Specimen collection is essential for modern science.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Influence of dengue virus serotypes on the abundance of Aedes aegypti insect-specific viruses (ISVs).

A comprehensive understanding of the virome in mosquito vectors is crucial for assessing the potential transmission of viral agents, designing effective vector control strategies, and advancing our knowledge of insect-specific viruses (ISVs). In this study, we utilized Oxford Nanopore Technologies metagenomics to characterize the virome of Aedes aegypti mosquitoes collected in various regions of Colombia, a country hyperendemic for dengue virus (DENV). Analyses were conducted on groups of insects with previous natural DENV infection (DENV-1 and DENV-2 serotypes), as well as mosquito samples that tested negative for virus infection (DENV-negative). Our findings indicate that the Ae. aegypti virome exhibits a similar viral composition at the ISV family and species levels in both DENV-positive and DENV-negative samples across all study sites. However, differences were observed in the relative abundance of viral families such as Phenuiviridae, Partitiviridae, Flaviviridae, Rhabdoviridae, Picornaviridae, Bromoviridae, and Virgaviridae, depending on the serotype of DENV-1 and DENV-2. In addition, ISVs are frequently found in the core virome of Ae. aegypti, such as Phasi Charoen-like phasivirus (PCLV), which was the most prevalent and showed variable abundance in relation to the presence of specific DENV serotypes. Phylogenetic analyses of the L, M, and S segments of the PCLV genome are associated with sequences from different regions of the world but show close clustering with sequences from Brazil and Guadeloupe, indicating a shared evolutionary relationship. The profiling of the Ae. aegypti virome in Colombia presented here improves our understanding of viral diversity within mosquito vectors and provides information that opens the way to possible connections between ISVs and arboviruses. Future studies aimed at deepening our understanding of the mechanisms underlying the interactions between ISVs and DENV serotypes in Ae. aegypti could provide valuable information for the design of effective vector-borne viral disease control and prevention strategies.IMPORTANCEIn this study, we employed a metagenomic approach to characterize the virome of Aedes aegypti mosquitoes, with and without natural DENV infection, in several regions of Colombia. Our findings indicate that the mosquito virome is predominantly composed of insect-specific viruses (ISVs) and that infection with different DENV serotypes (DENV-1 and DENV-2) could lead to alterations in the relative abundance of viral families and species constituting the core virome in Aedes spp. The study also sheds light on the identification of the genome and evolutionary relationships of the Phasi Charoen-like phasivirus in Ae. aegypti in Colombia, a widespread ISV in areas with high DENV incidence.

New daily persistent headache after SARS-CoV-2 infection in Latin America: a cross-sectional study.

BACKGROUND: Persistent headache is a frequent symptom after coronavirus disease 2019 (COVID-19) and there is currently limited knowledge about its clinical spectrum and predisposing factors. A subset of patients may be experiencing new daily persistent headache (NDPH) after COVID-19, which is among the most treatment-refractory primary headache syndromes. METHODS: We conducted a cross-sectional study in Latin America to characterize individuals with persistent headache after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and to identify factors associated with NDPH. Participants over 18 years old who tested positive for SARS-CoV-2 infection and reported persistent headache among their symptoms completed an online survey that included demographics, past medical history, persistent headache clinical characteristics, and COVID-19 vaccination status. Based on participants' responses, NDPH diagnostic criteria were used to group participants into NDPH and non-NDPH groups. Participant data was summarized by descriptive statistics. Student's t and Mann-Whitney U tests were used according to the distribution of quantitative variables. For categorical variables, Pearson's chi-square and Fisher's exact tests were used according to the size of expected frequencies. Binomial logistic regression using the backward stepwise selection method was performed to identify factors associated with NDPH. RESULTS: Four hundred and twenty-one participants from 11 Latin American countries met the inclusion criteria. One in four participants met the NDPH diagnostic criteria. The mean age was 40 years, with most participants being female (82%). Over 90% of the participants reported having had mild/moderate COVID-19. Most participants had a history of headache before developing COVID-19 (58%), mainly migraine type (32%). The most predominant clinical characteristics in the NDPH group were occipital location, severe/unbearable intensity, burning character, and radiating pain (p < 0.05). A higher proportion of anxiety symptoms, sleep problems, myalgia, mental fog, paresthesia, nausea, sweating of the face or forehead, and ageusia or hypogeusia as concomitant symptoms were reported in participants with NDPH (p < 0.05). Palpebral edema as a concomitant symptom during the acute phase of COVID-19, occipital location, and burning character of the headache were risk factors associated with NDPH. CONCLUSION: This is the first study in Latin America that explored the clinical spectrum of NDPH after SARS-CoV-2 infection and its associated factors. Clinical evaluation of COVID-19 patients presenting with persistent headache should take into consideration NDPH.

Description of pathogenic bacteria in patients with respiratory symptoms associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Colombia.

Viral respiratory infections may predispose to co-infections with other pathogenic microorganisms. In this study, pathogenic respiratory bacteria were detected using commercial kit Allplex™ Respiratory Panel 4 from nasopharyngeal samples from individuals suffering respiratory symptoms with and without severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Patients without respiratory symptoms were included as controls. Haemophilus influenzae and Streptococcus pneumoniae were detected from 12 patients (6%) in both, patients with respiratory symptoms (including hospitalized) (n = 6) and individual without symptoms (n = 6). Pathogenic bacteria possibly proliferate due to the limited immune response of patients with SARS-CoV-2, perhaps due to dysbiosis generated by the viral infection.

The first report of Dirofilaria repens infection in dogs from Colombia.

Dirofilariasis is a mosquito-borne disease caused by Dirofilaria parasites, affecting both wild and domestic animals, including humans considered as accidental hosts. Dirofilaria repens is the principal causative agent of dirofilariasis in the Old World, with increasing reports of the parasite in countries where it has not been previously identified, due to several factors such as the expansion of mosquito vectors' geographical distribution. By utilizing newly designed primers for molecular detection and confirming through next-generation sequencing, here, we report the first plausible cases of D. repens in dogs from Colombia. Our results support the classification of this species as an emergent pathogen in the Americas. Finally, we encourage an increase in diagnostic and surveillance efforts to prevent and control the current and future dirofilariasis cases in this region.

Impact of SARS-CoV-2 Mu variant on vaccine effectiveness: A comparative genomics study at the peak of the third wave in Bogota, Colombia.

We assessed the circulation of severe acute respiratory syndrome coronavirus-2 variants amongst vaccinated military personnel in Bogotá, Colombia to evaluate the mutations of certain variants and their potential for breakthrough infection in vaccinated subjects. We observed that in vaccinated individuals the most frequent infecting lineage was Mu (B.1.621 and B.1.621.1). The above is possibly associated with specific mutations that confer it with vaccine-induced immune escape ability. Our findings highlight the importance of how genomic tracking coupled with epidemiological surveillance can assist in the study of novel emerging variants (e.g., Omicron) and their impact on vaccination efforts worldwide.

Hotspots for SARS-CoV-2 Omicron variant spread: Lessons from New York City.

The coronavirus disease-2019 (COVID-19) pandemic is still challenging public health systems worldwide, particularly with the emergence of novel SARS-CoV-2 variants with mutations that increase their transmissibility and immune escape. This is the case of the variant of concern Omicron that rapidly spread globally. Here, using epidemiological and genomic data we compared the situations in South Africa as the epicenter of emergence, United Kingdom, and with particular interest New York City. This rapid global dispersal from the place of first report reemphasizes the high transmissibility of Omicron, which needed only two weeks to become dominant in the United Kingdom and New York City. Our analyses suggest that as SARS-CoV-2 continues to evolve, global authorities must prioritize equity in vaccine access and continued genomic surveillance. Future studies are still needed to fully unveil the biological properties of Omicron, but what is certain is that vaccination, large-scale testing, and infection prevention efforts are the greatest arsenal against the COVID-19 pandemic.

Safety and efficacy of convalescent plasma for severe COVID-19: a randomized, single blinded, parallel, controlled clinical study.

BACKGROUND: Convalescent plasma (CP) has been widely used to treat COVID-19 and is under study. However, the variability in the current clinical trials has averted its wide use in the current pandemic. We aimed to evaluate the safety and efficacy of CP in severe coronavirus disease 2019 (COVID-19) in the early stages of the disease. METHODS: A randomized controlled clinical study was conducted on 101 patients admitted to the hospital with confirmed severe COVID-19. Most participants had less than 14 days from symptoms onset and less than seven days from hospitalization. Fifty patients were assigned to receive CP plus standard therapy (ST), and 51 were assigned to receive ST alone. Participants in the CP arm received two doses of 250 mL each, transfused 24 h apart. All transfused plasma was obtained from "super donors" that fulfilled the following criteria: titers of anti-SARS-CoV-2 S1 IgG ≥ 1:3200 and IgA ≥ 1:800 antibodies. The effect of transfused anti-IFN antibodies and the SARS-CoV-2 variants at the entry of the study on the overall CP efficacy was evaluated. The primary outcomes were the reduction in viral load and the increase in IgG and IgA antibodies at 28 days of follow-up. The per-protocol analysis included 91 patients. RESULTS: An early but transient increase in IgG anti-S1-SARS-CoV-2 antibody levels at day 4 post-transfusion was observed (Estimated difference [ED], - 1.36; 95% CI, - 2.33 to - 0.39; P = 0.04). However, CP was not associated with viral load reduction in any of the points evaluated. Analysis of secondary outcomes revealed that those patients in the CP arm disclosed a shorter time to discharge (ED adjusted for mortality, 3.1 days; 95% CI, 0.20 to 5.94; P = 0.0361) or a reduction of 2 points on the WHO scale when compared with the ST group (HR adjusted for mortality, 1.6; 95% CI, 1.03 to 2.5; P = 0.0376). There were no benefits from CP on the rates of intensive care unit admission (HR, 0.82; 95% CI, 0.35 to 1.9; P = 0.6399), mechanical ventilation (HR, 0.66; 95% CI, 0.25 to 1.7; P = 0.4039), or mortality (HR, 3.2; 95% CI, 0.64 to 16; P = 0.1584). Anti-IFN antibodies and SARS-CoV-2 variants did not influence these results. CONCLUSION: CP was not associated with viral load reduction, despite the early increase in IgG anti-SARS-CoV-2 antibodies. However, CP is safe and could be a therapeutic option to reduce the hospital length of stay. Trial registration NCT04332835.

First report and genome sequencing of SARS-CoV-2 in a cat (Felis catus) in Colombia.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus of zoonotic origin that can bind to ACE2 receptors on the cells of many wild and domestic mammals. Studies have shown that the virus can circulate among animals mutate, lead to animal-to-human zoonotic jump, and further onward spread between humans. Infection in pets is unusual, and there are few human-to-pet transmission reports worldwide. OBJECTIVE: To describe the SARS-CoV-2 infection in a domestic animal in Córdoba, Colombian Caribbean region. METHODS: A cross-sectional molecular surveillance study was carried out, oral and rectal swabs were taken from cats and dogs living with people diagnosed with coronavirus disease 2019 (COVID-19). RESULTS: SARS-CoV-2 was found in a cat living with a person with COVID-19. Genome sequencing showed that the B.1.111 lineage caused the infection in the cat. The owner's sample could not be sequenced. The lineage is predominant in Colombia, and this variant is characterised by the presence of the D614D and Q57H mutation. CONCLUSION: The present work is the first report of an infected cat with SARS-CoV-2 with whole-genome sequencing in Colombia. It highlights the importance of detecting SARS-CoV-2 mutations that could promote the transmissibility of this new coronavirus. There is still a significant information gap on human-to-cat-to-human infection; we encourage self-isolation measures between COVID-19 patients and companion animals. The findings of this study give a preliminary view of the current panorama of SARS-CoV-2 infection in animals in Colombia.

Evaluation of the diagnostic performance of nine commercial RT-PCR kits for the detection of SARS-CoV-2 in Colombia.

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has led to the design and development of multiple reverse-transcription polymerase chain reaction kits aimed to facilitate the rapid scale-up of molecular testing for massive screening. We evaluated the diagnostic performance of nine commercial kits, which showed optimal performance and high discriminatory power. However, we observed differences in terms of sensitivity, specificity, and E gene Ct Values and discuss these results in light of the influence of SARS-CoV-2 genetic variability and its potential impact in current molecular diagnostic assays.

RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens.

As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.

The arrival and spread of SARS-CoV-2 in Colombia.

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.

Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic.

BACKGROUND: There is limited and controverting evidence looking at possible associations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies and patient variables in large cohorts of symptomatic and asymptomatic patients. METHODS: We studied 2275 symptomatic and asymptomatic patients from Colombia with coronavirus disease 2019 (COVID-19) and analyzed the associations between RT-PCR cycle threshold (Ct) value with gender, age, comorbidities, symptomatology, and disease severity. RESULTS: 15.4 % of the samples (n = 428) reported at least one comorbidity. There were 2011 symptomatic cases (72.4 %), being the most common reported symptom cough (57.2 %, n = 1586). Respiratory distress was present in 21.4 % of patients (n = 595), and 435 patients (15.6 %) required hospital admission. We observed that patients with no prior medical history harbored higher RNA copies than patients with comorbidities (p = 0.02). No significant differences in RNA copies were observed between symptomatic and asymptomatic patients (p = 0.82). Strong correlations were detected between Ct values and the presence of odynophagia (p = 0.03), diarrhea (p = 0.04), and headache (p = 0.0008). An inverse association was found between RNA copy number and markers of disease severity, namely, respiratory distress (P < 0.0001) and hospitalization requirement (P < 0.0001). CONCLUSIONS: SARS-CoV-2 RT-PCR cycle thresholds reveal strong associations with a prior medical history, specific symptomatology, and disease severity markers. Further research controlling potential confounding variables needs to be conducted to evaluate the nature and usefulness of these associations in managing COVID-19 patients.

Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate.

Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.

In vitro culture of spermatogonial stem cells isolated from adult alpaca (Vicugna pacos) testes analysed with Dolichos biflorus by flow cytometry.

Spermatogonial stem cell (SSC) is known for its self-renewal capacity. We have studied the in vitro proliferation of isolated SSC from adult alpaca (Vicugna pacos) testes. A total of 107 samples were evaluated of which 31 were evaluated at baseline, 36 were cultivated in DMEM and 40 in STEMPRO media. Half of the cultivated samples was analysed after 14 days, and the rest after 21 days. Round cell subpopulations were identified with FITC-DBA by flow cytometry: strongly positive DBA (sDBA+) as SSC, weakly positive DBA (wDBA+) as in early differentiation and negative DBA as differentiated. At the beginning, 4.16% of the cells were SSC, 37.61% wDBA+ while 54.12% were DBA-. After 14 days, 42.28% of SSC, 44.68% wDBA+ and 11.07% DBA- were found in DMEM while 47.09% of SSC, 32.57% wDBA+ and 18.48% DBA- in STEMPRO. After 21 days 38.66% were SSC, 52.78% wDBA and 7.65% DBA- in DMEM and on STEMPRO media 47.92% SSC, 44.20% wDBA+, 4.93% DBA-. There is a significant difference between the number of initial and SSC cultivated, as well as between DBA- (p < 0.05), while there is no significant difference between the wDBA+ (p > 0.05). Our results suggest that both culture media are appropriate for the in vitro proliferation of alpacas SSC.

Assessment of Trace Metals in Soil, Vegetation and Rodents in Relation to Metal Mining Activities in an Arid Environment.

Areas where abandoned metal-extraction mines are located contain large quantities of mineral wastes derived from environmentally unsafe mining practices. These wastes contain many pollutants, such as heavy metals, which could be released to the environment through weathering and leaching, hence becoming an important source of environmental metal pollution. This study evaluates differences in the levels of lead, iron, nickel, manganese, copper and cadmium in rodents sharing the same type of diet under different microhabitat use in arid areas with past mining activities. Samples of soil, roots, branches and seeds of Palo Adán (Fouquieria diguetii) and specimens of two rodent species (Chaetodipus arenarius and C. spinatus) were collected in areas with impact from past metal mining activities as well as from areas with no mining impact. Both rodent species mirrored nickel and iron levels in soil and seeds, as well as lead levels in soil; however, C. arenarius accumulated higher levels of manganese, copper and cadmium.

Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle.

Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.

Molecular detection of intestinal parasites in a rural community of Colombia: A one health approach to explore potential environmental-zoonotic transmission.

AIMS: Protozoan and helminth parasitic infections pose significant public health challenges, especially in developing countries with rural populations marked by suboptimal hygiene practices and socio-economic constraints. The parasites are the etiological agents of these infections and have a notably elevated global prevalence. Therefore, this study focuses on estimating the frequency and transmission dynamics of several parasitic species, including Blastocystis, Giardia, Cryptosporidium spp., Entamoeba histolytica, Ascaris lumbricoides, Trichuris trichiura, Taenia spp. and hookworms, within a rural community in southwest Colombia with a particular emphasis on the One Health framework, considering environmental and zoonotic transmission potentials. METHODS AND RESULTS: This study involved the analysis of 125 samples, encompassing human participants (n = 99), their domestic pets (dogs) (n = 24) and water sources (n = 2). Parasite detection was carried out utilizing a combination of microscopy and molecular techniques. Furthermore, the characterization of Blastocystis subtypes (STs) was achieved through Oxford Nanopore sequencing of the rRNA-18S gene. The investigation also entailed the examination of potential associations between intestinal parasitism and various sociodemographic factors. Results revealed a high frequency of parasitic infections when employing molecular methods, with Blastocystis (n = 109/87%), Giardia (n = 20/16%), Ancylostoma duodenale (n = 28/22%), Ancylostoma ceylanicum (n = 7/5.6%), E. histolytica (n = 6/4.8%), Cryptosporidium spp. (n = 12/9.6%) and even Taenia (n = 1/0.8%) detected. Cryptosporidium spp. was also identified in water samples. Coinfections were prevalent, with 57% (n = 70) of samples exhibiting single-parasite infections and 43% (n = 53) showing various degrees of polyparasitism, emphasizing the complexity of transmission dynamics. Blastocystis subtyping, conducted via Oxford Nanopore sequencing, revealed a diversity of subtypes and coexistence patterns, with ST2 being the most prevalent. CONCLUSIONS: This research underscores the importance of using molecular techniques for frequency estimation, particularly emphasizing the relevance of zoonotic transmission in parasitic infections. It highlights the significance of the One Health approach in comprehending the circulation of parasites among animals, humans and environmental sources, thereby directly impacting public health and epidemiological surveillance.