given
isolates of IBV have different levels of similarity index of S1 gene sequence.
This table contains the already published Afghani IBV isolates with different Antigenic
variations
|
Country |
Strain |
Type |
Gene bank No. |
Reference |
|
Afghanistan |
Afghanistan/AFS21/2017 Afghanistan/AFS14/2017 Afghanistan/AFS20/2017 Afghanistan/AFS26/2017 Afghanistan/AFS29/2017 Afghanistan_AFS5_2017 IBV/Chicken/Afghanistan//AFS1/2016 IBV/Chicken/Afghanistan//AFS7/2016 IBV/Chicken/Afghanistan//AFS9/2016 IBV/Chicken/Afghanistan//AFS15/2016 IBV/Chicken/Afghanistan//AFS18/2016 IBV/Chicken/Afghanistan//AFS19/2016 IBV/Chicken/Afghanistan//AFS22/2016 IBV/Chicken/Afghanistan//AFS23/2016 |
LX4 Like (GI-19) LX4 Like |
MF322865MF322866MF322862
MF322853 MF322867 MF322856MF322857MF322858MF322859MF322860MF322861MF322863
MF322864 |
Sadri et al. (2019) |
%20465-473%20Rev_files/image002.png)
Fig. 1: Phylogenetic tree showing Antigenic diversity of the
S1 gene for IBV strains generated using neighbor-joining 100 bootstrap
replicates. The phylogenetic tree was constructed by using MEGA 11 software.
Ten (05) Pakistani IBV strains were compared with IBV strains in selected
countries of South-Asia. The Pakistani strains in this study were indicated by
black arrows, The Fig. 1 contains the already published IBV isolates with
different Antigenic variations in South-Asian region
classifying these variants and connecting the
results to the most effective vaccination plan for protection. However, genotyping
offers convenience and speed, the present review highlights requirement for a
standardized way of performing genotyping because different groups use
different parts such as the S1 region of the S gene for strain comparisons,
which makes the interpretation of outcomes very difficult. Another important
thing to keep in mind is that the level of cross-protection in a chicken is
determined solely by the vaccination, not by genetic or antigenic variations as
determined by genotyping or serotyping (Wit et al. 2011).
Cross-protection studies indicate that flocks can be protected against IS-1494
and QX by using heterologous vaccines with different genotypes, such as
Massachusetts and 4/91 (Habibi et al.
2017). Some published IBV isolates of
Afghanistan with accession numbers are given in Table 6.
Control strategies
The
first step to control this economically significant disease in poultry requires
identification of novel variant of IBV, which is linked to the disease outbreak
in vaccinated birds. It is the need of an hour to develop a vaccine in order to
control the newly circulating strain of IBV in particular area, because already
available vaccines are unable to offer sufficient protection. The killed
vaccines or attenuated live vaccines are usually developed for Novel IBV
strain. It should be worth mentioning that new vaccine development approaches
are obviously required in order to respond to disease outbreaks in a safe and
timely manner.
Conclusion
Infectious
bronchitis is a serious poultry disease with economic implications that mostly
impacts countries with large poultry production (Bande et al. 2017), but it also affects poultry sectors
globally (Jackwood and Wit 2013).
Currently, IBV strains are categorized using a phylogeny-based categorization
approach developed by Valastro and colleagues. The phylogenetic tree given in
Fig. 1 shows the antigenic diversity of S1 gene of infectious bronchitis virus
in South Asian region. The IBV variants or strains are currently classified
into eight genotypes (GI-GVIII), 39 different lineages (GI-1 to GI-31, GII-1,
GII-2, GIII-1, GIV-1, GV-1, GVI-1, GVII-1 and GVIII-1) as well as a large
number of inter-lineage recombinants that are not yet classified. Most IBV
lineages are limited to specific geographic regions, while certain countries
report the circulation of distinct lineages. On the other hand, the lineages
GI-1, GI-13, GI-16, and GI-19 are widely distributed (Krisztina et al. 2022). The
study conducted in Pakistan, evaluated the criteria using the 9 novel sequences
for all Pakistani isolates of IBV. Eigth sequences of IBV isolates out of nine
were grouped in GI-13 and one was placed in GI-24 lineage (Saleem et al. 2024). It suggested that Different IBV strains isolated and
identified in Pakistan are diverse in terms of genetics, offering a base for
re-combination and challenging the biological control protocols. Another
study showed that IBV strain (Pak-973) has diverse mutations when matched with
Mass and 4/91 strains which are being used as vaccine strains. The sequenced
isolate Pak-973 varied from other serotypes by an average of 7%. These
observable changes or substitutions in HVR1 and HVR2 ensure that this isolate
is distinct from the vaccination strains that are used in vaccines. This
demonstrates the importance of vaccine matching strategy before choosing a
strain to use as a vaccine seed when introducing a novel IBV vaccination strain
in a particular area. Conclusively, the major factors involved in the
prevalence of Infectious bronchitis are occurrence of multiple strains of IBV,
lower level of humoral immunity and emergence of novel IBV strains. This review
presented a little contribution in demonstrating the similarity index between
Pakistani IBV and strains of selected south Asian countries. This similarity
index was established through phylogenetic analysis of different IBV strains.
Furthermore, A detailed summary of the most recent findings regarding the
genetic group distribution of avian coronavirus which may be helpful in vaccine
production for different IBV strains circulating in selected South Asian
countries. It is very important that vaccine matching should be done before
vaccination. Vaccine matching is crucial for maintaining the efficacy of
vaccines, as it allows researchers and healthcare professionals to stay ahead
of the evolving nature of infectious agents and address emerging strains that
might pose challenges to existing vaccine formulations.
Acknowledgement
I would like to express my sincere
gratitude to the senior colleagues at the National Institute for Genomics and
Advanced Biotechnology, NARC, Islamabad, for their invaluable guidance and
support throughout the process of writing and analyzing the review paper. Their
expertise and insights have significantly contributed to the quality and depth
of this manuscript. I am also thankful to all my co-authors for their
collaboration and input, which have enriched the content of the review paper.
This work would not have been possible without their collective effort and
encouragement.
Author Contributions
BJ: Complete write up of original Article and Phylogenetic
Analysis and collection of relevant data, TK: Idea and conceptualization, FA:
Visualization (presentation of data, such as creating figures or tables), MNR:
technical Support, HMBA: Proof-reading of review paper.
Conflicts of Interest
The authors have no conflicts of interest
to declar.
Data Availability
The data used in this study can be
obtained from the corresponding author upon a reasonable request.
Ethics Approval
Not applicable
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