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.

Objective: To determine the prevalence of genital infections (GIs), including sexual transmitted STIs: Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Trichomonas vaginalis, and opportunistic pathogens that generally do not cause STIs, non-classic STI: Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma hominis, in women with high-risk oncogenic human papillomavirus (hr-HPV) infection and their association with cervical lesions. Methods: A cross-sectional study was carried out including 231 hr-HPV positive women. Of these, 46 has histologically confirmed cervical intraepithelial neoplasia 3 (CIN3) or more (including CIN3 and cervical cancer lesions-CIN3+). GIs were detected by multiplex real time PCR. Odds ratios (OR) were estimated to explore possible associations between GIs and the presence or absence of CIN3+ lesions. Additionally, we examined associations between sociodemographic, sexual, and clinical characteristics and the presence of GIs. Results: In total, there were 174/231 cases of GIs corresponding to an overall prevalence of 75.3% (95%CI: 69.4–80.4), being non-classic STIs the most common (72.3%) compared to STIs (12.6%). The most prevalent non-classic STI and STI were U. parvum (49.8%) and C. trachomatis (7.4%), respectively. The odds of presenting GIs were 3 times higher in women under 46 years compared to older counterparts (OR: 3.32, 95%CI: 1.74–6.16), and in women with a normal Pap smear with inflammation compared to those without inflammation (OR: 3.31, 95%CI: 1.15–9.77). GIs were equally present in women with and without CIN3+ lesions. Conclusion: We observed an association of GIs with inflammation in the Pap smear, but no association with CIN3+, as some of them are very common and likely part of the normal vaginal flora, suggesting that such infections do not appear to be cofactors in cervical carcinogenesis, although larger prospective studies are needed.

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.

A descriptive, retrospective, cross-sectional study was conducted, evaluating data from newborn (NB) samples sent to the PNDN between January 2018 and December 2023. Samples taken by heel prick on Whatman 903 filter paper and analyzed by fluorometric immunoassay for the quantification of immunoreactive trypsin (IRT) were included. An IRT(+)/IRT(+) strategy was adopted, with diagnostic confirmation by sweat test. Descriptive statistics were used to analyze the incidence of CF. Variability in the incidence of CF was observed between 2018 and 2023, with a peak in 2020 (1/4,431) followed by a decrease in subsequent years. In the temporal trend analysis, it was observed that the incidence of CF does not follow a simple linear trend, indicating more complex fluctuations over time, but with an increase in the average incidence being statistically significant (p=0.0385). Management indicators showed improvements in sample processing and analysis times over the years. The distribution of confirmed CF cases by health region did not reflect statistically significant differences, with a higher concentration in the Central Department (26%). The incidence of CF in Paraguay shows a stable trend in recent years. Improvements in management indicators and regional disparities in disease incidence highlight the need for differentiated approaches to CF detection.

Human papillomavirus Type 16 (HPV16) variants are classified into four lineages (A–D) and 16 sublineages: A1–3 (European), A4 (Asian), B1–4 and C1–4 (African), and D1–4 (Asian‐American). This study investigated the genetic HPV16 variability through sequencing of the complete long control region (LCR), in 44 cervical samples from Paraguayan women, including 19 without cervical intraepithelial neoplasia grade 2 (<CIN2) and 25 with CIN2 or worse (CIN2+: 1 CIN2, 16 CIN3, and 8 invasive cancers). Sublineages A1 (81.8%), A4 (2.3%), D2 (2.3%), D3 (11.4%), and D4 (2.3%) were detected. A total of 48 point mutations were detected, of which 11 showed nominal association with CIN2+ ( p < 0.05), although none remained statistically significant after correction for multiple comparisons. Notably, most of these mutations were predominantly observed in non‐A1–A3 variants. An exploratory association was observed between non‐A1–A3 variants and the presence of CIN2+ ( p = 0.0065). Functional analysis revealed that the A4 variant, detected in a woman with cancer, exhibited the highest transcriptional activity (2.34 ± 0.78), followed by D3 (0.72 ± 0.21) and A1 (0.03 ± 0.02), corresponding to samples from women with CIN3 and without lesions, respectively. In conclusion, we report for the first time the detection of an A4 HPV16 variant in Paraguay, which exhibited the highest transcriptional activity among the variants analyzed. These findings suggest potential functional differences among HPV16 variants and are consistent with a possible relevance of non‐A1–A3 variants in cervical lesion severity. However, these results should be interpreted with caution as exploratory and hypothesis‐generating.