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Article ; Online: Cloning, expression and seroreactivity of the recombinant lipopolysaccharide assembly protein - D (LptD) from Bartonella bacilliformis.

Flores-Nuñez, Astrid / Ventura, Gladis / Bailon, Henri / Marcelo, Adolfo / Sandoval, Gustavo / Padilla-Rojas, Carlos

Revista peruana de medicina experimental y salud publica

2022 Volume 39, Issue 1, Page(s) 15–23

Abstract: Objective.: To evaluate in silico and at the serological level the antigenic potential of the recombinant extracellular domain of the lipopolysaccharide assembly protein - D (LptD) of Bartonella bacilliformis (dexr_LptD).: Materials and methods.: ... ...

Title translation	Clonamiento, expresión y seroreactividad de la proteína recombinante de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis.
Abstract	Objective.: To evaluate in silico and at the serological level the antigenic potential of the recombinant extracellular domain of the lipopolysaccharide assembly protein - D (LptD) of Bartonella bacilliformis (dexr_LptD). Materials and methods.: Through in silico analysis, we selected a B. bacilliformis protein with antigenic and immunogenic potential. The selected protein gene was cloned into Escherichia coli TOP10 and expressed in Escherichia coli BL21 (DE3) pLysS. Recombinant protein was expressed using isopropyl-β-D-1-thiogalactopyranoside (IPTG) and induction conditions were optimized. Finally, it was purified with Ni-IDA resin (His60 Ni Superflow) and a Western Blot assay was conducted. Results.: In silico, the selected protein was LptD because it is located in the outer membrane and is antigenic and immunogenic. Optimized conditions for dexr_LptD induction were 0.5 mM IPTG, 16 hours, TB (Terrific Broth) medium, 3% (v/v) ethanol, 28 ºC, OD600: 1-1.5 and 200 rpm. Purification was carried out under denaturating conditions on a small scale and we obtained 2.6 μg/mL of partially purified dexr_LptD. The Western Blot assay showed a positive reaction between the sera from patients with Carrión's Disease and dexr_LptD, which shows the antigenicity of dexr_LptD. Conclusions.: The dexr_LptD shows antigenicity both in silico and at the serological level, these results are the basis for further studies on vaccine candidates against Carrion's Disease.
MeSH term(s)	Bacterial Outer Membrane Proteins/genetics ; Bacterial Outer Membrane Proteins/metabolism ; Bartonella Infections ; Bartonella bacilliformis/genetics ; Cloning, Molecular ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Humans ; Isopropyl Thiogalactoside/metabolism ; Lipopolysaccharides/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Escherichia coli Proteins ; Lipopolysaccharides ; LptD protein, E coli ; Recombinant Proteins ; Isopropyl Thiogalactoside (367-93-1)
Language	English
Publishing date	2022-06-24
Publishing country	Peru
Document type	Journal Article
ZDB-ID	2120092-0
ISSN	1726-4642 ; 1726-4642
ISSN (online)	1726-4642
ISSN	1726-4642
DOI	10.17843/rpmesp.2022.391.9292
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Article ; Online: Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology.

Molina, Iris S / Jimenez-Vasquez, Victor / Lizarraga, Wendy / Sevilla, Nieves / Hurtado, Veronica / Padilla-Rojas, Carlos

Journal of medical virology

2023 Volume 95, Issue 9, Page(s) e29056

Abstract: During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen ... ...

Abstract	During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.
MeSH term(s)	Male ; Humans ; Adult ; Female ; Phylogeny ; Mpox (monkeypox) ; Pandemics ; COVID-19 ; Databases, Factual
Language	English
Publishing date	2023-09-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.29056
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Article ; Online: Reinfections Are More Frequent Than Currently Considered in Countries With High Incidence of Coronavirus Disease 2019 (COVID-19) Cases Due to Stringent Definitions.

Pampa-Espinoza, Luis / Silva-Valencia, Javier / Fernandez-Navarro, Manuel / Padilla-Rojas, Carlos / Solari, Lely

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 74, Issue 8, Page(s) 1505–1506

MeSH term(s)	COVID-19 ; Humans ; Incidence ; Reinfection ; SARS-CoV-2
Language	English
Publishing date	2021-07-10
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciab783
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Article ; Online: Clonamiento, expresión y seroreactividad de la proteína recombinante de ensamblaje de lipopolisacáridos – D (LptD) de Bartonella bacilliformis

Astrid Flores-Nuñez / Gladis Ventura / Henri Bailon / Adolfo Marcelo / Gustavo Sandoval / Carlos Padilla-Rojas

Revista Peruana de Medicina Experimental y Salud Pública, Vol 39, Iss 1, Pp 15-

2022 Volume 23

Abstract: Objetivo. Evaluar in silico y a nivel serológico el potencial antigénico del dominio extracelular recombinante de la proteína de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis (dexr_LptD). Materiales y métodos. Mediante el ... ...

Abstract	Objetivo. Evaluar in silico y a nivel serológico el potencial antigénico del dominio extracelular recombinante de la proteína de ensamblaje de lipopolisacáridos - D (LptD) de Bartonella bacilliformis (dexr_LptD). Materiales y métodos. Mediante el análisis in silico se realizó la selección de una proteína de B. bacilliformis con potencial antigénico e inmunogénico. El gen de la proteína seleccionada se clonó en Escherichia coli TOP10 y se expresó en Escherichia coli BL21 (DE3) pLysS. La proteína recombinante fue expresada usando isopropil-β-D-1-tiogalactopiranósido (IPTG) y se optimizaron las condiciones de inducción. Por último, se purificó con resina Ni-IDA (His60 Ni Superflow) y se realizó un ensayo de Western Blot. Resultados: In silico, la proteína seleccionada fue LptD por estar localizada en la membrana externa y ser antigénica e inmunogénica. Las condiciones optimizadas para la inducción del dexr_LptD fueron 0,5 mM IPTG, 16 h, medio TB (Terrific Broth), etanol al 3% (v/v), 28 ºC, OD600: 1-1,5 y 200 r.p.m. La purificación se realizó en condiciones denaturantes a pequeña escala y se obtuvo 2,6 μg/mL de dexr_LptD parcialmente purificada. El ensayo de Western Blot mostró una reacción positiva entre los sueros provenientes de pacientes con la enfermedad de Carrión y dexr_LptD, ello evidencia la antigenicidad del dexr_LptD. Conclusiones. El dexr_LptD muestra antigenicidad in silico y a nivel serológico, estos resultados son base para posteriores estudios sobre candidatos vacunales contra la enfermedad de Carrión.
Keywords	infecciones por bartonella ; proteína lptd ; bartonella bacilliformis ; proteínas recombinantes ; antigenicidad vacunal ; biología computacional ; Medicine ; R ; Medicine (General) ; R5-920
Language	Spanish
Publishing date	2022-03-01T00:00:00Z
Publisher	Instituto Nacional de Salud
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Notes from the Field: Dengue Outbreak - Peru, 2023.

Munayco, César V / Valderrama Rosales, Betsabet Yadira / Mateo Lizarbe, Susan Yanett / Yon Fabian, Carmen Rosa / Peña Sánchez, Ricardo / Vásquez Sánchez, César Henry / García, Maria Paquita / Padilla-Rojas, Carlos / Suárez, Victor / Sánchez-González, Liliana / Jones, Forrest K / Kohatsu, Luciana / Adams, Laura E / Morgan, Juliette / Paz-Bailey, Gabriela

MMWR. Morbidity and mortality weekly report

2024 Volume 73, Issue 4, Page(s) 86–88

MeSH term(s)	Humans ; Peru/epidemiology ; Disease Outbreaks ; Dengue/epidemiology
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	412775-4
ISSN	1545-861X ; 0149-2195
ISSN (online)	1545-861X
ISSN	0149-2195
DOI	10.15585/mmwr.mm7304a4
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Article ; Online: Validation and evaluation of RT-PCR real time in house test to detection of SARS-CoV-2 using specific RdRp gene and GAPDH endogen control.

Rojas-Serrano, Nancy / Lope-Pari, Priscila / Huaringa-Nuñez, Maribel / Marques Simas, Paulo Vitor / Palacios-Salvatierra, Rosa / Balbuena-Torres, Johanna / Caceres Rey, Omar Alberto / Padilla-Rojas, Carlos

Revista peruana de medicina experimental y salud publica

2022 Volume 38, Issue 4, Page(s) 595–600

Abstract: The present work validated and evaluated a duplex real-time RT-PCR using specific primers and probes for genes RdRp from SARS-CoV-2 and GAPDH from humans; the latter was used as an endogenous control in all reactions. We evaluated the specificity, the ... ...

Title translation	Validación y evaluación de una prueba de RT-PCR en tiempo real in house para la detección de SARS-CoV-2 usando un gen específico RdRp y control endógeno GAPDH.
Abstract	The present work validated and evaluated a duplex real-time RT-PCR using specific primers and probes for genes RdRp from SARS-CoV-2 and GAPDH from humans; the latter was used as an endogenous control in all reactions. We evaluated the specificity, the sensitivity, the robustness, the reproducibility, the repeatability, the comparability, and the limit of detection. The predictive positive and negative values (PPV and PNV, respectively) and all the parameters evaluated using our duplex real-time RT-PCR was 100%. The detection limit was 100 copies/µL according to the acceptance criteria established for the validation of this protocol. Our duplex real-time RT-PCR demonstrated to be a good alternative for the diagnosis of COVID-19; in addition, this PCR was used adequately in suspicion of COVID-19, allowing it to control the number of false-negatives.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing/methods ; COVID-19 Testing/standards ; Humans ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/genetics ; Sensitivity and Specificity
Chemical Substances	RNA, Viral ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-04-01
Publishing country	Peru
Document type	Journal Article
ZDB-ID	2120092-0
ISSN	1726-4642 ; 1726-4642
ISSN (online)	1726-4642
ISSN	1726-4642
DOI	10.17843/rpmesp.2021.384.7596
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Article ; Online: Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru.

Padilla-Rojas, Carlos / Lope-Pari, Priscila / Vega-Chozo, Karolyn / Balbuena-Torres, Johanna / Caceres-Rey, Omar / Bailon-Calderon, Henri / Huaringa-Nuñez, Maribel / Rojas-Serrano, Nancy

Microbiology resource announcements

2020 Volume 9, Issue 19

Abstract: A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from ... ...

Abstract	A near-complete genome sequence was obtained for a novel coronavirus (SARS-CoV-2) strain obtained from an oropharyngeal swab from a Peruvian patient with coronavirus syndrome (COVID-19) who had contact with an individual who had returned to Peru from travel to Italy.
Keywords	covid19
Language	English
Publishing date	2020-05-07
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00303-20
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Article ; Online: Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern.

Padilla-Rojas, Carlos / Jimenez-Vasquez, Victor / Hurtado, Veronica / Mestanza, Orson / Molina, Iris S / Barcena, Luis / Morales Ruiz, Sandra / Acedo, Steve / Lizarraga, Wendy / Bailon, Henri / Cáceres, Omar / Galarza, Marco / Rojas-Serrano, Nancy / Vargas-Herrera, Natalia / Lope-Pari, Priscila / Huayra, Joseph / Solari, Lely

Journal of medical virology

2021 Volume 93, Issue 12, Page(s) 6845–6849

Abstract: The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they ... ...

Abstract	The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Genome, Viral/genetics ; Genomics/methods ; Humans ; Mutation/genetics ; Pandemics/prevention & control ; Peru/epidemiology ; SARS-CoV-2/genetics
Language	English
Publishing date	2021-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.27261
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Article ; Online: Genomic surveillance of the Lambda SARS-CoV-2 variant in a global phylogenetic context.

Journal of medical virology

2022 Volume 94, Issue 10, Page(s) 4689–4695

Abstract: The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in ... ...

Abstract	The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS-CoV-2 wave.
MeSH term(s)	COVID-19/epidemiology ; Chile ; Genome, Viral ; Genomics ; Humans ; Mutation ; Phylogeny ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-06-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.27889
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Article: Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections After a Second Wave With Predominance of Lambda in Lima and Callao, Peru.

Open forum infectious diseases

2022 Volume 9, Issue 6, Page(s) ofac134

Abstract: Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the ... ...

Abstract	Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru. Methods: We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections. Results: There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases. Conclusions: We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru's second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.
Language	English
Publishing date	2022-03-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofac134
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