Genetic characterization of the complete genome of a
strain of Chikungunya virus circulating in Brazil
Caracterización genética del genoma completo de una cepa del virus
Chikungunya circulante en Brasil
Caracterização genética do genoma completo de uma cepa do vírus
Chikungunya que circula no Brasil
ABSTRACT
The Chikungunya virus (CHIKV) is a single-stranded posi-
tive-sense RNA virus that belongs to the Alphavirus genus
of the Togaviridae family. It is primarily transmitted by Ae-
des aegypti and albopictus mosquitoes. Its genome encodes
four non-structural proteins (NSP 1-4) and three structural
proteins (C, E1, and E2). Four lineages of this virus have been
identified, namely the West African, East African, Central and
South African (ECSA), Asian (AL), and Indian Ocean Lineages
(IOL). CHIKV is an endemic arbovirus circulating in 51 coun-
tries in the Americas. Clinical manifestations attributed to it
include high fever, rash, myalgia, and episodes of arthralgia,
which subsequently lead to chronic pain and disability, es-
pecially in the joints. Sequencing the complete genome of
the Chikungunya virus is essential to understand its biology,
evolution, and spread and to develop effective strategies
for prevention, diagnosis, and treatment. This information is
crucial for combating the disease and minimizing its impact
on public health. For these reasons, the complete genome
of the Chikungunya virus strain br33, identified in the north-
eastern city of Recife, in the state of Pernambuco, Brazil, was
sequenced. The genome has a size of 11,601 nucleotides and
Rafael Guillermo Villarreal-Julio1
Jonny Andrés Yepes-Blandón2
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OPEN ACCESS
Como Citar (Norma Vancouver): Villarreal-Julio RG, Yepes-Blandón JA. Genetic characterization
of the complete genome of a strain of Chikungunya virus circulating in Brazil. Orinoquia,
2023;27(2):e-789 https://doi.org/10.22579/20112629.789
Artículo de investigación
Recibido: 26 de septiembre de 2023
Aceptado: 18 de noviembre de 2023
1 CES University, Graduate School, Doctorate
in Health Sciences, Medellín, Colombia
-BIOTECH MOLECULAR, Molecular, Genetic
and Computational Biology Unit; Medellín,
Colombia. - University of Antioquia, School of
Medicine, Program for the Study and Control
of Tropical Diseases (PECET); Medellín,
Colombia - International Internships in the
Gehrke Laboratory at the Massachusetts
Institute of Technology (MIT), Cambridge,
MA, USA and Harvard Medical School (HMS),
Boston, Massachusetts. USA. Email: rafael.
[email protected] ORCID: https://orcid.
org/0000-0002-9009-1086
2 Animal Scientist, Project Management
Specialist, Master's in Biology and
Ph.D. in Biology. Grupo de Investigación en
Organismos Acuáticos Nativos y Exóticos
- GIOANE, Facultad de Ciencias Agrarias,
Escuela de Producción Agropecuaria,
Universidad de Antioquia. Email: jonny.
[email protected] ORCID: https://orcid.
org/0000-0001-6276-5488
2Caracterización genética d el genoma c o m p leto d e una c epa d el v irus C h ikungunya c irculante en B rasil Vol 27 No. 2 - e-789 julio diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
contains coding regions for two polyproteins. A phylogenetic analysis indicates
that the recent Brazilian strain of CHIKV belongs to the East, Central, and South
African lineage (ECSA). This phylogenetic identification is important because this
particular genotype has been associated with greater damage and clinical severity.
Until 2016, the CHIKV virus was directly associated with travel, and its transmission
was limited. Subsequently, the largest outbreak occurred in the state associated
with the introduction of a new ECSA lineage, as identified in this study. It is highly
likely that new CHIKV outbreaks will occur in the near future due to the abundance
of competent vectors in Brazil and a susceptible population, exposing more than 11
million inhabitants to an increasing risk of infection.
Keywords: Emerging alphaviruses, Chikungunya fever, Genome, Sequencing
RESUMEN
El virus Chikungunya (CHIKV) es un virus de ARN monocatenario de sentido positivo
que pertenece al género Alphavirus de la familia Togaviridae. Se transmite princi-
palmente por mosquitos Aedes aegypti y albopictus. Su genoma codifica cuatro
proteínas no estructurales (NSP 1-4) y tres proteínas estructurales (C, E1 y E2). Se
han identificado cuatro linajes de este virus que son los linajes de África occidental,
África oriental, central y sudafricana (ECSA), asiático (AL) y del océano Índico (IOL).1.
CHIKV es un arbovirus endémico circulante en 51 países de las Américas. Las mani-
festaciones clínicas que se le atribuyen son; fiebre alta, erupción cutánea, mialgia y
episodios de artralgia, que en consecuencia provocan dolor crónico y discapacidad,
especialmente en articulaciones. La secuenciación del genoma completo del virus
del Chikungunya es esencial para comprender su biología, evolución y propagación,
y para desarrollar estrategias efectivas de prevención, diagnóstico y tratamiento.
Esta información es fundamental para combatir la enfermedad y minimizar su im-
pacto en la salud pública. Por esas razones se secuenció el genoma completo del vi-
rus Chikungunya br33, identificada en la ciudad nororiental de Recife, en el estado
de Pernambuco, Brasil. El genoma tiene un tamaño de 11601 nucleótidos y fragmen-
tos que codifican para dos poliproteínas.
Se realizó un análisis filogénico que indica que la reciente cepa brasileña del CHIKV
pertenece al linaje del este, centro y sur de África (ECSA). Dicha identificación filo-
genética es importante porque este genotipo en particular ha sido asociado a ma-
yor daño y severidad clínica.
Hasta 2016, el virus CHIKV estaba asociadas directamente a viajes y la transmisión
era limitada. Posteriormente se produjo el brote más grande en el estado asocia-
do con la introducción de un nuevo linaje ECSA como el indetificado en este estu-
dio. Es muy probable que se produzcan nuevos brotes de CHIKV en un futuro cer-
cano debido a la abundancia de vectores competentes en brazil y a una población
susceptible, exponiendo a más de 11 millones de habitantes a un riesgo de infección
cada vez mayor.
Palabras clave: Alfavirus emergentes, Fiebre Chikungunya, Genoma, Secuenciación
DOI: https://doi.org/ 10.22579/20112629.789
contains coding regions for two polyproteins. A phylogenetic analysis indicates
that the recent Brazilian strain of CHIKV belongs to the East, Central, and South
African lineage (ECSA). This phylogenetic identification is important because this
particular genotype has been associated with greater damage and clinical severity.
Until 2016, the CHIKV virus was directly associated with travel, and its transmission
was limited. Subsequently, the largest outbreak occurred in the state associated
with the introduction of a new ECSA lineage, as identified in this study. It is highly
likely that new CHIKV outbreaks will occur in the near future due to the abundance
of competent vectors in Brazil and a susceptible population, exposing more than 11
million inhabitants to an increasing risk of infection.
Keywords: Emerging alphaviruses, Chikungunya fever, Genome, Sequencing
RESUMEN
El virus Chikungunya (CHIKV) es un virus de ARN monocatenario de sentido positivo
que pertenece al género Alphavirus de la familia Togaviridae. Se transmite princi-
palmente por mosquitos Aedes aegypti y albopictus. Su genoma codifica cuatro
proteínas no estructurales (NSP 1-4) y tres proteínas estructurales (C, E1 y E2). Se
han identificado cuatro linajes de este virus que son los linajes de África occidental,
África oriental, central y sudafricana (ECSA), asiático (AL) y del océano Índico (IOL).1.
CHIKV es un arbovirus endémico circulante en 51 países de las Américas. Las mani-
festaciones clínicas que se le atribuyen son; fiebre alta, erupción cutánea, mialgia y
episodios de artralgia, que en consecuencia provocan dolor crónico y discapacidad,
especialmente en articulaciones. La secuenciación del genoma completo del virus
del Chikungunya es esencial para comprender su biología, evolución y propagación,
y para desarrollar estrategias efectivas de prevención, diagnóstico y tratamiento.
Esta información es fundamental para combatir la enfermedad y minimizar su im-
pacto en la salud pública. Por esas razones se secuenció el genoma completo del vi-
rus Chikungunya br33, identificada en la ciudad nororiental de Recife, en el estado
de Pernambuco, Brasil. El genoma tiene un tamaño de 11601 nucleótidos y fragmen-
tos que codifican para dos poliproteínas.
Se realizó un análisis filogénico que indica que la reciente cepa brasileña del CHIKV
pertenece al linaje del este, centro y sur de África (ECSA). Dicha identificación filo-
genética es importante porque este genotipo en particular ha sido asociado a ma-
yor daño y severidad clínica.
Hasta 2016, el virus CHIKV estaba asociadas directamente a viajes y la transmisión
era limitada. Posteriormente se produjo el brote más grande en el estado asocia-
do con la introducción de un nuevo linaje ECSA como el indetificado en este estu-
dio. Es muy probable que se produzcan nuevos brotes de CHIKV en un futuro cer-
cano debido a la abundancia de vectores competentes en brazil y a una población
susceptible, exponiendo a más de 11 millones de habitantes a un riesgo de infección
cada vez mayor.
Palabras clave: Alfavirus emergentes, Fiebre Chikungunya, Genoma, Secuenciación
3Rafael G uillermo V illarreal-Julio & J o n n y A n d rés Yepes-Blandón
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
RESUMO
O vírus Chikungunya (CHIKV) é um vírus de RNA de sentido positivo de cadeia sim-
ples que pertence ao gênero Alphavirus da família Togaviridae. É transmitido prin-
cipalmente por mosquitos Aedes aegypti e albopictus. Seu genoma codifica quatro
proteínas não estruturais (NSP 1-4) e três proteínas estruturais (C, E1 e E2). Quatro
linhagens desse vírus foram identificadas, a saber: as linhagens da África Ocidental,
da África Oriental, da África Central e Sul (ECSA), Asiática (AL) e do Oceano Índico
(IOL). O CHIKV é um arbovírus endêmico que circula em 51 países das Américas. As
manifestações clínicas atribuídas a ele incluem febre alta, erupção cutânea, mialgia
e episódios de artralgia, que, subsequentemente, levam a dores crônicas e incapa-
cidade, especialmente nas articulações. A sequenciação completa do genoma do
vírus Chikungunya é essencial para compreender sua biologia, evolução e propa-
gação, além de desenvolver estratégias eficazes de prevenção, diagnóstico e tra-
tamento. Essas informações são cruciais para combater a doença e minimizar seu
impacto na saúde pública. Por essas razões, o genoma completo da cepa do vírus
Chikungunya br33, identificada na cidade nordestina de Recife, no estado de Per-
nambuco, Brasil, foi sequenciado. O genoma tem um tamanho de 11.601 nucleotídeos
e contém regiões de codificação para duas poliproteínas. Uma análise filogenética
indica que a recente cepa brasileira do CHIKV pertence à linhagem da África Orien-
tal, Central e Sul (ECSA). Essa identificação filogenética é importante porque esse
genótipo em particular tem sido associado a maiores danos e gravidade clínica. Até
2016, o vírus CHIKV estava diretamente associado a viagens, e sua transmissão era
limitada. Posteriormente, ocorreu o maior surto no estado associado à introdução
de uma nova linhagem ECSA, como identificada neste estudo. É altamente provável
que novos surtos de CHIKV ocorram em um futuro próximo devido à abundância de
vetores competentes no Brasil e a uma população suscetível, expondo mais de 11
milhões de habitantes a um risco crescente de infecção.
Palavras chave: Vírus alfa emergentes, febre de Chikungunya, genoma,
sequenciamento
INTRODUCTION
Chikungunya virus (CHIKV) is an alphavirus that
produces a reemerging infection transmitted to
humans by the mosquito vectors Aedes aegypti
and Ae. Albopictus (Carrillo et al., 2023; Nunes et
al., 2015)an outbreak of Chikungunya virus (CHIKV.
CHIKV infection is a significant public health issue
in tropical and subtropical regions. An infection by
CHIKV is characterized by an acute fever, rash, and
arthralgia, most commonly known as joint pain,
often accompanied by headache, swelling of the
joints, and conjunctivitis (Hakim & Aman, 2022;
Nunes et al., 2015).
As far as we know, three different CHIKV phyloge-
netic groups with differing antigenic properties
have been identified: the East, Central, and South
African (ECSA) genotypes. The first cases of au-
tochthonous CHIKV in Brazil were confirmed in the
city of Oiapoque, in the state of Amapá, back in
September 2014 Where two genotypes of CHIKV
were identified, ECSA and Asian (Alguridi et al.,
2023; Nunes et al., 2015; Volk et al., 2010)
In this document, we present the complete ge-
nomic sequence of the BR33 genotype ECSA iso-
lated on March 3, 2016, from a pregnant patient in
Brazil, in the city of Recife, state of Pernambuco,
initially suspected of being infected with the Zika
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
RESUMO
O vírus Chikungunya (CHIKV) é um vírus de RNA de sentido positivo de cadeia sim-
ples que pertence ao gênero Alphavirus da família Togaviridae. É transmitido prin-
cipalmente por mosquitos Aedes aegypti e albopictus. Seu genoma codifica quatro
proteínas não estruturais (NSP 1-4) e três proteínas estruturais (C, E1 e E2). Quatro
linhagens desse vírus foram identificadas, a saber: as linhagens da África Ocidental,
da África Oriental, da África Central e Sul (ECSA), Asiática (AL) e do Oceano Índico
(IOL). O CHIKV é um arbovírus endêmico que circula em 51 países das Américas. As
manifestações clínicas atribuídas a ele incluem febre alta, erupção cutânea, mialgia
e episódios de artralgia, que, subsequentemente, levam a dores crônicas e incapa-
cidade, especialmente nas articulações. A sequenciação completa do genoma do
vírus Chikungunya é essencial para compreender sua biologia, evolução e propa-
gação, além de desenvolver estratégias eficazes de prevenção, diagnóstico e tra-
tamento. Essas informações são cruciais para combater a doença e minimizar seu
impacto na saúde pública. Por essas razões, o genoma completo da cepa do vírus
Chikungunya br33, identificada na cidade nordestina de Recife, no estado de Per-
nambuco, Brasil, foi sequenciado. O genoma tem um tamanho de 11.601 nucleotídeos
e contém regiões de codificação para duas poliproteínas. Uma análise filogenética
indica que a recente cepa brasileira do CHIKV pertence à linhagem da África Orien-
tal, Central e Sul (ECSA). Essa identificação filogenética é importante porque esse
genótipo em particular tem sido associado a maiores danos e gravidade clínica. Até
2016, o vírus CHIKV estava diretamente associado a viagens, e sua transmissão era
limitada. Posteriormente, ocorreu o maior surto no estado associado à introdução
de uma nova linhagem ECSA, como identificada neste estudo. É altamente provável
que novos surtos de CHIKV ocorram em um futuro próximo devido à abundância de
vetores competentes no Brasil e a uma população suscetível, expondo mais de 11
milhões de habitantes a um risco crescente de infecção.
Palavras chave: Vírus alfa emergentes, febre de Chikungunya, genoma,
sequenciamento
INTRODUCTION
Chikungunya virus (CHIKV) is an alphavirus that
produces a reemerging infection transmitted to
humans by the mosquito vectors Aedes aegypti
and Ae. Albopictus (Carrillo et al., 2023; Nunes et
al., 2015)an outbreak of Chikungunya virus (CHIKV.
CHIKV infection is a significant public health issue
in tropical and subtropical regions. An infection by
CHIKV is characterized by an acute fever, rash, and
arthralgia, most commonly known as joint pain,
often accompanied by headache, swelling of the
joints, and conjunctivitis (Hakim & Aman, 2022;
Nunes et al., 2015).
As far as we know, three different CHIKV phyloge-
netic groups with differing antigenic properties
have been identified: the East, Central, and South
African (ECSA) genotypes. The first cases of au-
tochthonous CHIKV in Brazil were confirmed in the
city of Oiapoque, in the state of Amapá, back in
September 2014 Where two genotypes of CHIKV
were identified, ECSA and Asian (Alguridi et al.,
2023; Nunes et al., 2015; Volk et al., 2010)
In this document, we present the complete ge-
nomic sequence of the BR33 genotype ECSA iso-
lated on March 3, 2016, from a pregnant patient in
Brazil, in the city of Recife, state of Pernambuco,
initially suspected of being infected with the Zika
Caracterización genética del genoma completo de una cepa del virus Chikungunya circulante en Brasil4 Vol 27 No. 2 - e-789 julio diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
virus. The patient was initially diagnosed with
CHIKV through PCR via reverse transcription (RT-
PCR), amplifying a section of the gene E1 designed
and standardized by the Gehrke Laboratory at the
Massachusetts Institute of Technology (MIT).
METHODS
The CHIKV strain was propagated in Vero-E6 cells
(Vero) that were maintained in minimal essential
medium (MEM) (Sigma), supplemented with 5%
to 10% fetal bovine serum and antibiotics at 37° in
5% CO2. C6/36 cells were maintained in Leibovitz’s
L-15 medium (Invitrogen, Carlsbad, California, USA)
supplemented with 10% fetal bovine serum, antibi-
otics, and 1% TPB (Sigma, St. Louis, Missouri, USA)
at 32°C. collected 7 days after infection or after
displaying cytopathogenic effect (Ang et al., 2016;
Miller et al., 2018). All experiments were carried out
in a biosafety level 3 laboratory. RNA extraction was
performed using QIAamp Viral RNA mini kit from
Qiagen, following instructional directions. Novo
sequencing of the entire genome was performed
in an Illumina HiSeq 2500 system (Conteville et
al., 2016; Xf et al., 2023) using the Trinity RNA seq
assembly method (Haas et al., 2013; Hartline et al.,
2023), and version r2013-02-25. Sequencing and
assembly were undertaken at the Massachusetts
Institute of Technology (MIT) facilities.
Characterization was performed using the ViPR da-
tabase (www.viprbrc.org). The function was gener-
ated by the InterPro program (http://www.ebi.ac.uk/
interpro/protein/A0A192GR82). Phylogenetic anal-
ysis was carried out using the software Molecular
Evolutionary Genetics Analysis (MEGA) version 7.0
(7-17) with the neighbor-joining tree method.
RESULTS
The complete genome sequence was called Chi-
kungunya virus isolate BR33, and it was submitted
to the NCBI GenBank, with the accession number:
KX228391.1.
The genome has a size of 11 601 nucleotides, and
two open reading frames that encode for two poly-
protein precursors evidenced, these are the struc-
tural and non-structural polyprotein of Chikungun-
ya. The first is a nonstructural polyprotein ranging
from nucleotide position 80 to 7504. The product
is called CHIKVgp1, and its ID is ANK58564.1 (Fig
1). The second structural polyprotein ranges from
nucleotide position 7570 to 11 316, the product is
called CHIKVgp2, and its ID is ANK58565.1 (Table
1). Functional and structural characteristics are
described in detail (Fig 1-4). In addition, the phylo-
genetic classification of Chikungunya virus isolate
BR33 was performed (Fig 5).
Table 1. Physical and functional characteristics of anno-
tation and search of CHIKV BR33.
a.
General Info
Genome ID 371.244.891
Genome Name Chikungunya virus BR33
Taxonomy Info
Taxon ID 37124
Superkingdom Viruses
Kingdom Orthornavirae
Phylum Kitrinoviricota
Class Alsuviricetes
Order Martellivirales
Family Togaviridae
Genus Alphavirus
Species Chikungunya virus
Status
Genome Status Complete
Type Info
Strain BR33
Database Cross Reference
Completion Date 6/20/2016
Genbank Accessions KX228391
Sequence Info
Sequencing Platform Illumina
Assembly Method trinityrnaseq v.
r2013-02-25
Genome Statistics
Chromosomes 1
Contigs 1
Genome Length 11601
GC Content 5.027.153
Contig L50 1
Contig N50 11601
DOI: https://doi.org/ 10.22579/20112629.789
virus. The patient was initially diagnosed with
CHIKV through PCR via reverse transcription (RT-
PCR), amplifying a section of the gene E1 designed
and standardized by the Gehrke Laboratory at the
Massachusetts Institute of Technology (MIT).
METHODS
The CHIKV strain was propagated in Vero-E6 cells
(Vero) that were maintained in minimal essential
medium (MEM) (Sigma), supplemented with 5%
to 10% fetal bovine serum and antibiotics at 37° in
5% CO2. C6/36 cells were maintained in Leibovitz’s
L-15 medium (Invitrogen, Carlsbad, California, USA)
supplemented with 10% fetal bovine serum, antibi-
otics, and 1% TPB (Sigma, St. Louis, Missouri, USA)
at 32°C. collected 7 days after infection or after
displaying cytopathogenic effect (Ang et al., 2016;
Miller et al., 2018). All experiments were carried out
in a biosafety level 3 laboratory. RNA extraction was
performed using QIAamp Viral RNA mini kit from
Qiagen, following instructional directions. Novo
sequencing of the entire genome was performed
in an Illumina HiSeq 2500 system (Conteville et
al., 2016; Xf et al., 2023) using the Trinity RNA seq
assembly method (Haas et al., 2013; Hartline et al.,
2023), and version r2013-02-25. Sequencing and
assembly were undertaken at the Massachusetts
Institute of Technology (MIT) facilities.
Characterization was performed using the ViPR da-
tabase (www.viprbrc.org). The function was gener-
ated by the InterPro program (http://www.ebi.ac.uk/
interpro/protein/A0A192GR82). Phylogenetic anal-
ysis was carried out using the software Molecular
Evolutionary Genetics Analysis (MEGA) version 7.0
(7-17) with the neighbor-joining tree method.
RESULTS
The complete genome sequence was called Chi-
kungunya virus isolate BR33, and it was submitted
to the NCBI GenBank, with the accession number:
KX228391.1.
The genome has a size of 11 601 nucleotides, and
two open reading frames that encode for two poly-
protein precursors evidenced, these are the struc-
tural and non-structural polyprotein of Chikungun-
ya. The first is a nonstructural polyprotein ranging
from nucleotide position 80 to 7504. The product
is called CHIKVgp1, and its ID is ANK58564.1 (Fig
1). The second structural polyprotein ranges from
nucleotide position 7570 to 11 316, the product is
called CHIKVgp2, and its ID is ANK58565.1 (Table
1). Functional and structural characteristics are
described in detail (Fig 1-4). In addition, the phylo-
genetic classification of Chikungunya virus isolate
BR33 was performed (Fig 5).
Table 1. Physical and functional characteristics of anno-
tation and search of CHIKV BR33.
a.
General Info
Genome ID 371.244.891
Genome Name Chikungunya virus BR33
Taxonomy Info
Taxon ID 37124
Superkingdom Viruses
Kingdom Orthornavirae
Phylum Kitrinoviricota
Class Alsuviricetes
Order Martellivirales
Family Togaviridae
Genus Alphavirus
Species Chikungunya virus
Status
Genome Status Complete
Type Info
Strain BR33
Database Cross Reference
Completion Date 6/20/2016
Genbank Accessions KX228391
Sequence Info
Sequencing Platform Illumina
Assembly Method trinityrnaseq v.
r2013-02-25
Genome Statistics
Chromosomes 1
Contigs 1
Genome Length 11601
GC Content 5.027.153
Contig L50 1
Contig N50 11601
Rafael Guillermo Villarreal-Julio & Jonny Andrés Yepes-Blandón5
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Annotation Statistics
CDS 2
CDS Ratio 0.17239892
Genome Quality
None available
Isolate Info
Collection Date 3/03/2016
Collection Year 2016
Isolation Country Brazil
Geographic Group South America
Geographic Location Brazil: Pernambuco
Host Info
Host Name Homo sapiens
Host Common Name Human
Host Group Human
b.
Source
CDS
Region in
Nucleotide
Protein Name Organism
INSDC KX228391.1 ANK58564.1 CHIKVgp1 Chikungun-
ya virus80-7504 (+)
INSDC KY704954.1 ASM47579.1
nonstruc-
tural
polyprotein
Chikungun-
ya virus75-7499 (+)
INSDC MH000700.1 QBM78314.1 nonstructur-
al protein
Chikungun-
ya virus57-7481 (+)
INSDC MH000703.1 QBM78318.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000704.1 QBM78320.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000705.1 QBM78322.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000706.1 QBM78324.1 nonstructur-
al protein
Chikungun-
ya virus19-7443 (+)
Figure 1.
Structural (a) and Genetic characteristics (b,c) of CHIKV BR33. Organization of the CHIKV Genome and Gene Products: The genomic organization
of the chikungunya virus (CHIKV) resembles that of other alphaviruses. It consists of two open reading frames (ORFs), both flanked by 5’ cap
structures and a 3’ poly(A) tail. The regions proximal to the 5’ and 3’ ends of the CHIKV genome contain nontranslated regions (NTR), with the
junction region (J) also being noncoding.
The 5’ ORF is translated directly from the genomic RNA and encodes four nonstructural proteins (nsP1, nsP2, nsP3, and nsP4). In contrast, the
3’ ORF is translated from a subgenomic 26S RNA and codes for several structural proteins, including the capsid protein (C), two surface enve-
lope glycoproteins (E1 and E2), and two small peptides known as E3 and 6k. These non-structural and structural proteins, namely nsP1 to nsP4,
and C, E1, E2, E3, and 6k, are produced through proteolytic cleavage of polyprotein precursors. This genomic organization and the subsequent
protein synthesis are fundamental aspects of the CHIKV life cycle and play a crucial role in its pathogenicity and interactions with the host.
https://viralzone.expasy.org/625?outline=all_by_species
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Annotation Statistics
CDS 2
CDS Ratio 0.17239892
Genome Quality
None available
Isolate Info
Collection Date 3/03/2016
Collection Year 2016
Isolation Country Brazil
Geographic Group South America
Geographic Location Brazil: Pernambuco
Host Info
Host Name Homo sapiens
Host Common Name Human
Host Group Human
b.
Source
CDS
Region in
Nucleotide
Protein Name Organism
INSDC KX228391.1 ANK58564.1 CHIKVgp1 Chikungun-
ya virus80-7504 (+)
INSDC KY704954.1 ASM47579.1
nonstruc-
tural
polyprotein
Chikungun-
ya virus75-7499 (+)
INSDC MH000700.1 QBM78314.1 nonstructur-
al protein
Chikungun-
ya virus57-7481 (+)
INSDC MH000703.1 QBM78318.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000704.1 QBM78320.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000705.1 QBM78322.1 nonstructur-
al protein
Chikungun-
ya virus80-7504 (+)
INSDC MH000706.1 QBM78324.1 nonstructur-
al protein
Chikungun-
ya virus19-7443 (+)
Figure 1.
Structural (a) and Genetic characteristics (b,c) of CHIKV BR33. Organization of the CHIKV Genome and Gene Products: The genomic organization
of the chikungunya virus (CHIKV) resembles that of other alphaviruses. It consists of two open reading frames (ORFs), both flanked by 5’ cap
structures and a 3’ poly(A) tail. The regions proximal to the 5’ and 3’ ends of the CHIKV genome contain nontranslated regions (NTR), with the
junction region (J) also being noncoding.
The 5’ ORF is translated directly from the genomic RNA and encodes four nonstructural proteins (nsP1, nsP2, nsP3, and nsP4). In contrast, the
3’ ORF is translated from a subgenomic 26S RNA and codes for several structural proteins, including the capsid protein (C), two surface enve-
lope glycoproteins (E1 and E2), and two small peptides known as E3 and 6k. These non-structural and structural proteins, namely nsP1 to nsP4,
and C, E1, E2, E3, and 6k, are produced through proteolytic cleavage of polyprotein precursors. This genomic organization and the subsequent
protein synthesis are fundamental aspects of the CHIKV life cycle and play a crucial role in its pathogenicity and interactions with the host.
https://viralzone.expasy.org/625?outline=all_by_species
Caracterización genética del genoma completo de una cepa del virus Chikungunya circulante en Brasil6 Vol 27 No. 2 - e-789 julio diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 2.
GO term prediction
Biological Process
Molecular Function
Cellular Component
transcription, DNA-templated
RNA processing
RNA binding
RNA-directed 5`-3`RNA polymerase activity
ATP binding
mRNA methyltransferase activity
None predicted
viral RNA genome replication
mRNA methylation
GO: 0006351
GO: 0006396
GO: 0039694
GO: 0080009
GO: 0003723
GO: 0003968
GO: 0005524
GO: 0008174
Gene Ontology Classification of protein CHIKgp1, divided into functional biological, molecular, and cellular components. Gene Ontology (GO):
Gene Ontology (GO) stands as a cornerstone in the realm of biological information by offering precise definitions of protein functions. GO is
an organized and regulated lexicon consisting of terms known as GO terms. It’s categorized into three distinct and non-overlapping ontologies:
Molecular Function (MF), Biological Process (BP), and Cellular Component (CC). The structure of GO is represented as a Directed Acyclic Graph
(DAG), where terms take the form of nodes, and relationships among terms form the edges. This framework offers greater flexibility than a tra-
ditional hierarchy, as each term can have multiple connections to broader parent terms as well as more specific child terms (du Plessis et al.,
2011). Genes or proteins become associated with GO terms through an annotation process, which serves as a linkage. Each GO annotation has an
attributed source and database entry. These sources can range from literature references to database references and computational evidence.
Every biological molecule is linked to the most specific set of terms that accurately depict its functional attributes. Consequently, if a biological
molecule is associated with a particular term, it will be inherently connected to all the parent terms within that term’s hierarchical structure (du
Plessis et al., 2011). This comprehensive system enables the precise classification of biological functions and greatly aids in the understanding
of gene and protein functionality.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 2.
GO term prediction
Biological Process
Molecular Function
Cellular Component
transcription, DNA-templated
RNA processing
RNA binding
RNA-directed 5`-3`RNA polymerase activity
ATP binding
mRNA methyltransferase activity
None predicted
viral RNA genome replication
mRNA methylation
GO: 0006351
GO: 0006396
GO: 0039694
GO: 0080009
GO: 0003723
GO: 0003968
GO: 0005524
GO: 0008174
Gene Ontology Classification of protein CHIKgp1, divided into functional biological, molecular, and cellular components. Gene Ontology (GO):
Gene Ontology (GO) stands as a cornerstone in the realm of biological information by offering precise definitions of protein functions. GO is
an organized and regulated lexicon consisting of terms known as GO terms. It’s categorized into three distinct and non-overlapping ontologies:
Molecular Function (MF), Biological Process (BP), and Cellular Component (CC). The structure of GO is represented as a Directed Acyclic Graph
(DAG), where terms take the form of nodes, and relationships among terms form the edges. This framework offers greater flexibility than a tra-
ditional hierarchy, as each term can have multiple connections to broader parent terms as well as more specific child terms (du Plessis et al.,
2011). Genes or proteins become associated with GO terms through an annotation process, which serves as a linkage. Each GO annotation has an
attributed source and database entry. These sources can range from literature references to database references and computational evidence.
Every biological molecule is linked to the most specific set of terms that accurately depict its functional attributes. Consequently, if a biological
molecule is associated with a particular term, it will be inherently connected to all the parent terms within that term’s hierarchical structure (du
Plessis et al., 2011). This comprehensive system enables the precise classification of biological functions and greatly aids in the understanding
of gene and protein functionality.
Rafael Guillermo Villarreal-Julio & Jonny Andrés Yepes-Blandón7
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 3.
Genomic Annotation*1
CDS CDS
Start
CDS
End CDS Length (nt) Protein Lenght (aa) Codon Start View Sequence and Design Primers Source
CHIKVgp2 7570 11316 3747 11248 1 CDS | Protein GenBank
Isoelectric Point/Molecular Weight (SOP)
Isoelectric pt Molecular Weught Evidence Code
8.7 138351.1 RCA
Other Domains/Motifs (SOP)
Domain/Motif Start End Program
transmembrane 733 755 tmhmm
transmembrane 690 7112 tmhmm
transmembrane 794 816 tmhmm
low_complexity 780 791 seg
transmembrane 1223 1245 tmhmm
transmembrane 765 7787 tmhmm
low_complexity 57 99 seg
low_complexity 20 44 seg
low_complexity 693 707 seg
low_complexity 1224 1241 seg
Functional features of annotating and searching for domains of the CHIKgp2 protein. Sequence annotations provide detailed information about
specific regions or features within a protein sequence. These annotations encompass a wide range of elements, including post-translational
modifications, binding sites, enzyme active sites, local secondary structures, and other characteristics that are either reported in the cited refe-
rences or predicted. Additionally, any discrepancies or conflicts in the sequence information between different references are also documented
in this manner.
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 3.
Genomic Annotation*1
CDS CDS
Start
CDS
End CDS Length (nt) Protein Lenght (aa) Codon Start View Sequence and Design Primers Source
CHIKVgp2 7570 11316 3747 11248 1 CDS | Protein GenBank
Isoelectric Point/Molecular Weight (SOP)
Isoelectric pt Molecular Weught Evidence Code
8.7 138351.1 RCA
Other Domains/Motifs (SOP)
Domain/Motif Start End Program
transmembrane 733 755 tmhmm
transmembrane 690 7112 tmhmm
transmembrane 794 816 tmhmm
low_complexity 780 791 seg
transmembrane 1223 1245 tmhmm
transmembrane 765 7787 tmhmm
low_complexity 57 99 seg
low_complexity 20 44 seg
low_complexity 693 707 seg
low_complexity 1224 1241 seg
Functional features of annotating and searching for domains of the CHIKgp2 protein. Sequence annotations provide detailed information about
specific regions or features within a protein sequence. These annotations encompass a wide range of elements, including post-translational
modifications, binding sites, enzyme active sites, local secondary structures, and other characteristics that are either reported in the cited refe-
rences or predicted. Additionally, any discrepancies or conflicts in the sequence information between different references are also documented
in this manner.
Caracterización genética del genoma completo de una cepa del virus Chikungunya circulante en Brasil8 Vol 27 No. 2 - e-789 julio diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 4.
GO term prediction
Biological Process
Molecular Function
Cellular Component
proteolysis
serine-type endopeptidase activity
structural molecule activity
protein dimerization activity
GO: 0006508
GO: 0004252
GO: 0005198
GO: 0046983
viral capsid
virion membrane
GO: 0019028
GO: 0055036
Name GO ID Annotation Source Evidence
Biological Process
virion attachment to host cell surface receptor GO: 0019062 UniProtKB - N/A -
Molecular Function
serine - type endopeptidase activity GO: 0004252 UniProtKB IEA
structural molecule activity GO: 0005198 UniProtKB IEA
Cellular Component
host cell membrane GO: 0033644 UniProtKB IEA .Interpro
integral to membrane GO: 0016021 UniProtKB IEA
viral capsid GO: 0019028 UniProtKB IEA
virion membrane GO: 0055036 UniProtKB IEA .UniProtKB - SubCell
Gene Ontology Classification of protein CHIKgp2, divided into functional biological, molecular, and cellular components.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 4.
GO term prediction
Biological Process
Molecular Function
Cellular Component
proteolysis
serine-type endopeptidase activity
structural molecule activity
protein dimerization activity
GO: 0006508
GO: 0004252
GO: 0005198
GO: 0046983
viral capsid
virion membrane
GO: 0019028
GO: 0055036
Name GO ID Annotation Source Evidence
Biological Process
virion attachment to host cell surface receptor GO: 0019062 UniProtKB - N/A -
Molecular Function
serine - type endopeptidase activity GO: 0004252 UniProtKB IEA
structural molecule activity GO: 0005198 UniProtKB IEA
Cellular Component
host cell membrane GO: 0033644 UniProtKB IEA .Interpro
integral to membrane GO: 0016021 UniProtKB IEA
viral capsid GO: 0019028 UniProtKB IEA
virion membrane GO: 0055036 UniProtKB IEA .UniProtKB - SubCell
Gene Ontology Classification of protein CHIKgp2, divided into functional biological, molecular, and cellular components.
Rafael Guillermo Villarreal-Julio & Jonny Andrés Yepes-Blandón9
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 5.
Phylogenetic Analysis Details (Serotype). Bayesian filament of CHIKV BR33 including the three genotypes: West African (WA), East-Central-
South Africa (ECSA) and South East (SE) Asian. The red box shows CHIKV BR33.
Results showed that the isolated CHIKV BR33
strain belongs to the genotype ECSA (Fig 5). A que-
ry search using the nucleotide search tool, BLASTn
( Huh, J. E. et al 2021), revealed that the strain an-
alyzed is closely related to the CHIKV virus strain
BHI3734/H804698, with the GenBank accession
number: KP164568.1 it was isolated in Brazil from a
patient from Feira de Santana-BA and was submit-
ted to the NCBI by the Center for Technological In-
novation, Evandro Chagas Institute. It has a size of
11812 base pairs and phylogenetically belongs to
the ECSA genotype. Other strains isolated by the
same research group in 2015, in Feira de Santana,
a municipality in the state of Bahia, also located
in the northeastern region of Brazil (Nunes et al.,
2015), showed a 99% similarity regarding nucleo-
tide identity.
DISCUSSION
The detection of this CHIKV strain serves as com-
pelling evidence of its current circulation within
Brazil, giving rise to significant implications for
both virus dissemination and public health. Key
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Figure 5.
Phylogenetic Analysis Details (Serotype). Bayesian filament of CHIKV BR33 including the three genotypes: West African (WA), East-Central-
South Africa (ECSA) and South East (SE) Asian. The red box shows CHIKV BR33.
Results showed that the isolated CHIKV BR33
strain belongs to the genotype ECSA (Fig 5). A que-
ry search using the nucleotide search tool, BLASTn
( Huh, J. E. et al 2021), revealed that the strain an-
alyzed is closely related to the CHIKV virus strain
BHI3734/H804698, with the GenBank accession
number: KP164568.1 it was isolated in Brazil from a
patient from Feira de Santana-BA and was submit-
ted to the NCBI by the Center for Technological In-
novation, Evandro Chagas Institute. It has a size of
11812 base pairs and phylogenetically belongs to
the ECSA genotype. Other strains isolated by the
same research group in 2015, in Feira de Santana,
a municipality in the state of Bahia, also located
in the northeastern region of Brazil (Nunes et al.,
2015), showed a 99% similarity regarding nucleo-
tide identity.
DISCUSSION
The detection of this CHIKV strain serves as com-
pelling evidence of its current circulation within
Brazil, giving rise to significant implications for
both virus dissemination and public health. Key
Caracterización genética del genoma completo de una cepa del virus Chikungunya circulante en Brasil10 Vol 27 No. 2 - e-789 julio diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
considerations involve the transmission dynam-
ics: Chikungunya, primarily transmitted by Aedes
aegypti and Aedes albopictus mosquitoes, is fa-
cilitated by the prevalence of these vectors in
Brazil and other tropical and subtropical regions.
The introduction of an African strain augments
the virus’s genetic diversity, potentially affecting
its capacity to infect and spread among humans.
This diverse genetic landscape poses a challenge
in managing the virus, as infected individuals be-
come reservoirs for mosquito-borne transmis-
sion, elevating the risk of localized outbreaks, par-
ticularly in densely populated urban areas (Hakim
& Aman, 2022; Nunes et al., 2015).. The genetic
diversity also influences immune responses and
vaccine efficacy, with varying susceptibility and
disease severity among individuals. Moreover, dif-
ferent strains may exhibit differential responses
to existing treatments, complicating the devel-
opment of effective therapies. In terms of public
health, the presence of an African Chikungunya
strain underscores the critical need for vector con-
trol measures, encompassing mosquito breeding
site elimination and public education on mosquito
bite prevention. These measures are paramount
in curtailing virus spread and averting potential
outbreaks. Vigilant epidemiological surveillance
is essential, especially in areas where the African
strain is prevalent, enabling early and effective
responses to contain virus transmission. In sum-
mary, the introduction of an African Chikungun-
ya strain in Brazil presents additional challenges
to public health and disease control. Addressing
virus spread and genetic diversity necessitates
a coordinated response at local, national, and in-
ternational levels, emphasizing continual monitor-
ing, research, and collaborative efforts to tackle
this global health concern (Hakim & Aman, 2022;
Nunes et al., 2015)..
The detection of this specific Chikungunya strain
in Brazil warrants a deeper exploration of its clin-
ical implications, particularly regarding its viru-
lence and its association with the severity of the
disease. Understanding the virulence of this strain
is crucial, as it can significantly impact the clinical
outcomes in infected individuals. Virulence refers
to the ability of the virus to cause disease and the
severity of that disease. Investigating whether
this strain exhibits enhanced virulence compared
to other Chikungunya strains is essential for pre-
dicting the potential impact on public health. Fur-
thermore, assessing the relationship between this
strain and the severity of the disease is pivotal.
Some Chikungunya strains have been associated
with more severe clinical manifestations, such as a
higher incidence of severe joint pain, arthritis, and
neurological complications. If this African strain
shows a stronger correlation with severe disease,
it could have important implications for health-
care systems and clinical management strategies
in regions affected by the virus. In addition, the
genetic diversity of the virus could potentially
influence the effectiveness of diagnostic tests,
treatment approaches, and vaccine development.
A comprehensive study of the specific genetic
characteristics of this strain is warranted to eval-
uate these aspects thoroughly. By delving deeper
into the clinical implications, we can gain valuable
insights into the potential impact of this African
Chikungunya strain on the health of affected pop-
ulations and, consequently, inform more targeted
and effective public health interventions and clin-
ical management strategies (Lima-Camara, 2016;
Zerfu et al., 2023).
No vaccines are currently available for use as a
prophylactic method, and no effective antiviral
drugs are available for the treatment of a CHIKV
infection. Thus, evidence such as the presented in
this document is crucial for the continuous alert
and vigilance of national and international disease
control agencies, for the prevention of new cases
that could collapse the health services during si-
multaneous explosive epidemics circulating in the
country (Lima-Camara, 2016; Zerfu et al., 2023). It
is important to identify phylogenetically the circu-
lating genotype in Brazil’s outbreak, because the
presence of particular genotypes has been asso-
ciated with more dangerous and severe clinical
manifestations, mortality, high pathogenicity, and
even an increase of mosquito infectivity, followed
DOI: https://doi.org/ 10.22579/20112629.789
considerations involve the transmission dynam-
ics: Chikungunya, primarily transmitted by Aedes
aegypti and Aedes albopictus mosquitoes, is fa-
cilitated by the prevalence of these vectors in
Brazil and other tropical and subtropical regions.
The introduction of an African strain augments
the virus’s genetic diversity, potentially affecting
its capacity to infect and spread among humans.
This diverse genetic landscape poses a challenge
in managing the virus, as infected individuals be-
come reservoirs for mosquito-borne transmis-
sion, elevating the risk of localized outbreaks, par-
ticularly in densely populated urban areas (Hakim
& Aman, 2022; Nunes et al., 2015).. The genetic
diversity also influences immune responses and
vaccine efficacy, with varying susceptibility and
disease severity among individuals. Moreover, dif-
ferent strains may exhibit differential responses
to existing treatments, complicating the devel-
opment of effective therapies. In terms of public
health, the presence of an African Chikungunya
strain underscores the critical need for vector con-
trol measures, encompassing mosquito breeding
site elimination and public education on mosquito
bite prevention. These measures are paramount
in curtailing virus spread and averting potential
outbreaks. Vigilant epidemiological surveillance
is essential, especially in areas where the African
strain is prevalent, enabling early and effective
responses to contain virus transmission. In sum-
mary, the introduction of an African Chikungun-
ya strain in Brazil presents additional challenges
to public health and disease control. Addressing
virus spread and genetic diversity necessitates
a coordinated response at local, national, and in-
ternational levels, emphasizing continual monitor-
ing, research, and collaborative efforts to tackle
this global health concern (Hakim & Aman, 2022;
Nunes et al., 2015)..
The detection of this specific Chikungunya strain
in Brazil warrants a deeper exploration of its clin-
ical implications, particularly regarding its viru-
lence and its association with the severity of the
disease. Understanding the virulence of this strain
is crucial, as it can significantly impact the clinical
outcomes in infected individuals. Virulence refers
to the ability of the virus to cause disease and the
severity of that disease. Investigating whether
this strain exhibits enhanced virulence compared
to other Chikungunya strains is essential for pre-
dicting the potential impact on public health. Fur-
thermore, assessing the relationship between this
strain and the severity of the disease is pivotal.
Some Chikungunya strains have been associated
with more severe clinical manifestations, such as a
higher incidence of severe joint pain, arthritis, and
neurological complications. If this African strain
shows a stronger correlation with severe disease,
it could have important implications for health-
care systems and clinical management strategies
in regions affected by the virus. In addition, the
genetic diversity of the virus could potentially
influence the effectiveness of diagnostic tests,
treatment approaches, and vaccine development.
A comprehensive study of the specific genetic
characteristics of this strain is warranted to eval-
uate these aspects thoroughly. By delving deeper
into the clinical implications, we can gain valuable
insights into the potential impact of this African
Chikungunya strain on the health of affected pop-
ulations and, consequently, inform more targeted
and effective public health interventions and clin-
ical management strategies (Lima-Camara, 2016;
Zerfu et al., 2023).
No vaccines are currently available for use as a
prophylactic method, and no effective antiviral
drugs are available for the treatment of a CHIKV
infection. Thus, evidence such as the presented in
this document is crucial for the continuous alert
and vigilance of national and international disease
control agencies, for the prevention of new cases
that could collapse the health services during si-
multaneous explosive epidemics circulating in the
country (Lima-Camara, 2016; Zerfu et al., 2023). It
is important to identify phylogenetically the circu-
lating genotype in Brazil’s outbreak, because the
presence of particular genotypes has been asso-
ciated with more dangerous and severe clinical
manifestations, mortality, high pathogenicity, and
even an increase of mosquito infectivity, followed
Rafael Guillermo Villarreal-Julio & Jonny Andrés Yepes-Blandón11
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
by Asian strains (Hakim & Aman, 2022; Kumar et al.,
2014; Spicher et al., 2021).
The present study helps to better understand the
pathophysiology and molecular aspects of the dis-
ease by achieving a complete genetic and functional
description of the virus and its structural proteins.
CONCLUSION
As far as we know, this is the first report of a com-
plete genome of CHIKV, isolated in Brazil, in 2016.
The sequence described, the additional phyloge-
netic analyzes of these genomes, and the other
sequences will be detailed in future publications.
Sequencing the complete genome of the Chikun-
gunya virus is of paramount importance for sev-
eral reasons. Firstly, it allows the identification of
different strains and mutations of the virus. This
is crucial for comprehending the genetic diversity
of the virus and its capacity for evolution, enabling
effective surveillance of mutations, which is vital
for predicting the virus’s spread and developing
more effective prevention and treatment strate-
gies. Furthermore, genomic sequencing facilitates
diagnosis and the development of specific tests.
These tests play a fundamental role in detecting
the presence of the virus in infected patients, en-
abling swift and precise decision-making regard-
ing control measures. Additionally, this genomic
information is essential in designing vaccines
against Chikungunya. A detailed understanding of
the viral genome allows the creation of vaccines
capable of eliciting effective and specific immune
responses against the virus. Genomic sequencing
also provides valuable insights into epidemiolog-
ical studies and understanding the virus’s spread
in different regions, which is essential for the im-
plementation of control and prevention measures,
especially in areas where the virus is endemic.
Knowledge of the Chikungunya virus’s genetics is
crucial in the development of effective antiviral
treatments. These medications can target specific
components of the viral genome to inhibit its rep-
lication. Finally, genomic sequencing allows us to
monitor the potential emergence of resistance to
antiviral medications used in Chikungunya treat-
ment, which is essential for adjusting treatments
and ensuring their efficacy over time. In summa-
ry, sequencing the Chikungunya virus genome is a
critical component in the fight against this disease
and in safeguarding public health.
ACKNOWLEDGEMENTS
The authors particularly acknowledge to Dr. Irene
Bosch at the Columbia Mailman School of Pub-
lic Health, New York, NY, USA and Dr. Lee Gehrke,
director of Gehrke Laboratory at Harvard Med-
ical School (HMS), Boston, Massachusetts, USA
and Massachusetts Institute of Technology (MIT),
Cambridge, MA, USA for the academic formation,
methodological advice and equipment loan for the
realization of this research.
CONFLICT OF INTEREST
The authors declare they have no conflict of
interest.
AUTHOR CONTRIBUTIONS
RVJ and JYB designed the study; collected and pre-
pared the materials; performed the experiments;
performed data analyses; drafted and wrote the
manuscript. All authors read, edited, and approved
the final draft.
REFERENCES
Alguridi HI, Alzahrani F, Altayb HN, Almalki S,
Zaki E, Algarni S, Assiri A, Memish ZA. The
First Genomic Characterization of the
Chikungunya Virus in Saudi Arabia. Jour-
nal of Epidemiology and Global Health,
2023;13(2):191–199. https://doi.org/10.1007/
s44197-023-00098-0
Ang SK, Lam S, Chu JJH. Propagation of Chikungunya
Virus Using Mosquito Cells. Methods in Mo-
lecular Biology (Clifton, N.J.), 2016;1426:87–
92. https://doi.org/10.1007/978-1-4939-
3618-2_8
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
by Asian strains (Hakim & Aman, 2022; Kumar et al.,
2014; Spicher et al., 2021).
The present study helps to better understand the
pathophysiology and molecular aspects of the dis-
ease by achieving a complete genetic and functional
description of the virus and its structural proteins.
CONCLUSION
As far as we know, this is the first report of a com-
plete genome of CHIKV, isolated in Brazil, in 2016.
The sequence described, the additional phyloge-
netic analyzes of these genomes, and the other
sequences will be detailed in future publications.
Sequencing the complete genome of the Chikun-
gunya virus is of paramount importance for sev-
eral reasons. Firstly, it allows the identification of
different strains and mutations of the virus. This
is crucial for comprehending the genetic diversity
of the virus and its capacity for evolution, enabling
effective surveillance of mutations, which is vital
for predicting the virus’s spread and developing
more effective prevention and treatment strate-
gies. Furthermore, genomic sequencing facilitates
diagnosis and the development of specific tests.
These tests play a fundamental role in detecting
the presence of the virus in infected patients, en-
abling swift and precise decision-making regard-
ing control measures. Additionally, this genomic
information is essential in designing vaccines
against Chikungunya. A detailed understanding of
the viral genome allows the creation of vaccines
capable of eliciting effective and specific immune
responses against the virus. Genomic sequencing
also provides valuable insights into epidemiolog-
ical studies and understanding the virus’s spread
in different regions, which is essential for the im-
plementation of control and prevention measures,
especially in areas where the virus is endemic.
Knowledge of the Chikungunya virus’s genetics is
crucial in the development of effective antiviral
treatments. These medications can target specific
components of the viral genome to inhibit its rep-
lication. Finally, genomic sequencing allows us to
monitor the potential emergence of resistance to
antiviral medications used in Chikungunya treat-
ment, which is essential for adjusting treatments
and ensuring their efficacy over time. In summa-
ry, sequencing the Chikungunya virus genome is a
critical component in the fight against this disease
and in safeguarding public health.
ACKNOWLEDGEMENTS
The authors particularly acknowledge to Dr. Irene
Bosch at the Columbia Mailman School of Pub-
lic Health, New York, NY, USA and Dr. Lee Gehrke,
director of Gehrke Laboratory at Harvard Med-
ical School (HMS), Boston, Massachusetts, USA
and Massachusetts Institute of Technology (MIT),
Cambridge, MA, USA for the academic formation,
methodological advice and equipment loan for the
realization of this research.
CONFLICT OF INTEREST
The authors declare they have no conflict of
interest.
AUTHOR CONTRIBUTIONS
RVJ and JYB designed the study; collected and pre-
pared the materials; performed the experiments;
performed data analyses; drafted and wrote the
manuscript. All authors read, edited, and approved
the final draft.
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nprot.2013.084
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and Immune Pathogenesis of Chikungun-
ya Virus Infection for Diagnostic and Vac-
cine Development. Viruses, 2022;15(1):48.
https://doi.org/10.3390/v15010048
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A resource for the discovery of novel genes.
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public health challenges in Brazil. Revis-
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2018;7(3): gix135. https://doi.org/10.1093/
gigascience/gix135
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Nunes BTD, Cardoso JF, Tesh RB, Hay SI, da
Costa-Vasconcelos PF. Emergence and po-
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Brazil. BMC Medicine, 2015;13(1):102. https://
doi.org/10.1186/s12916-015-0348-x
Spicher T, Delitz M, Schneider AdeB, Wolfinger MT.
Dynamic Molecular Epidemiology Reveals
Lineage-Associated Single-Nucleotide Va-
riants That Alter RNA Structure in Chikun-
gunya Virus. Genes, 2021;12(2):239. https://
doi.org/10.3390/genes12020239
Volk SM, Chen R, Tsetsarkin KA, Adams AP, Gar-
cia TI, Sall AA, Nasar F, Schuh AJ, Holmes
EC, Higgs S, Maharaj PD, Brault AC, Weaver
SC. Genome-scale phylogenetic analyses
of Chikungunya virus reveal independent
emergences of recent epidemics and va-
rious evolutionary rates. Journal of Viro-
logy, 2010;84(13):6497–6504. https://doi.
org/10.1128/JVI.01603-09
Xf T, Yh H, Yf S, Pf Z, Lz H, Hs LHP. The transcriptome
of Icerya aegyptiaca (Hemiptera: Monophle-
bidae) and comparison with neococcoids
reveal genetic clues of evolution in the scale
insects. BMC Genomics, 2023;24(1):https://
doi.org/10.1186/s12864-023-09327-z
Rafael Guillermo Villarreal-Julio & Jonny Andrés Yepes-Blandón13
Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
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Vol 27 No. 2 e-789 julio - diciembre 2023.
DOI: https://doi.org/ 10.22579/20112629.789
Zerfu B, Kassa T, Legesse M. Epidemiology, biology,
pathogenesis, clinical manifestations, and
diagnosis of dengue virus infection, and its
trend in Ethiopia: A comprehensive litera-
ture review. Tropical Medicine and Health,
2023;51(1):11. https://doi.org/10.1186/
s41182-023-00504-0
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SARS-CoV-2, SARS-CoV and MERS-CoV.
BMC Research Notes, 2021;14(1):doi:10.1186/
s13104-021-05561-4