{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:06:46Z","timestamp":1772168806215,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/f1000research.110361.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,7,19]],"date-time":"2023-07-19T00:00:00Z","timestamp":1689724800000}},{"DOI":"10.12688\/f1000research.110361.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,7,19]],"date-time":"2023-07-19T00:00:00Z","timestamp":1689724800000}}],"reference-count":56,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,7,19]],"date-time":"2023-07-19T00:00:00Z","timestamp":1689724800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministerio de Ciencia Tecnolog\u00eda e Innovaci\u00f3n de Colombia","award":["Project. Code: 622177757170"],"award-info":[{"award-number":["Project. Code: 622177757170"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    <ns3:italic>Antecedentes<\/ns3:italic>\n                  <\/ns3:p>\n                  <ns3:p>\n                    La malaria urbana es un problema de salud p\u00fablica en Colombia y a\u00fan existe desconocimiento sobre sus caracter\u00edsticas epidemiol\u00f3gicas, las cuales son clave para la implementaci\u00f3n de medidas de control. La presencia de casos de malaria urbana y el diagn\u00f3stico de la enfermedad son algunos de los desaf\u00edos que enfrentan los programas de eliminaci\u00f3n de la malaria. El objetivo de esta investigaci\u00f3n fue estimar la prevalencia de malaria, explorar factores asociados y detectar genes\n                    <ns3:italic>pfhrp<\/ns3:italic>\n                    <ns3:italic>2\/3<\/ns3:italic>\n                    , en la zona urbana de Tumaco entre julio y diciembre de 2019.\n                  <\/ns3:p>\n                  <ns3:p\/>\n                  <ns3:p>\n                    <ns3:italic>M\u00e9todos<\/ns3:italic>\n                  <\/ns3:p>\n                  <ns3:p>Se realiz\u00f3 un estudio de prevalencia utilizando un muestreo probabil\u00edstico aleatorio estratificado. Se administraron encuestas estructuradas y se tomaron muestras de sangre y se examinaron mediante microscop\u00eda \u00f3ptica, pruebas de diagn\u00f3stico r\u00e1pido (RDT) y reacci\u00f3n en cadena de la polimerasa (PCR). Se utiliz\u00f3 un modelo de regresi\u00f3n log\u00edstica para explorar los factores asociados.<\/ns3:p>\n                  <ns3:p\/>\n                  <ns3:p>\n                    <ns3:italic>Resultados<\/ns3:italic>\n                  <\/ns3:p>\n                  <ns3:p>\n                    Se encuest\u00f3 a 1.504 personas que viv\u00edan en 526 hogares. La prevalencia global fue del 2,97% (IC 95%: 2,1 - 4,3%). Fue mayor en varones, en el grupo de edad de 10 a 19 a\u00f1os y en casos asintom\u00e1ticos. La prevalencia de la amplificaci\u00f3n de\n                    <ns3:italic>pfhrp2<\/ns3:italic>\n                    fue del 2,16 % (IC del 95 %: 1,6 - 2,9 %). Los hogares con tres o m\u00e1s personas ten\u00edan un mayor riesgo de infecci\u00f3n por paludismo (odds ratio ajustado [ORa] 4,05; intervalo de confianza [IC] del 95%: 1,57-10,43). Todos los casos se debieron a\n                    <ns3:italic>P.<\/ns3:italic>\n                    <ns3:italic>falciparum<\/ns3:italic>\n                    .\n                  <\/ns3:p>\n                  <ns3:p\/>\n                  <ns3:p>\n                    <ns3:italic>Conclusiones<\/ns3:italic>\n                  <\/ns3:p>\n                  <ns3:p>\n                    La prevalencia de malaria urbana fue baja. Las estrategias para eliminar la malaria en \u00e1reas urbanas deben ajustarse considerando el acceso al diagn\u00f3stico temprano, la infecci\u00f3n asintom\u00e1tica y las PDR utilizadas para detectar la presencia del gen\n                    <ns3:italic>pfhrp2<\/ns3:italic>\n                    .\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.110361.3","type":"journal-article","created":{"date-parts":[[2023,7,19]],"date-time":"2023-07-19T06:49:34Z","timestamp":1689749374000},"page":"448","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Malaria prevalence in Commune 5 in Tumaco (Nari\u00f1o, Colombia)"],"prefix":"10.12688","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2498-4721","authenticated-orcid":false,"given":"Pablo Enrique","family":"Chaparro Narv\u00e1ez","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monica Marcela","family":"Jimenez-Serna","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Luz","family":"Gunturiz Albarracin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9449-4931","authenticated-orcid":false,"given":"Gabriel","family":"Carrasquilla Gutierrez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2023,7,19]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1186\/s12936-015-0956-0","article-title":"Is there malaria transmission in urban settings in Colombia?.","volume":"14","author":"J Padilla","year":"2015","journal-title":"Malar. 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These are our answers: Some questions were not answered by the authors and thus, new doubts arose: the main question is in the interpretation of pfhrp2\/3 prevalence\u2019s (and malaria prevalence): 1) In total, how many samples were actually positive? What is the denominator? table 5 shows 39 positive samples. If denominator is 1,504, the prevalence was 2.59 and not 2.97%. Please add all the information and clarify the number and prevalence of positive samples. <b>Answer:<\/b> The prevalence of 2.97% corresponds to the stratified multistage random sampling with proportional assignment used by us. We have indicated in the methods section. The prevalence of 2.59% would correspond to a simple random sampling that was not used in this study. On the other hand, it is assumed that all <i>P. falciparum<\/i> should have the pfhrp2\/3 gene. Its absence indicates a deletion of this gene or that the PCR used was not able to detect it. What was the PCR protocol used for detection of pfhrp2\/3?. Please, add the reference. These data are extremely important for quality of the work. Was it and &quot;in house&quot; method?. If this was the case, the complete protocol must be added to methods sections. <b>Answer:<\/b> As indicated in the methods section, PCRs were performed for the individual amplification of the HRP2 and HRP3 genes. It is not possible to confirm the deletion of these genes with this study, since the sequencing of the complete genes was not carried out, but only fragments of them. It is probably that authors used as denominator for pfhrp2 gene detection, almost all the samples collected (n=1.492). As authors only found 39 <i>P. falciparum<\/i> positive samples, the denominator for PfHRP amplification should be 39 (as in table 5) and not 1.492. Maybe this is the cause of finding only 2.16% PfHRP gene amplification. As data are incomplete this is an assumption. Authors must clarify. It is very confusing. <b>Answer:<\/b> The prevalence for the detection of the pfhrp2 gene was also calculated taking into account multistage stratified random sampling with proportional assignment. Minor English and taxonomic corrections are necessary: All taxonomic names with only generic names must have spp. at the end (ex. Anopheles spp.). <b>Answer<\/b>: The adjustment was made on pages 9, 15, 16, 19. page 6\/40: &quot;In this city, 70% of malaria cases are reported from Commune 5 in the last ten years&quot;. As authors are talking about malaria in the last ten years (in past), the verb should be written in past time: ...In this city, 70% of malaria cases were reported. <b>Answer:<\/b> The adjustment was made. Page 6\/40: &quot;Polymerase chain reaction (PCR) For PCR, two drops of blood were obtained from the same finger puncture and were then put on the filter paper. 10 mm2 of Whatman #3 filter paper impregnated with blood were taken and genomic DNA extraction was performed according to the protocol described in the article&quot;. Authors did not give information about this article. Please add a reference. <b>Answer:<\/b> The adjustment was made. Pag 6\/40: Authors said that: &quot;Standardization of protocols for genomic DNA extraction from whole blood and filter paper samples&quot;. However, methods only explain about DNA extraction and PCR from filter paper samples. No mention about whole blood experiments was found in the manuscript. If authors collected whole blood samples (not filter paper) these data should be in the methods. If not, this part of the sentence should be excluded. <b>Answer<\/b>: The adjustment was made. The whole blood extraction was eliminated since it is not mentioned in the manuscript. Page 7\/40: The sentence: &quot;For the amplification of the different fragments of the genes mentioned, we designed the specific primers and the PCR conditions for each of them were standardized. For the design of the primers, the GC content, dimer formation, loop formation, palindromes and Tm were taken into account. The sequences of the HRP2\/HRP3 and PvSSU genes published in the Genbank were used, an alignment was performed using clustalW (Refseq) and the primers were designed from conserved regions of the sequences obtained&quot; is repeated at the end of page 6. Please excluded the repeated sentence. <b>Answer:<\/b> Removed the repeated paragraph. Discussion: Page 16\/40: Authors said: &quot;In terms of case detection, as in other studies, PCR had the highest diagnostic performance,40 followed by microscopy. When comparing microscopy\/RDT results with PCR results, lack of concordance was observed. Those with a positive diagnosis through microscopy\/RDT were not detected through PCR and those with a positive diagnosis through PCR were not detected through microscopy\/RDT. It is possible that people who were positive according to microscopy\/RDT did not have the parasite's DNA so it could not be detected through PCR, as described by Mudare et al.,51 or the sample may have had a low amount of parasitic DNA or it may have degraded. Another possibility is that there were changes in the primer ringing site, which would prevent amplification of the gene fragment under study.&quot;. This part is a little confusing. For better clarification, we suggested to separate RDT results, thick smear results and PCR results and to discuss each finding (negative RDT with positive PCR, etc.). <b>Answer:<\/b> The adjustment was made. The correlation between techniques is made to be able to explain why there is not a 100% positivity between tests. Specifically, for negative PCR results it can be inferred that: 1. The ringing site of the primers may have some modification that does not allow their hybridization. 2. Although the degradation of genomic DNA is improbable because the verification of its quality and integrity was carried out through quantification and the 260\/280 ratio, which for all DNA was between 1.8 and 2.0 and by electrophoresis, respectively, but it is not unlikely that the reactions have contaminants that interfere with amplification. 3. The sequences of the selected fragments may contain variable regions that are not recognized by the designed primers.","URL":"https:\/\/f1000research.com\/articles\/11-448\/v3#referee-comment-9920","order":1,"name":"referee-comment-9920","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.138123.r149866, Meor Termizi Farah Haziqah, School of Biological Sciences, Universiti Sains Malaysia, Penang, 09 Sep 2022, version 2, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/11-448\/v2#referee-response-149866","order":2,"name":"referee-response-149866","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.144551.r245104, Ebenezer Krampah Aidoo, Accra Technical University, Accra, 01 Mar 2024, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/11-448\/v3#referee-response-245104","order":3,"name":"referee-response-245104","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This study was funded by Minciencias \u201cMalaria Elimination: A Challenge for Colombia\u201d Project. Code: 622177757170. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}