Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant-calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller and use of replicate sequencing have the most significant impact on single-nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false-negative rates. When replicates are not available, using a combination of multiple callers with more stringent cutoffs is recommended. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intra-host viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intra-host variation, viral diversity, and viral evolution. IMPORTANCE When viruses replicate inside a host cell, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus nor strongly beneficial can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in the inclusion of false-positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant-calling tools. We used simulated and synthetic data to test their performance against a true set of variants and then used these studies to inform variant identification in data from SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.

Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care

OBJECTIVE

The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis.

METHODS

We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded.

RESULTS

We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers.

CONCLUSION

In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.

Genetic characterization of Dibothriocephalus latus and Dibothriocephalus dendriticus (Cestoda: Diphyllobothriidae) from Chile based on haplotype analysis using mitochondrial DNA markers

Dibothriocephalus latus and Dibothriocephalus dendriticus are found throughout the temperate and sub-arctic zones of the northern hemisphere, but they are also found in the southern core countries of South America, Chile and Argentina. Genetic characteristics of D. latus and D. dendriticus from South America have yet to be fully defined. The present study aimed to understand the genetic characteristics of D. latus and D. dendriticus from Chile by haplotype network analysis of mitochondrial cytochrome c oxidase subunit I gene (cox1) and cytochrome b gene (cob), as well as their origins. Dibothriocephalus latus and D. dendriticus plerocercoid larvae were obtained from feral and/or wild salmonids captured in Lake Llanquihue in Región de Los Lagos, and Lake Panguipulli in Región de Los Ríos, located south of central Chile. Haplotype analysis of D. latus revealed that H1 in cox1 and H2 in cob are the key haplotypes common to D. latus across the world, including Chile, and both genes exhibited limited genetic diversity in D. latus. It was assumed that D. latus was brought into South America by European and Russian immigrants in the 19th century as previously reported. In contrast, both the cox1 and cob of D. dendriticus display considerable genetic diversity, with no common haplotypes between D. dendriticus populations from Chile and the northern hemisphere. More intriguingly, two cob haplotypes (H24, H25) detected in Chilean D. dendriticus were closely linked to haplotypes (H30,H31) detected in North American D. dendriticus, strongly implying that D. dendriticus in Chile was brought by piscivorous migrating birds from North America. It has also been estimated that the D. dendriticus from Chile genetically diverged from the D. dendriticus from the northern hemisphere approximately 1.11 million years ago, long before humans migrated to the southern parts of South America.

Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry

BACKGROUND

Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months.

METHODS

We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed.

RESULTS

We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05).

CONCLUSION

While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data

High error rates of viral RNA-dependent RNA polymerases lead to diverse intra-host viral populations during infection. Errors made during replication that are not strongly deleterious to the virus can lead to the generation of minority variants. However, accurate detection of minority variants in viral sequence data is complicated by errors introduced during sample preparation and data analysis. We used synthetic RNA controls and simulated data to test seven variant calling tools across a range of allele frequencies and simulated coverages. We show that choice of variant caller, and use of replicate sequencing have the most significant impact on single nucleotide variant (SNV) discovery and demonstrate how both allele frequency and coverage thresholds impact both false discovery and false negative rates. We use these parameters to find minority variants in sequencing data from SARS-CoV-2 clinical specimens and provide guidance for studies of intrahost viral diversity using either single replicate data or data from technical replicates. Our study provides a framework for rigorous assessment of technical factors that impact SNV identification in viral samples and establishes heuristics that will inform and improve future studies of intrahost variation, viral diversity, and viral evolution.

IMPORTANCE

When viruses replicate inside a host, the virus replication machinery makes mistakes. Over time, these mistakes create mutations that result in a diverse population of viruses inside the host. Mutations that are neither lethal to the virus, nor strongly beneficial, can lead to minority variants that are minor members of the virus population. However, preparing samples for sequencing can also introduce errors that resemble minority variants, resulting in inclusion of false positive data if not filtered correctly. In this study, we aimed to determine the best methods for identification and quantification of these minority variants by testing the performance of seven commonly used variant calling tools. We used simulated and synthetic data to test their performance against a true set of variants, and then used these studies to inform variant identification in data from clinical SARS-CoV-2 clinical specimens. Together, analyses of our data provide extensive guidance for future studies of viral diversity and evolution.

Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis

BACKGROUND

Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry.

METHODS

In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months.

RESULTS

One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability.

CONCLUSION

High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.

Morphological observation and molecular phylogeny of Spirometra decipiens complex 1 (Cestoda: Diphyllobothriidae) found in cat from Chile

The systematics of tapeworms in the genus Spirometra has been progressing with the accumulation of molecular genetics data, but the taxonomic status of many nominal species remains under debate. We report morphological and molecular-phylogenetic data for a Spirometra species collected from a domestic cat (Felis silvestris catus) in Chiloé Island, Chile. The Spirometra species was shown to be genetically conspecific with Spirometra decipiens complex 1 found in a Pampas fox (Lycalopex gymnocercus) from Argentina, and was closely related to a Hoary fox (Lycalopex vetulus) and rattlesnake (Crotalus durissus) from Brazil. Therefore, the presence of S. decipiens complex 1 was molecularly confirmed for the first time in Chile. The findings of the present study add useful information for the systematics of poorly known Spirometra species in South America.

Determination of subtypes of Blastocystis sp. in Chilean patients with and without inflammatory bowel syndrome, A preliminary report

Background & methods

Blastocystis sp. is one of the most prevalent unicellular eukaryote of the human large intestine in Chile and worldwide. It is classified in subtypes (STs), where using the polymorphic sequences of its 18S rRNA genes currently recognizes 22. STs 1–9 and ST12 have been reported in humans. It has been hypothesized that different STs of Blastocystis sp. differentially affect the clinical severity of the digestive disease in Irritable Bowel Syndrome (IBS) patients, but more studies ar4e needed to establish this statement. To contribute in the elucidation of the potential relationship between Blastocystis sp. subtypes and IBS severity, 37 IBS patient fecal samples were collected at hospitals in Santiago (Chile) and were screened for the presence of vacuolated forms of Blastocystis sp. by using conventional microscopy. Positive samples were submitted to PCR and sequencing for determining STs. The same procedure was performed in fecal samples from five non-IBS Blastocystis sp. carriers for preliminary comparative purpose.

Results and discussion

Four out of the 37 samples from the IBS patients were found positive for Blastocystis sp. (10.81%) by using microscopy. The presence of this microorganism in these four samples were confirmed by PCR and sequencing. Subtypes and their respective closest match alleles were searched and the ST1, ST2 and ST4 subtypes were found in these patients. ST4 subtype is scarcely detected in South America countries, being reported previously only in Colombia and Brazil. In this ST4 subtype we determined the allele 42 which is the most frequent allele observed in human Blastocystis isolates. In the non-IBS individuals' carriers, three subtypes were found: ST1, ST2 and ST3, even belonging to the same family group. Closest match alleles: 2, 12 and 34 here detected were also commonly reported globally. Instead of the small number of IBS patients studied here, the frequency of blastocystosis detected (10.81%) was lower than the prevalence of Blastocystis sp. infections described for the Chilean general population (30.4%). In Chile, clear correlation of Blastocystis sp. subtypes and IBS severity is still lacking with this study but it may lead and contribute to a better understanding of its pathogenicity and worldwide epidemiology.

Presence of anisakid larvae in commercial fishes landed in the Pacific coast of Ecuador and Colombia

Introduction: Anisakidosis is a zoonotic disease caused by the consumption of raw or undercooked fish or crustaceans parasitized by nematode larvae of the Anisakidae family. In this study, the presence of anisakid larvae was identified in fish species of consumer of the Pacific coast in Ecuador and Colombia.Methods: We obtained 438 samples grouped into twenty species of fish caught in the fishing ports of Manta, Santa Rosa, Buenaventura and Tumaco. The morphological identification of the larvae was made by taxonomy and the percentage of infection, were calculated. For the identification of species, a multiplex PCR was carried.Results: The taxonomic review identified eight species of fish as hosts of the genders Anisakis andPseudoterranova. The larvae were isolated mainly from  the intestine with a percentage of infection between 18 and 100%. The percentage of infection and identification of anisakids in these fish will aid in the prevention and control of anisakiasis as a possible emerging disease for this area of the Pacific. With the multiplex PCR, A. pegreffii, A. physeteris, and P. decipiens were identified.Conclusion: The identification of these species is reported for the first time in this geographical area, providing the basis for future research into the Anisakidae family.

First reporting of Anisakis sp. in the Armed Snook fish (Centropomus armatus) caught and commercialized in Buenaventura, Colombia

Objective: Nematodes of the Anisakidae family are parasites found in aquatic organisms. The lack of studies on anisakidosis and Anisakis in Colombia has meant this type of parasitosis is not widely known by health personnel and underreporting of the disease is highly likely. The objective of this study was to identify anisakid nematodes in the armed snook fish (Centropomus armatus) obtained by artisanal fishing and sold commercially in the coastal port city of Buenaventura.Material and methods: Morphological identification of these worms was performed using taxonomic keys and supplemented with microscopic study using the histochemical Hematoxylin-Eosin technique.Results: Nematodes of the genus Anisakis were found in 42% and the mean abundance was 2.8 in the C. armatus.Conclusions: The findings confirm the presence of Anisakis sp. in fish for human consumption in Buenaventura, the main fishing port in the Colombian Pacific region. This finding in itself warrants further investigation into the possibility of an emerging disease in Colombia.

[Morphological and molecular identification of canine filariae in a semi-rural district of the Metropolitan Region in Chile]

INTRODUCTION

To date, there has been no definitive confirmation of the presence of zoonotic dirofilariasis in dogs in Chile.

OBJECTIVES

To study the presence of dirofilarias in blood samples from dogs collected in a semi-rural district near Santiago and to compare their frequency in dogs with and without dermatological manifestations.

METHODS

We examined 100 blood samples for dog filariae infections using microscopic methods (modified Knott technique). 50 dogs presented dermatological symptoms or signs compatible with filarial infections and 50 were asymptomatic. ITS-2 and 12s rDNA gene amplification by PCR and sequencing were performed in samples microscopically positive for microfilariae. Results. We observed microfilariae in 22 dogs (22%). Of these, 16/50 (32%) were symptomatic and 6/50 (12%) were asymptomatic (p = 0.02). Morphologically, the majority of micro-filariae were similar to Dirofilaria repens, although many had a bigger size than previously described. Nucleotide sequencing of the amplified genes showed no more than 95% homology with the D. repens sequences available for comparison. D. reconditum and D. dracunculoides infections were also identified.

CONCLUSIONS

These features might indicate the presence of new species of Dirofilaria or a D. repens close related variant in Chile.

Cryptosporidium parvum in diarrheic calves detected by microscopy and identified by immunochromatographic and molecular methods

Cryptosporidium is an important protozoan parasite that causes diarrhea in neonates and young bovines. The objective of the present study was to determine the frequency of Cryptosporidium infection in animals of dairy farms of the Metropolitan Region (Santiago), Chile. Fecal samples of 205 newborn calves with diarrhea were studied and used for comparing the efficiency of two microscopic staining methods for diagnosis of the parasite, the auramine (AU) and a modified Ziehl-Neelsen (ZN) procedure. Out of the 205 fecal samples, we detected oocysts in 115 (56.1%) with AU and 102 (49.8%) with ZN. Comparison of results obtained with the two microscopic techniques showed significant difference (p<0.05), AU being more sensitive. On the other hand, concordance between the two methods was almost perfect (kappa value of 0.83). The results with these two operator dependent methods were confirmed using an operator independent immunochromatographic (IC) method. The IC method also enabled us to determine the identity of the parasite species as that of Cryptosporidium parvum. Identification of the parasite species was further corroborated by performing a Cryptosporidium species-specific polymerase chain reaction (PCR) test on few samples taken at random. Overall, the results showed a high number of infected animals suggesting the parasite C. parvum as a major parasitic disease agent of neonatal calves with diarrhea in dairy farms of the Metropolitan Region (Santiago) of Chile.

Ectopic pregnancy early diagnosis markers

Ectopic pregnancy (EP) is a high-risk medical condition with an incidence of 1.9% in reported pregnancies, and has proven to be the most common cause of pregnancy-related deaths in the first trimester. The clinical symptoms can mimic non-EP conditions, thus creating a challenge for developing diagnostic criteria and new diagnostic tools. Early diagnosis of ectopic pregnancy is essential in order to minimize the morbidity and to assess the need for urgent surgical intervention. Currently, ultrasound and serum biomarkers are used by clinicians for early detection and diagnosis. This review summarizes and comments on the available literature on the various markers including their utility and their statistical parameters.

Comparison of bronchoscopic bronchoalveolar lavage vs blind lavage with a modified nasogastric tube in the etiologic diagnosis of ventilator-associated pneumonia

OBJECTIVE

Our objective was to compare the results of a blind lavage vs a bronchoscopic-guided bronchoalveolar lavage for the etiologic diagnosis of ventilator-associated pneumonia (VAP).

DESIGN

Prospective study in consecutive patients with high probability of VAP. Every patient underwent both procedures, in a formally randomized fashion. The interpretation of quantitative cultures was done in a blind fashion.

SETTING

Single center study, with a 20 bed medical and surgical Intensive Care Unit of the University Hospital in Monterrey, Mexico.

PATIENTS

Twenty-five patients with high probability of VAP.

INTERVENTIONS

Every patient underwent blind bronchoalveolar lavage with a modified nasogastric tube, and a bronchoscopic-guided bronchoalveolar lavage.

RESULTS

Twenty-one patients underwent both procedures. Four patients were excluded due to contamination of the cultures. The quantitative cultures were compared in a paired fashion. Only two patients had discordant cultures. The correlation coefficient between the number of colonies was very high, r=0.90 (95% confidence interval [CI], 0.77-0.96; p=0.0001).

CONCLUSIONS

The blind bronchoalveolar lavage with a modified nasogastric tube is a valuable tool for the identification of etiologic agent in VAP, particularly when trained bronchoscopists or the necessary resources for bronchoscopic-guided bronchoalveolar lavage are not readily available.

[Parasitological and epidemiological aspects of Trypanosoma cruzi seropositive blood donors]

BACKGROUND

After the interruption of the transmission of Chagas disease via vector insects in Chile, there is little available epidemiological information about this parasitosis in blood banks.

AIM

To update the rates of T cruzi positive blood donors. To measure parasitological and epidemiological parameters in blood donors with anti T cruzi antibodies.

MATERIAL AND METHODS

An ELISA-T cruzi test was carried out in 30,309 blood donors between 2000 and 2004. In 75 blood donors with an ELISA-T cruzi positive test and 79 donors with negative ELISA (controls), a survey about personal or parental history of biting by a kissing bug (Triatomine), was performed. A blood sample was also obtained to perform Polymerase Chain Reaction (PCR) for T cruzi and a xenodiagnostic test.

RESULTS

Annual frequency of positive ELISA for T cruzi serum antibodies in blood donors varied from 0.31% to 0.45%. Twenty eight percent of subjects with positive and 6% of subjects with negative specific antibodies answered the survey about biting. PCR and xenodiagnostic test were positive in 52 (69%) and 16 (21%) of positive ELISA-T cruzi test blood donors, respectively. Xenodiagnostic was also positive in 5 individuals who had a negative PCR.

CONCLUSIONS

Seroprevalence of T cruzi antibodies decreased from 3% in 1968 to 0.3% in 2004.

Cryptosporidium hominis infection of the human respiratory tract

Cryptosporidium oocysts, observed in a natural sputum sample of a patient with HIV, were further studied by using DNA markers to determine the species of the parasite. C. hominis was identified as the species infecting the patient’s respiratory tract, a finding that strengthens evidence regarding this pathogen’s role in human disease.

Seroepidemiological aspects of human Strongyloides stercoralis infections in Chile

To determine the frequency of Strongyloides stercoralis antibodies by means of the enzyme linked immunosorbent assay (ELISA) in Chile, in 2001-2003, 675 blood samples of patients of two psychiatric hospitals and 172 of healthy individuals (doctors, nurses and paramedicals) of these institutions, and 1,200 serum samples of blood donors of Northern region (Arica and Antofagasta), Central region (Valparaiso and Santiago) and Southern region (La Union) were collected. ELISA showed positivity of 12.1% in psychiatric hospitalized patients, none (0%) in the health personnel and 0.25% in blood donors (p < 0.05). Only in blood donors of Arica (1%) and La Union (0.5%) the ELISA test was positive suggesting that strongyloidiasis is focalized in determinate zones of the country. In Chile, human infections by S. stercoralis are endemic with very low frequency in apparently healthy individuals and high prevalence in risk groups such as the mentally ill hospitalized patients.

Microsurgical considerations of the anterior spinal and the anterior-ventral spinal arteries

BACKGROUND

There are few data describing the microanatomy of the anterior-ventral spinal (AVSA) and anterior spinal arteries (ASA) and discussing their clinical and surgical implications. We describe the anatomical features of this arterial complex, and highlight their use when planning and performing surgical approaches to lesions involving the ventral aspect of the medulla and the foramen magnum.

METHOD

The microsurgical anatomy and branching pattern of the AVSA and the ASA from fifty human cadaver brain stems is described using a surgical microscope.

RESULTS

We found one anterior-ventral spinal artery at each side in 30 of the brain stems (60%). The ASA was a direct branch emerging from the left vertebral artery (VA) in 15 (30%), from the right VA in 4 (8%), and from the basilar artery (BA) in one brain stem (2%). The previously described as "typical pattern" of the junction of the AVS arteries from both sides, was observed only in 9 brain stems (18%). The anterior communicating spinal artery (ACoSA) was observed in 15 brain stems (30%). Also multiple ACoS arteries were described in one brain stem. Both, the AVSA and the ASA were observed to send long circumferential branches that supplied irrigation to the olive in 42 (84%) brain stems.

CONCLUSIONS

This anatomical study gives important information for a better understanding of the clinical picture of ischemic lesions of the brain stem, such as the medial medullary syndrome, and highlights the remarkable role of the AVSA and ASA as anatomical landmarks during the surgical approaches to lesions involving the ventral aspect of the medulla and the foramen magnum.

First record of human trichinosis in Chile associated with consumption of wild boar (Sus scrofa)

The first South American case of human trichinosis, resulting from the consumption of roast wild boar (Sus scrofa) is reported in Chile. The patient presented fever, diarrhea, myalgias, facial edema, sub-conjunctival reddening, photophobia, eosinophilia, and elevated glutamic oxalacetic transaminase. The diagnosis was confirmed by two immunoenzymatic tests (ELISA) using somatic and excretion-secretion antigens.

Exposure to larva migrans syndromes in squares and public parks of cities in Chile

Between November 2001 and December 2002, 600 dog fecal samples were collected in main squares and public parks of 13 cities in Chile, from the extreme north to the extreme south of the country. The samples were processed in the laboratory by centrifugal sedimentation and the Harada-Mori methods. T. canis eggs were found in 12 cities. Detection rates ranged from 1.9 to 12.5% with an average of 5.2%. Seven percent of the samples had eggs and 9.5% had rhabditoid and/or filariform larvae of Ancylostomatidae. Strongyloides stercoralis were not found. Squares and public parks in Chile pose a potential risk of exposure to visceral, ocular, and/or cutaneous larva migrans syndromes.

Vascular anatomy of the foramen of Vicq d'Azyr: a microsurgical perspective

INTRODUCTION

The foramen of Vicq d'Azyr, is a triangular-shaped area located rostral to the ventral median fissure of the medulla oblongata. Its importance relies on the fact that it is penetrated by small vessels from the vertebrobasilar axis that nourish vital pontine nuclei and tracts. We described the microvascular anatomy of the perforating vessels of the foramen of Vicq d'Azyr (FVA).

MATERIALS AND METHODS

The vertebrobasilar junction arteries and the perforating arteries of the foramen of Vicq d'Azyr were examined using a surgical microscope in 21 formalin-fixed brain stems.

RESULTS

The total number of perforating branches found was 286 in the 21 brains, an average of 13.6 perforators per brain, range 7 to 22. They arose as distal branches of 73 main trunks, average of 3.5 per brain, range 2 to 5, originating mainly from the basilar artery in 41 (56.1 %); the left ventral spinal artery in 12 (16.4 %), and the left vertebral artery in 8 (11 %). The average outer diameters of the left and right vertebral arteries were 3.2 mm and 2.9 mm, 4.1 mm for the basilar artery, and 0.6 mm for the right and left ventral spinal arteries. The branching pattern and interesting anatomic variations of the main vessels of the vertebro-basilar junction are also described.

DISCUSSION

The vascular anatomy of the infratentorial compartment is highly variable. These variations should be kept in mind to avoid pitfalls during vascular or tumor surgery. In contrast, the entering locations of perforating vessels remain constant, referring to these zones as key areas when planning or doing surgical procedures in this region.

[Immunodiagnosis of Strongyloides stercoralis infections in Chile using ELISA test]

BACKGROUND

Strongyloides stercoralis is a world wide distributed small intestinal nematode parasite. In immunocompetent individuals S stercoralis can produce asymptomatic infections or a moderate clinical picture of diarrhea, some cases become chronic. In immunocompromised patients, a disseminated disease may appear, sometimes fatal. In Chile, there is little epidemiological information about S stercoralis infections and appropriate diagnostic techniques are usually not used.

AIM

To evaluate the yield of an ELISA test for the diagnosis of strongyloidiasis in Chilean patients.

MATERIAL AND METHODS

Ten serum samples from patients with S stercoralis infections confirmed by a positive stool examination, 66 samples from individuals with other infections by tissue helminthes (24 toxocariasis, 15 trichinellosis, 11 hydatidosis, 12 fascioliasis and 4 cysticercosis), 13 samples from subjects with autoimmune diseases and 49 samples from apparently healthy individuals with a normal eosinophil count, were studied. ELISA antigen was prepared using a filariform larval extract obtained from a murine species of Strongyloides, maintained in laboratory animals.

RESULTS

Using 0.33 optical density units as a cut off value, 9 of 10 sera of S stercoralis infected individuals, had a positive ELISA test. No cross reactions were observed with sera of patients with other helminthic infections, autoimmune diseases or in healthy individuals. Thus, specificity, positive and negative predictive values were 100%.

CONCLUSIONS

The results obtained are similar with those found by other investigators. ELISA test for strongyloidiasis is a useful tool for the diagnosis of clinical cases and for seroepidemiological studies of this nematode infection in Chile.

[Current epidemiological situation of trichinosis in Chile. 1991-2000]

BACKGROUND

Human and animal trichinosis has been recorded in Chile since the late XIX century and is irregularly distributed along the country. From high rates of infection in the early 1900, the frequency of this parasitosis in man has progressively decreased.

AIM

To describe and discuss the epidemiological situation of trichinosis in Chile during the decade 1991-2000.

MATERIAL AND METHODS

Human infection was assessed using annual incidence and lethality reports provided by the Ministry of Health, periodic photostrichinoscopies in corpses of non selected individuals autopsied at the Medico Legal Service and periodic national serologic surveys. The advise of one of the authors in an epidemic that occurred in 1999 in the VIII Region was also used. Animal infection was assessed using the annual prevalence of infection in pigs slaughtered in abattoirs, furnished by the Ministry of Health.

RESULTS

A total of 631 clinical cases with 4 deaths (0.6%) was recorded. A decline in the incidence, from 0.7 x 100,000 in 1991 to 0.2 x 100,000 in 2000 was recorded. The higher frequency of the parasitosis was observed in the Metropolitan, VI, VIII and X regions. Although human trichinosis has been observed in all seasons, its frequency increases in close relation with the higher pork consumption in cold seasons (45.8% in winter and 37.5% in spring). There has been a decrease of infection rates in pigs from 0.17@1000 in 1991 to 0.04@1000 in 1998-2000.

CONCLUSIONS

The incidence and prevalence of trichinosis shows a constant decline in Chile. Considering the geographical characteristics of Chile, it is possible that an undetermined number of pigs are home reared and butchered without veterinary control, constituting an important source of human trichinosis.

Human infection by Pseudoterranova decipiens (Nematoda, Anisakidae) in Chile: report of seven cases

From 1997 to 1999, we identified seven human cases of infection by fourth stage larvae of Pseudoterranova decipiens in Chile. All identified larvae were coughed up by the patients. Subjects were 10-55 years old; five were female. Some patients complained of coughing, expectoration, pharyngeal pain, nausea or anal and nasal pruritus. Larvae of three patients were coughed up from 36 h to 7 days after having eaten raw (cebiche or sushi) or lightly fried fish. P. decipiens has a marine life cycle. Infective third stage larva develop to adult stage in pinniped mammals. The nematode eggs are voided with the host faeces and develop and hatch releasing third stage larvae. Some crustaceans and fish act as hosts of third stage larvae. Man is an accidental host for third or fourth stage larvae.

Early programming of T cell populations responding to bacterial infection

The duration of infection and the quantity of Ag presented in vivo are commonly assumed to influence, if not determine, the magnitude of T cell responses. Although the cessation of in vivo T cell expansion coincides with bacterial clearance in mice infected with Listeria monocytogenes, closer analysis suggests that control of T cell expansion and contraction is more complex. In this report, we show that the magnitude and kinetics of Ag-specific T cell responses are determined during the first day of bacterial infection. Expansion of Ag-specific T lymphocyte populations and generation of T cell memory are independent of the duration and severity of in vivo bacterial infection. Our studies indicate that the Ag-specific T cell response to L. monocytogenes is programmed before the peak of the innate inflammatory response and in vivo bacterial replication.

[Environmental contamination with Toxocara sp. eggs in public squares and parks from Santiago, Chile, 1999]

Most of cases of visceral larva migrans syndrome are caused by Toxocara canis larvae. Man acquires the infection by accidental ingestion of ripe eggs of the helminth. In order to find out the frequency of the presence of Toxocara sp. eggs in dog fecal specimens from public places of Santiago city in 1999 july-september a study was carried out in 84 squares and 12 parks from 32 counties. Three fecal samples were collected in each of these places, making a total of 288. Each sample was processed according to a modified Telemann method and three smears of each were microscopically examined. Toxocara sp. eggs were found in 39 (13.5%) fecal specimens. In 28/84 (33.3%) squares and in 8/12 (66.7%) parks these eggs were detected. These results make necessary the control of dogs and cats populations with the aim of reduce the presence of animals without responsible owners. It should be advisable to prevent dogs and cats defecation in public areas grounds, trying to exclude these animals from recreation areas.

MHC class I restricted T cell responses to Listeria monocytogenes, an intracellular bacterial pathogen

Studies of the murine immune response to infection with the intracellular bacterial pathogen Listeria monocytogenes have provided a wealth of information about innate and acquired immune defenses in the setting of an infectious disease. Our studies have focused on the MHC class I restricted, CD8+ T cell responses of Balb/c mice to L. monocytogenes infection. Four peptides that derive from proteins that L. monocytogenes secretes into the cytosol of infected cells are presented to cytotoxic T lymphocyte (CTL) by the H2-Kd major histocompatibility complex (MHC) class I molecule. We have found that bacterially secreted proteins are rapidly degraded in the host cell cytosol by proteasomes that utilize, at least in part, the N-end rule to determine the rate of degradation. The MHC class I antigen processing pathway is remarkably efficient at generating peptides that bind to MHC class I molecules. The magnitude of in vivo T cell responses, however, is influenced to only a small degree by the amount of antigen or the efficiency of antigen presentation. Measurements of in vivo T cell expansion following L. monocytogenes infection indicate that differences in the sizes of peptide-specific T cell responses are more likely owing to differences in the repertoire of naive T cells than to differences in peptide presentation. This notion is supported by our additional finding that dominant T cell populations express a more diverse T cell receptor (TCR) repertoire than do subdominant T cell populations.

Regulation of glial Na+/K+-ATPase by serotonin: identification of participating receptors

The purpose of the present study was the characterization of the receptors participating in the regulatory mechanism of glial Na+/K+-ATPase by serotonin (5-HT) in rat brain. The activity of the Na+ pump was measured in four brain regions after incubation with various concentrations of serotoninergic agonists or antagonists. A concentration-dependent increase in enzyme activity was observed with the 5-HT1A agonist R (+)-2-dipropylamino-8-hydroxy-1,2,3, 4-tetrahydronaphthalene hydrobromide (8-OH-DPAT) in homogenates or in glial membrane enriched fractions from cerebral cortex and in hippocampus. Spiperone, a 5-HT1A antagonist, completely inhibited the response to 8-OH-DPAT but had no effect on Na+/K+-ATPase activity in cerebellum where LSD, a 5-HT6 agonist, elicited a dose-dependent response similar to that of 5-HT. In brainstem, a lack of response to 5-HT and other agonists was confirmed. Altogether, these results show that serotonin modulates glial Na+/K+-ATPase activity in the brain, apparently not through only one type of 5-HT receptor. It seems that the receptor system involved is different according to the brain region. In cerebral cortex, the response seems to be mediated by 5-HT1A as well as in hippocampus but not in cerebellum where 5-HT6 appears as the receptor system involved.

[Seasonal variation of intestinal protozoa infections in outpatients of the north section of Santiago, Chile. 1995-1996]

Formalin preserved fecal samples from 6,058 and 5,863 outpatients were examined for intestinal parasites during 1995 and 1996 respectively. Prevalence rates of infections by intestinal protozoa in both years were similar. By age group (0-9, 10-19 and > 20 years old) Blastocystis hominis was observed in 18.6-19.3, 37.0-31.1 and 25.3-25.4% in 1995-1996 respectively. Prevalence of Giardia intestinalis infections decreased from 16.6-17.4% in the 0-9 year-old children group to 4.1-4.5% in patients over 20 years. Overall percentages of infection by Entamoeba histolytica varied between 4.2 and 10.9. Rates of infections by G. intestinalis, E. histolytica, and Entamoeba coli observed during rainy-cold months (april-september) of the year versus drywarmy period (october-march) were the same. On the contrary, more cases of B. hominis infection 25.8% versus 18.2% (this difference being statistically significant, p > 0.001) were observed during rainy-cold months of the year.

Comparison in systemic hypertension of left ventricular mass and geometry with systolic and diastolic function in patients <65 to > or = 65 years of age

Previous studies have differed on the independent effect of age and gender to left ventricular (LV) mass. Data on ventricular remodeling in hypertensive patients > or = 65 years of age is lacking. Similarly, the systolic and diastolic interaction in older hypertensives is not well defined. In a prospective study, we examined the relation of LV mass, relative wall thickness, and systolic and diastolic interaction in 508 hypertensive patients between 50 and 80 years of age who were divided according to age (<65 and > or = 65 years) and gender. LV mass, geometric classification, systolic wall stress, and Doppler filling were obtained according to standard Doppler echocardiographic criteria. In men, most measurements were similarly distributed. However, women > or = 65 years of age had smaller LV systolic dimensions, thicker ventricular septums, higher endocardial and midwall fractional shortenings, and lower end-systolic wall stress. Although LV mass was higher in men, there was no age difference within the same sex. The most common LV geometric remodeling was increased relative wall thickness in the form of concentric hypertrophy or concentric remodeled. The predominant mitral flow pattern was "impaired relaxation"; however, older patients had even shorter E waves, taller A waves, and lower E/A ratios. Thus, patients > or = 65 years of age had an even higher prevalence of this pattern (men, 89% vs 73%, p <0.001, and women, 91% vs 77%, p <0.001). Delayed LV relaxation with preservation of systolic ejection indexes is an early abnormality in essential hypertension, which lasts an undetermined time with further progression as patients aged. As a result, hypertensive patients > or = 65 years of age had the most pronounced structural and functional changes, an observation particularly noted in women. In those > or = 65 years, data from the Doppler E wave and A wave do not distinguish the physiologic process of aging from the pathologic changes of pressure overload.

Serotonin modulation of low-affinity ouabain binding in rat brain determined by quantitative autoradiography

Previous results showed that Na+/K+-ATPase may have a functional relationship with the neurotransmitter serotonin which activates the glial sodium pump in the rat brain. Both the reaction rate (V) of Na+/K+-ATPase activity and [3H]ouabain binding were significantly increased in the presence of serotonin. It is not known, however, which alpha isoform is involved in the Na+/K+-ATPase response to serotonin and its regional distribution. Quantitative autoradiography of [3H]ouabain binding to rat brain slices was employed at different [3H]ouabain concentrations in order to gain information on both the distribution and the possible isoform involved. The results showed that 1500 nM [3H]ouabain binding was sensitive to serotonin 10(-3) M and significantly increased in the following brain regions: frontal cortex, areas CA1, CA2, and CA3 of the hippocampus, presubiculum, zona incerta, caudate putamen and the amygdaloid area, confirming and extending previous results. An effect of serotonin on brain but not kidney tissue at high, 1500 nM, and the lack of effect at low, 50 nM [3H]ouabain concentrations, strongly suggests the participation of the alpha2 isoform in the response of the pump to the neurotransmitter. Glial cells showed stimulation of ouabain binding by serotonin at ouabain concentrations above 350 nM. The present results open interesting questions related to the brain regions involved and the K+ handling by the glial alpha2 isoform of the pump.

Regulated release of serotonin from axonal growth cones isolated from the fetal rat brain

In the present work we propose an hypothetical model related to a molecular recognizing system for serotonin in isolated growth cone particles. This model is supported by previous results from our laboratory plus new ones which show that growth cones release serotonin tonically and such release can be stimulated by potassium in a calcium-dependent manner. The present results, together with other author's data, suggest a physiological basis for the putative role of serotonin as a trophic factor during nervous system development.

Pattern of deletions of the dystrophin gene in Mexican Duchenne/Becker muscular dystrophy patients: the use of new designed primers for the analysis of the major deletion "hot spot" region

We have analyzed 59 unrelated Mexican Duchenne/Becker muscular dystrophy patients (DMD/BMD) using PCR analysis of the 2 prone deletion regions in the DMD gene. Thirty one (52%) of the patients had a deletion of one or several of the exons. Most of the alterations (87%) were clustered in exons 44-52, this being the highest percentage reported until now. In order to improve the molecular diagnosis in the Mexican population, we designed a new multiplex assay to PCR amplify exons 44-52. This assay allowed for the identification of a greater number of deletions in this region compared with the 9 and 5-plex assays previously described and to determine most of the deletion end boundaries. This is a reliable alternative for the initial screening of the DMD patients in the Mexican population.

Human case of gastric infection by a fourth larval stage of Pseudoterranova decipiens (Nematoda, Anisakidae)

Only three cases of human infection by anisakid nematodes have been reported in Chile since 1976. In the present case, an anisakid worm, identified as a fourth-stage Pseudoterranova decipiens larva, was removed with a gastroendoscopic biopsy clipper from the stomach of a 45 year-old man from southern Chile. The patient, who presented acute epigastric pain and a continuous sensation of having an empty stomach, reported having eaten smoked fish. The worm was fixed in 70% ethanol and cleaned in lactophenol for morphological study. The morphometric characteristics of the worm are described and drawn. Anisakid larvae in fish flesh can be killed by freezing or cooking.

[Human infection by intestinal protozoa and helminths in Calbuco County, X Region, Chile, 1997]

By the performance of parasitological examination of one fecal sample per individual, a total of 256 persons from a rural county in the X Region (41 degrees 50 minutes South lat., 73 degrees 05 minutes West long.) were studied. The general rates of infection by intestinal parasite and/or commensal protozoa and helminths found were: Giardia intestinalis 14.1%, Entamoeba histolytica 11.7%, Blastocystis hominis 36.0%, Entamoeba coli 9.8%, Endolimax nana 16.4%, Iodamoeba buetschlii 1.2%, Chilomastix mesnili 0.8%, Ascaris lumbricoides 13.7% and Trichuris trichiura 9.8%. The prevalence rates of intestinal infection led us to conclude that environmental conditions favorable for its transmission remain and show that intestinal parasitoses are still a public health problem in this region, affecting mostly children.

[Various epidemiological aspects of Enterobius vermicularis infection inpatients served at public outpatient clinics and hospitals from the northern section of Santiago, Chile, 1995]

During 1995, we examined 2,666 Graham's tests (five perianal swabs with adhesive cellulose tape) prescribed to ambulatory patients attended in 14 public outpatient clinics and four hospitals from the north section of Santiago. The infection rates found by age groups were the following: 6.1% in infants (< 2 years old), 20.9% in pre-schoolchildren (2 < 6 years old), 35.2% in elementary schoolchildren (6 < 15 years old) and 15.2% in adults (> 15 years old). Similar percentages of E. vermicularis infections were observed in females and males patients. Frequency of infection in each month of the year varied between 17.4 and 26.8%, with no seasonal variation. This study and previous surveys are stressing that E. vermicularis is the most frequent helminthic agent found in Chile, specially in elementary school children.

Radiofrequency field surveys in hospitals

The authors surveyed levels of radiofrequency (RF) fields in the frequency range 0.1-1,000 MHz in four hospitals in the Philadelphia area, to obtain background information related to the possible interference of radiofrequency fields with medical equipment. Two large center-city hospitals, a regional county hospital, and two suburban hospitals were surveyed. Measurements were made at six to 12 sites in each hospital, in each of the three frequency bands. More limited additional measurements were conducted in a fifth hospital as well. Sites were selected to include areas where strong RF signals from transmitting antennas might be expected to be present (e.g., locations close to windows in upper stories of buildings near paging antennas) as well as other representative sites in the hospital. The median RF field strengths were quite low (0.1-0.5 V/m), but at specific locations the RF signals from broadcast sources exceeded 1 V/m. Much stronger fields were recorded close to electrosurgical units and hand-held transmitters (cellular telephones and UHF transceivers).

[Taenia sp and other intestinal cestode infections in individuals from public outpatient clinics and hospitals from the northern section of Santiago, Chile (1985-1994)]

During 1985-1994 period, 70,642 parasitological stool examinations were performed. The exam was made to each patient which presenting gastrointestinal symptoms or nutritional problems, specially in children. 59,960 out of the 70,642 examinations corresponded to 1 month--15 years old children, 4,280 to 16-30 years old individuals and 6.402 to up to 30 years old adults. The infection rates (x 100,000) were: Taenia sp., 86; Hymenolepis nana, 1,165; Diphyllobotrium sp., 4 and Hymenolepis diminuta, 1. In this period, 11 cases of infection by Taenia saginata were detected, and none Taenia sodium infection. Although infections rates by intestinal cesdodes were higher in males than females, in the Taenia sp. infection the difference was not statistical significative. Médico-veterinary control of animals slaughtered in abbatoirs and the improvement of sanitary conditions in the last two decades have contributed to the control of most of human intestinal cestodiases.