Reduced neutralization against Delta, Gamma, Mu, and Omicron BA.1 variants of SARS-CoV-2 from previous non-Omicron infection.

The understanding of the host immune response to SARS-CoV-2 variants of concern is critical for improving diagnostics, therapy development, and vaccines. Here, we analyzed the level of neutralizing antibodies against SARS-CoV-2 D614G, Delta, Gamma, Mu, and Omicron variants in D614G infected healthcare workers during a follow-up up to 6 months after recovery. We followed up 76 patients: 60.5% were women and 39.5% men. The 96.1% and 3.9% were symptomatic and asymptomatic, respectively. The most frequent symptoms were headache, myalgia, and cough. The 65.8%, 65.8%, and 92.1% of the infected individuals were positive for neutralizing antibodies against D614G variant at 2, 4, and 6 months of follow-up, respectively. The 26.3%, 48.7% and 65.8% of patients neutralized Delta variant, 19.7%, 32.9% and 52.6% of patients neutralized Gamma, 7.9%, 19.7% and 44.7% of patients neutralized Mu, and 4.0%, 9.2% and 15.8% of patients neutralized Omicron. Low neutralization against Gamma and Mu variants was observed during the follow-up, and very low against the Omicron variant was detected during the same period. The median of neutralizing antibody titers against D614G and Delta variants increased significantly during the follow-up. An association was observed between the levels of neutralizing antibodies against D614G and Delta variants and the severity of the disease. Our results suggest an immune escape from neutralizing antibodies with the Omicron variant because of the many mutations localized in the S protein.

Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies.

Vaccination generates a neutralizing immune response against SARS-CoV-2. The genomic surveillance is showing the emergence of variants with mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we report the neutralization potency against alpha, gamma, and D614G SARS-CoV-2 variants in 44 individuals that received two doses of CoronaVac vaccine, an inactivated SARS-CoV-2 vaccine. Plasma samples collected at 60 days after the second dose of CoronaVac were analyzed by the reduction of cytopathic effect in Vero E6 cells with the three infectious variants of SARS-CoV-2. Plasma showed lower neutralization with alpha (geometric mean titer [GMT] = 18.5) and gamma (GMT = 10.0) variants than with D614G (GMT = 75.1) variant. Efficient neutralization against the alpha and gamma variants was not detected in 31.8% and 59.1% of plasma, respectively. These findings suggest the alpha and gamma variants could escape from neutralization by antibodies elicited by vaccination. Robust genomic and biological surveillance of viral variants could help to develop effective strategies for the control of SARS-CoV-2.

Detection and quantitation of human papillomavirus DNA in peripheral blood mononuclear cells from blood donors.

Human papillomavirus (HPV) is the etiological agent of cervical cancer. Also, HPV has been associated with anogenital cancer, oropharyngeal cancer, genital warts, and other dermatological diseases. HPV infects epithelial cells and their replication is closely linked to epithelial differentiation. The presence of HPV DNA in peripheral blood mononuclear cells (PBMC) has been reported in some patients with head and neck cancer, cervical cancer, and other genital diseases. However, the presence of HPV DNA in blood in asymptomatic subjects is still unresolved. The objective of this study was to evaluate the presence of HPV DNA in PBMC from asymptomatic blood donors. Blood samples were collected from 207 healthy Chilean blood donors. Genomic DNA was extracted from PBMC and HPV DNA detection was performed by real-time quantitative polymerase chain reaction assays with GP5+/6+ primers. HPV typing was carried out by genetic sequencing of a 140 to 150 bp fragment of the L1 gene. HPV DNA was detected in 6.8% (14/207) of blood donors. Single HPV infections were detected in seven blood donors. High-risk HPV was found in 6.3% (13/207) of cases: nine blood donors were infected with HPV-16, five with HPV-18, two with HPV-51, and one case was infected with either 32, 33, 45, 59, 66, 70, or 82. The median viral load value was 21.3 copies/mL blood or 13.4 HPV (+) cells per 10 4 PBMC. These results show that HPV DNA is present in PBMC from healthy blood donors and it suggests that blood could be a new route of HPV dissemination.

Genetic variability of human papillomavirus type 66 L1 gene among women presenting for cervical cancer screening in Chile.

The high-risk human papillomaviruses (HR-HPVs) are involved in the development of cervical cancer. Nevertheless, there are differences in the oncogenic potential among them. HPV-16 and HPV-18 are associated with approximately 70% of cancer worldwide, and both types are the most extensively studied HR-HPV. Great variations in the prevalence of HR-HPV have been described in different countries. The impact of these variations on the epidemiology of lesions and cervical cancer is currently unknown. A high prevalence of HPV-66 has been detected in Chile. Here, we have analyzed the genetic variability of the L1 gene from HPV-66-infected Chilean women. Higher order interactions between identified mutations were analyzed by co-variation and cluster analyses. Antigenic-index alterations following L1 mutations and B-cell epitopes were predicted by BcePred algorithm. HPV-66 L1 sequences clustered phylogenetically into two main clades. The genetic variability in the HPV-66 L1 gene involved thirty nucleotide changes. Four of these were for the first time identified in this study. Some of these variants are embedded in the B-cell epitope regions. Amino acid homology in the immunodominant epitopes of HPV-66 L1 protein (DE, FG and H1 loops) was 42.9-59.1% and 28.6-68.9% compared with HPV-16 and HPV-18, respectively. The results of this research suggest that the neutralizing epitopes of HPV-66 are antigenically different compared to HPV-16 and HPV-18. Our findings show the need to perform new structural and immunological studies on HPV-66 L1 protein to evaluate the cross-protection conferred by current HPV vaccines.

Detection and genotyping of HPV in urine samples from Chilean women attending primary health care centers.

Cervical cancer is the second most common malignant neoplasm in women worldwide representing approximately 10% of all types of cancers. Triage of women through cervical cytology has been an important strategy for the surveillance and control of new cases of cervical cancer. However, in many regions around the world cervical cytology has a low coverage compared to developed countries. The molecular detection of HPV is the most effective method to increase the screening sensitivity of women at risk of developing cervical cancer. There are very few studies about the efficacy of urine testing for detection of HPV in women followed up in primary health care centers. Consequently, the efficacy of using urine HPV screening in these populations has not been addressed yet. Here, we compared the detection of HPV in simultaneous urine and cervical samples of women followed up in primary health care centers. Urine and cervical samples were analyzed in 543 women attending at primary health care centers. HPV was detected by real time PCR, and HPV typing performed by PCR-RLB. A general HPV concordance of 86.2% (κ = 0.72) was determined between urine and cervical samples. The concordance for HPV-16 and 18 was almost perfect (κ = 0.82) and strong (κ = 0.77), respectively. The sensitivity and specificity for all HPV genotypes in urine using cervical samples as reference were 82.1 and 93.7%, respectively. The results showed that urine is a good alternative as clinical sample for HPV screening in women attending primary health care centers. Therefore, urine should be used as an alternative sample for increasing triage coverage either in refractory women participating in Pap surveillance programs or when cervical samples are not available.

Prevalence of Human Papillomavirus infection among Chilean women from 2012 to 2016.

Here, we evaluated the prevalence of Human Papillomavirus (HPV) in two groups of Chilean women. The first group consisted of 3235 women aged 18-64 years attended in six primary care centers of Santiago. The second group consisted of 456 women 18-85 aged who consulted the Gynaecology Department of the Reference Hospital of Santiago. Samples were collected from October 2012 to February 2016. Cervical swabs were analyzed both HPV genotyping by PCR and Reverse Line Blot, and cervical cytology by Pap testing. Results showed a prevalence of 12.0% HPV positive, 10.3% high-risk (HR) HPV types positive, 3.9% low-risk (LR) HPV types positive, and 1.0% Pap positive in group 1. The most frequent types were 16, 66, and 59, with a prevalence of 3.0%, 1.6%, and 1.5%, respectively. The prevalence were 71.9% HPV positive, 67.3% HR-HPV types positive, 13.6% LR-HPV types positive, and 62.5% Pap positive in group 2. The most frequent types were 16, 31, and 58, with prevalence of 33.6%, 10.5%, and 7.0%, respectively. Among infected women with HPV: 7.6% were infected with HPV16 or HPV18, 3.0% with HPV31, HPV33 or HPV45, and 6.7% with any other HR-HPV. These findings show great difference in HPV prevalence and types between primary care and reference center, and provide useful epidemiological information to assess the impact of HPV vaccination in the future.

Prevalence of human papillomavirus infection among women presenting for cervical cancer screening in Chile, 2014-2015.

Cervical cancer is the fourth most common malignancy in women worldwide. In Chile, cervical cancer is the second leading cause of death among women of reproductive age, causing more than 600 deaths annually. This study was carried out to determine the burden and confirm the predominant human papillomavirus (HPV) genotypes among women presenting for cervical cancer screening in public health services in Chile. Women aged 18-64 years residing in the north and central areas covered by six primary care centers of Santiago, Chile, were invited to participate from March 2014 to August 2015. Cervical swabs were examined both HPV genotyping by PCR and Reverse Line Blot, and cervical cytology by Pap testing. A total of 1738 women were included in this study: 11.1 % were HPV positive, 9.7 % were high-risk types positive, 3.2 % were low-risk types positive, 1.4 % were Pap positive and 0.9 % were positive by both tests. The four most predominant genotypes were 16, 66, 51 and 59, with prevalence of 2.8, 1.4, 1.2 and 1.2 %, respectively. Multiple HPV infections were detected among 3.8 % participants. Age-specific prevalence of HPV showed a peak in HPV infection at younger ages (≤30 years), declining to a plateau in middle age. Among women with normal cytology, the 9.4 % were HPV positive, while 58.3 % of women with abnormal cytology were HPV positive. These findings show new epidemiological data confirming HPV 16 and 66 as the most predominant genotypes in Chile. These data are important for design successful strategies for prevention of cervical cancer in Chile.

Human T-Lymphotropic Virus Type 1 and 2 Seroprevalence among first-time blood donors in Chile, 2011-2013.

Infection with human T-lymphotropic virus type 1/2 (HTLV-1/2) is a major health problem. HTLV-1/2 infection is endemic in Chile but representative donor prevalence data are lacking. Data on all blood donors in a large network of Chilean blood centers were examined during 2011-2013. Screening of HTLV-1/2 antibodies were measured by enzyme immunoassay (EIA) at all blood banks. Blood samples with anticoagulants from initially reactive blood donors were analyzed by serological confirmation tests (immunofluorescence or recombinant immunoblot) at the HTLV National Reference Laboratory of the Public Health Institute of Chile. Additionally, detection of HTLV-1 and HTLV-2 provirus in peripheral blood mononuclear cells (PBMCs) was performed in all blood donors as confirmatory test. Prevalence rates were calculated. Among 694,016 donors, 706 were seropositive for HTLV-1 (prevalence, 1.02 cases per 1,000; 95% confidence interval [CI], 0.94-1.09), and 97 were seropositive for HTLV-2 (prevalence, 0.14 cases per 1,000; 95%CI, 0.11-0.17). Prevalence of HTLV-1 differed considerably by region, from 0.51 to 1.69 per 1,000. Prevalence of HTLV-2 was similar across the country (0.12-0.16). HTLV-1 prevalence was associated with female sex, older age, and residence in the north of Chile. HTVL-2 prevalence was associated with older age. The HTLV-1 prevalence among Chilean blood donors was relatively high and could be reduced by improving donor recruitment and selection in high prevalence areas. Blood center data may contribute to surveillance for HTLV-1 and HTLV-2 infections.

[Genetic characterization of the virus causing H1N1 influenza pandemic in Chile: analysis of the first detected cases]. / Inicio del brote de Influenza A (H1N1) pandémica en Chile: caracterización genética de los primeros casos detectados.

BACKGROUND: Following the announcement of the Influenza A(H1N1) pandemic by the World Health Organization in April 2009, a surveillance program was carried out in Chile to detect the introduction of the virus in the country and to monitor its propagation and impact. AIM: To describe the onset of the outbreak and the genetic characterization of the pandemic H1N1 influenza virus in the first detected cases in Chile. MATERIAL AND METHODS: Analysis of18 clinical samples coming from suspicious patients, received in a National Reference Laboratory. RNA reverse transcription and real time influenza gene DNA amplification was carried out in a 7500 Fast and Step One Real Time PCR Systems of Applied Biosystems and MxPro-Mx3000P thermocycler from Stratagene. Super Script III Platinum One-Step Quantitative RT-PCR was used. RESULTS: The virus was first detected in three persons returning from the Dominican Republic via Panamá and a child from the east zone of Santiago. Genetic characterization of the virus showed that the child was infected by a different variant of the pandemic virus than the three persons returning from the Caribbean. CONCLUSIONS: The onset of the Influenza outbreak in Chile apparently carne from two different epidemiological groups. The spread of the virus detected in the voyagers was limited immediately However the virus of the fourth case was found in different regions of Chile.

Inicio del brote de Influenza A (H1N1) pandémica en Chile: caracterización genética de los primeros casos detectados / Genetic characterization of the virus causing H1N1 influenza pandemic in Chile: Analysis of the first detected cases

Background: Following the announcement of the Influenza A(H1N1) pandemic by the World Health Organization in April 2009, a surveillance program was carried out in Chile to detect the introduction of the virus in the country and to monitor its propagation and impact. Aim: To describe the onset of the outbreak and the genetic characterization of the pandemic H1N1 influenza virus in the first detected cases in Chile. Material and Methods: Analysis of18 clinical samples coming from suspicious patients, received in a National Reference Laboratory. RNA reverse transcription and real time influenza gene DNA amplification was carried out in a 7500 Fast and Step One Real Time PCR Systems of Applied Biosystems and MxPro-Mx3000P thermocycler from Stratagene. Super Script III Platinum One-Step Quantitative RT-PCR was used. Results: The virus was first detected in three persons returning from the Dominican Republic via Panamá and a child from the east zone of Santiago. Genetic characterization of the virus showed that the child was infected by a different variant of the pandemic virus than the three persons returning from the Caribbean. Conclusions: The onset of the Influenza outbreak in Chile apparently carne from two different epidemiological groups. The spread of the virus detected in the voyagers was limited immediately However the virus of the fourth case was found in different regions of Chile.

A pilot study on genetic variation in purine-rich elements in the nephrin gene promoter in type 2 diabetic patients.

Diabetic nephropathy (DN) is one of the major complications of type 2 diabetes and is associated with coronary disease. Nephrin, a protein mainly expressed in glomeruli, is decreased in DN and other kidney diseases. Since insulin levels are misregulated in type 2 diabetes, a possible connection between DN and its decreased nephrin expression could be the presence of regulatory elements responsive to insulin in the nephrin gene (NPHS1) promoter region. In this work, using bioinformatic tools, we identified a purine-rich GAGA element in the nephrin gene promoter and conducted a genomic study in search of the presence of polymorphisms in this element and its possible association with DN in type 2 diabetic patients. We amplified and sequenced a 514 bp promoter region of 100 individuals and found no genetic variants in the purine-rich GAGA-box of the nephrin gene promoter between groups of patients with diabetes type 2 with and without renal and coronary complications, control patients without diabetes and healthy controls.

A pilot study on genetic variation in purine-rich elements in the nephrin gene promoter in type 2 diabetic patients

Diabetic nephropathy (DN) is one of the major complications of type 2 diabetes and is associated with coronary disease. Nephrin, a protein mainly expressed in glomeruli, is decreased in DN and other kidney diseases. Since insulin levels are misregulated in type 2 diabetes, a possible connection between DN and its decreased nephrin expression could be the presence of regulatory elements responsive to insulin in the nephrin gene (NPHS1) promoter region. In this work, using bioinformatic tools, we identified a purine-rich GAGA element in the nephrin gene promoter and conducted a genomic study in search of the presence of polymorphisms in this element and its possible association with DN in type 2 diabetic patients. We amplified and sequenced a 514 bp promoter region of 100 individuals and found no genetic variants in the purine-rich GAGA-box of the nephrin gene promoter between groups of patients with diabetes type 2 with and without renal and coronary complications, control patients without diabetes and healthy controls.