The Experience of Testing for Coronavirus Disease (COVID-19) at a Single Diagnostic Center in Paraguay before the Introduction of Vaccination.

Soon after the declaration of the COVID-19 pandemic, the Institute for Health Sciences Research (IICS) of the National University of Asunción, Paraguay became a testing laboratory (COVID-Lab) for SARS-CoV-2. The COVID-Lab testing performance was assessed from 1 April 2020 to 12 May 2021. The effect of the pandemic on the IICS and how the COVID-Lab contributed to the academic and research activities of the institute were also assessed. IICS researchers and staff adjusted their work schedules to support the COVID-Lab. Of the 13,082 nasopharyngeal/oropharyngeal swabs processed, 2704 (20.7%) tested positive for SARS-CoV-2 by RT-PCR. Of the individuals testing positive, 55.4% were female and 48.3% were aged 21-40 years. Challenges faced by the COVID-Lab were unstable reagent access and insufficient staff; shifting obligations regarding research, academic instruction, and grantsmanship; and the continuous demands from the public for information on COVID-19. The IICS provided essential testing and reported on the progress of the pandemic. IICS researchers gained better laboratory equipment and expertise in molecular SARS-CoV-2 testing but struggled to manage their conflicting educational and additional research obligations during the pandemic, which affected their productivity. Therefore, policies protecting the time and resources of the faculty and staff engaged in pandemic-related work or research are necessary components of healthcare emergency preparedness.

SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol.

SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive for the SARS-CoV-2 N2 target and tested with the Spike SNP assay to detect mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Spike SNP calls were confirmed using amplicon (Sanger) sequencing and whole-genome (Nanopore) sequencing on a subset of samples with confirmed variant lineages. Samples had a mean N2 Ct of 20.8 (SD 5.6); 198/201 samples (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%), which was consistent with the P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%), and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). The results were confirmed using Sanger sequencing in 181/181 samples, and variant calls were consistent with Nanopore sequencing in 29/29 samples. The Spike SNP assay could improve population-level surveillance for mutations associated with SARS-CoV-2 variants and inform the judicious use of sequencing resources.

Detection and characterization of Plasmodium spp. by semi-nested multiplex PCR both in mosquito vectors and in humans residing in historically endemic areas of Paraguay.

In Paraguay, no cases of Malaria have been recorded since 2011. Microscopy and the SnM-PCR technique were implemented to detect and characterize Plasmodium spp. both in mosquitoes and in humans residing in historically endemic areas of Paraguay, to evaluate the possibility of finding asymptomatic cases and/or Plasmodium parasites circulating in anophelines. Between 2013 and 2015, 361 human blood samples were collected on filter paper, and between 2016 and 2017, 938 female Anopheles mosquitoes were captured in 15 Paraguayan localities. All the diagnostic techniques showed negative results. We observed no asymptomatic case or Plasmodium circulating in vectors.

Evaluación de primers reportados para detección de KDR en especies de Anopheles colectadas en los departamentos de Caaguazú y Alto Paraná en Paraguay / Evaluation of primers reported for KDR detection in Anopheles species collected in the departments of Caaguazú and Alto Paraná in Paraguay

Las mutaciones KDR en el gen del canal del sodio (VGSC) han sido ya detectadas en al menos 13 especies de mosquitos Anopheles en su mayoría especies de África, pero aún resta por determinar los cebadores específicos para la detección en especies de Latinoamérica. En nuestro país la especie Anopheles darlingi es el vector principal de la malaria, y el A. albitarsis, el vector secundario. Se emplearon muestras de mosquitos Anoheles de las especies A. strodei, A. albitarsis, A. fluminensis, A. evansae, A. nuneztovari, A. nyssorhynchela lutzi y A. oswaldoi capturadas en los departamentos de Caaguazú y Alto Paraná en Paraguay. Para la amplificación y secuenciación se usaron cebadores reportados para el gen VGSC de A. albimanus en Guatemala, que resultaron ser específicos solo para la especie A. strodei. La secuencia revela el codón TTA que codifica para una Leucina como la secuencia TTG, reportada para la versión susceptible en la posición L1014. El fragmento amplificado es de aproximadamente 225 pares de bases. A nuestro entender, esta es la primera caracterización del gen VGSC en mosquitos Anopheles del Paraguay y para la especie A. strodei

KDR mutations in the sodium channel gene (VGSC) have already been detected in at least 13 species of Anopheles mosquitoes, mostly African species, but the molecular techniques for detection in Latin American species have yet to be determined. In our country, Anopheles darlingi species is the main vector of Malaria, and A. albitarsis, the secondary vector. We used samples of Anoheles from the species A. strodei, A. albitarsis, A. fluminensis, A. evansae, A. nuneztovari, A. nyssorhynchela lutzi and A. oswaldoi collected at the departments of Caaguazú and Alto Paraná in Paraguay. For the amplification and sequentiation, primers reported for the VGSC gen of A. strodei in Guatemala were used and were specific only for A. strode in this case. The sequence revealed the TTA codon that codifies for a leucine as the TTG sequence, reported for the susceptible version at position L1014. The amplified fragment is approximately 225 base pairs. To our knowledge, this is the first characterization of the VGSC gene in Anopheles mosquitoes in Paraguay and for the species A. strodei

Vigilancia molecular de la malaria en potenciales reservorios silvestres que viven en una región históricamente endémica de Paraguay / Molecular surveillance of malaria in potential wild reservoirs that live in a historically endemic region of Paraguay

En Paraguay, no se han registrado casos autóctonos de malaria desde el 2011. Se realizó un estudio descriptivo observacional transversal en 6 monos y 23 aves que vivían en una región históricamente endémica de Paraguay para buscar presencia de reservorios silvestres de parásitos plasmodios causantes de la malaria. El ADN se extrajo por el método de Chelex a partir de una gota de sangre en un papel de filtro, y la detección del parásito se realizó mediante la PCR múltiple semianidada. Por este método, no se detectaron parásitos en ninguna de las 29 muestras. Se evaluó el riesgo potencial de circulación selvática de los parásitos que causan la malaria. Teniendo en cuenta la presencia de mosquitos anofelinos vectores en la zona, el hecho de que no se hayan observado casos positivos es un buen indicador teniendo en cuenta que nuestro país fue declarado recientemente como país libre de malaria por la OMS(AU)

In Paraguay, autochthonous cases of malaria have not been recorded since 2011. A cross-sectional observational descriptive study was conducted in 6 monkeys and 23 birds living in a historically endemic region of Paraguay to identify wild reservoirs of plasmodium parasites that cause malaria. DNA was extracted by the Chelex method from a blood drop in a filter paper, and parasite detection was performed by the seminested multiplex PCR. By this method, parasites were not detected in any of the 29 samples. The risk of potential sylvatic circulation of the parasites causing malaria was evaluated. Considering the presence of anopheline mosquitoes in the area, the fact that we did not find any positive cases is a good indicator as our country was recently certified as a malaria-free country by the WHO(AU)

Identificación molecular del sexo en 9 especies de aves del Centro de Investigación en Animales Silvestres de la hidroeléctrica de Itaipu, lado paraguayo / Sex identification by molecular methods in 9 species of birds from the wild animal research center of Itaipu dam on the paraguayan side

La importancia de determinar el sexo en especies monomórficas que viven en cautiverio conlleva a estrategias de apareamiento a fin de poder incentivar la reproducción. Existen métodos no moleculares de reconocimiento pero son factibles en edad adulta y mucho más difícil cuando son polluelos. Mediante la técnica molecular de PCR, se amplificó el gen de la Cromo Helicasa de Unión al ADN empleando los cebadores, 2550F/2718R. Por este método molecular se consiguió determinar el sexo en 19 de 23 especies de las cuales 3 son ejemplares de: Amazona aestiva, 1 de Pipile grayi, 1 de Bubo virginianus, 4 de Ara chloropterus, 6 de Crax fasciolata, 2 de Caracara plancus, 3 de Chauna torquata, 1 de Cariama cristata y 2 de Cairina moschata del Centro de Investigación de Animales Silvestres de ITAIPU binacional, del lado paraguayo. Nuestros resultados sugieren que el par de cebadores 2550F/2718R podría ser de utilidad para determinar el sexo en las especies estudiadas en el país.

In monomorphic species living in captivity, determining the sex is important because it may allow choosing mating strategies to enhance reproduction. Sex can be determined either by non-molecular recognition methods, which are only feasible in adult birds, or by molecular techniques, which may allow sexing monomorphic species at young ages. Thus, in this study, we used molecular techniques such PCR to amplifying the CHD gene by using 2550F/2718R primers. This method allowed us to determine the sex in 19 out of 23 bird specimens from the Centro de Investigación de Animales Silvestres (CIASI) of the ITAIPÚ BINACIONAL at Paraguayan side. The specimens belonged to the following species: Amazona aestiva (3), Pipile grayi (1), Bubo virginianus (1), Ara chloropterus (4), Crax fasciolata (6), Caracara plancus (2), Chauna torquata (3), Cariama cristata (1) and Cairina moschata (2). The 2550F/2718R primers were useful for determine the sex of the studied species.

21-Hydroxylase gene mutant allele CYP21A2*15 strongly linked to the resistant HLA haplotype B*14:02-DRB1*01:02 in chronic Chagas disease.

We previously reported protective haplotype HLA-B*14:02-DRB1*01:02 against chronic Chagas disease in Bolivia. The V281L mutant allele of the 21-Hydroxylase gene, CYP21A2*15, is reported to be located in the Class III region of the Human leukocyte antigen region and linked to the haplotype HLA-B*14:02-DRB1*01:02. The mutant allele might play a primary role in the pathogenesis of chronic Chagas disease in the associated HLA region. We analyzed the frequency of this allele in the same subjects for the previous one. The statistical analysis showed a significant association of the CYP21A2*15 with resistance to severe chronic Chagas disease (OR=0.207273; Pv=0.0041). However, there is no significant tendency of the mutant gene contribution to the resistance after the elimination of the HLA-B*14:02-DRB1*01:02 linked mutants (OR=0.38; Pv=0.1533). Although the frequency of the CYP21A2*15 was small, we found no primary contribution of this mutation to the protection against chronic Chagas disease.

Protective human leucocyte antigen haplotype, HLA-DRB1*01-B*14, against chronic Chagas disease in Bolivia.

BACKGROUND: Chagas disease, caused by the flagellate parasite Trypanosoma cruzi affects 8-10 million people in Latin America. The mechanisms that underlie the development of complications of chronic Chagas disease, characterized primarily by pathology of the heart and digestive system, are not currently understood. To identify possible host genetic factors that may influence the clinical course of Chagas disease, Human Leucocyte Antigen (HLA) regional gene polymorphism was analyzed in patients presenting with differing clinical symptoms. METHODOLOGY: Two hundred and twenty nine chronic Chagas disease patients in Santa Cruz, Bolivia, were examined by serological tests, electrocardiogram (ECG), and Barium enema colon X-ray. 31.4% of the examinees showed ECG alterations, 15.7% megacolon and 58.1% showed neither of them. A further 62 seropositive megacolon patients who had undergone colonectomy due to acute abdomen were recruited. We analyzed their HLA genetic polymorphisms (HLA-A, HLA-B, MICA, MICB, DRB1 and TNF-alpha promoter region) mainly through Sequence based and LABType SSO typing test using LUMINEX Technology. PRINCIPAL FINDINGS: The frequencies of HLA-DRB1*01 and HLA-B*14:02 were significantly lower in patients suffering from megacolon as well as in those with ECG alteration and/or megacolon compared with a group of patients with indeterminate symptoms. The DRB1*0102, B*1402 and MICA*011 alleles were in strong Linkage Disequilibrium (LD), and the HLA-DRB1*01-B*14-MICA*011 haplotype was associated with resistance against chronic Chagas disease. CONCLUSIONS: This is the first report of HLA haplotype association with resistance to chronic Chagas disease.

Association of MICA and MICB alleles with symptomatic dengue infection.

Dengue viruses (DV) are one of the most important arthropod-borne viral diseases in the developing world. DV can cause syndromes that are either self-limiting or severe. Allelic variants of human leukocyte antigen (HLA) genes have been demonstrated to be associated with disease susceptibility. Here we report the association of nonclassical HLA class I MICA-MICB genes with disease outcome during DV infection. A sequencing-based typing method and genotyping of MICA and MICB in a well-characterized group of Cuban individuals with dengue hemorrhagic fever (DHF), dengue fever (DF), or asymptomatic dengue infection (ADI) was performed. Statistical analysis revealed a tendency for MICA*008 and MICB*008 to associate with susceptibility to illness when symptomatic versus asymptomatic cases (odds ratio [OR] = 2.1, p(v) = 0.03, and OR = 10.4, p = 0.0096, respectively) were compared. Surprisingly, a stronger association of both allelic forms was observed for the DF patients compared with the ADI group (MICA*008, OR = 5.2, p = 0.0001; and MICB*008, OR = 13.2, p = 0.0025) rather than the severe cases. Major histocompatibility class I-related gene-related natural killer cells and/or γδ and αß T-cell activation might regulate the development of symptomatic DF and DHF.

Trypanosoma cruzi lineages detected in congenitally infected infants and Triatoma infestans from the same disease-endemic region under entomologic surveillance in Paraguay.

Trypanosoma cruzi II is associated with Chagas disease in the southern part of South America. We analyzed T. cruzi variants in field-collected triatomines and congenitally infected infants living in the same disease-endemic region in Paraguay. Results of polymerase chain reactions for T. cruzi kinetoplast DNA and satellite DNA were positive in 83 triatomine feces samples and 58 infant blood samples. However, lineages were detected in 33 and 38 samples, respectively. Trypanosoma cruzi genotypes were determined in 56 (97%) blood samples after hybridization by using specific probes. The Tc I genotype was not detected. The prevalent sublineage was Tc IId in triatomines (27 of 33) and infant blood (36 of 58) as assessed by amplification of the 24Salpha ribosomal RNA and the mini-exon region genes. The Tc IIc genotype was detected in 20 infant blood samples and in 1 triatomine. This study shows T. cruzi II is the predominant lineage circulating in triatomines and humans in endemic areas of eastern region of Paraguay.