Pre-1.91 Ga deformation and metamorphism in the Palaeoproterozoic Vammala Migmatite Belt, southern Finland, and implications for Svecofennian tectonics

A metamorphic event in the Vammala Migmatite Belt (VMB) at ~1.92 Ga, revealed by SHRIMP U-Pb analyses of both zircon overgrowths and monazite, is interpreted as post-depositional and is correlated with the development of the early high-grade schistosity. Neither this Early Svecofennian deformation and metamorphism, nor the associatedcomplex folding, is present in the overlying Tampere Schist Belt (TSB) sequence, consistent with the VMB being part of a pre-1.91 Ga basement complex. The ~1.92 Ga event provides a maximum deposition age for the TSB, confirming earlier age estimates. Earlier stratigraphic correlations between parts of the VMB and TSB, and associated tectonic interpretations, can no longer be sustained. The crustal thickening seen in the VMB, and previously attributed to arc accretion at ~1.89 Ga, is now attributed to accretion of a large Svionian marginal basin during the ‘Early Svecofennian’ orogenicphase at ~1.92 Ga. This is of similar age to the deformation and metamorphism associated with collision in the Lapland-Kola Orogen to the north of the Karelian Province. The well-known post-TSB orogenic phase was also identified in the VMB by a monazite age of 1881±6 Ma. A granitoid intrusion gave an emplacement age of 1888±5 Ma,comparable to the age of granitoid clasts in the upper part of the TSB succession. The detrital zircon data are interpreted to suggest that deposition of the precursor VMB sediments probably took place soon after an earlier pre-depositional metamorphism at ~1.98 Ga, which affected igneous source complexes dated at ~1.99 Ga and ~2.01 Ga. Mafic rocks in the southern part of the VMB, and probably also the Haveri basalts, represent a renewed episode of extensional magmatism, which might correlate with the 1.96–1.95 Ga Jormua and Outokumpu ophiolites. A pre-1.96 Ga older stage basin has an expression in Sweden and complexes of similar age occur in theconcealed Palaeoproterozoic basement south of the Gulf of Finland. Similar rocks, deformed and metamorphosed before ~1.96 Ga, might be present beneath the Central Finland granitoid complex and the late Svecofennian granite-migmatite zone, and were possibly more local sources for both the younger stage Svionian basin sediments andthe post-1.91 Ga Bothnian Basin sediments. The TSB and other post-accretionary volcanic sequences, and the associated plutonism,are interpreted to reflect a ~40 m.y. extensional period, inboard of the contemporaneous active margin, between orogenic phases at ~1.92 Ga and ~1.88 Ga. This interpretation provides a more satisfactory explanation of the major heat input to the crust over a very wide area than does the arc accretion hypothesis. The tectonic evolutionof the Svecofennian Province has strong similarities to that of the Palaeozoic Lachlan Fold Belt in eastern Australia

Hepatitis E virus in patients with acute hepatitis in Cape Town, South Africa, 2011

Background. Early hepatitis E virus (HEV) seroprevalence studies in South Africa (SA) showed seroprevalence rates of 2 - 10%, and suggested waterborne transmission. More recent studies in Cape Town, SA, reported HEV seroprevalence rates of 28% and 26% in outpatients without liver disease and blood donors, respectively. An association was found with eating pork or bacon/ham. Only 3 human cases of hepatitis E in SA have been reported in the literature.Objectives. To find evidence of HEV infection in hospitalised patients with acute hepatitis and no other identified cause.Methods. Leftover serum samples were retrieved for patients negative for hepatitis viruses A, B and C, where no other cause of hepatitis was identified. Samples were tested for HEV by polymerase chain reaction (PCR) and IgM and IgG enzyme-linked immunosorbent assay (ELISA).Results. Anti-HEV IgG was detected in 39/132 specimens (29.5%; 95% confidence interval (CI) 22.4 - 37.8), and anti-HEV IgM in 2/125 specimens (1.6%; 95% CI 0.4 - 5.7). No specimen tested positive by PCR.Conclusions. IgG seroprevalence found in this study was similar to that previously reported in Cape Town. IgM positivity in 2 patients was not confirmed by PCR. Locally, hepatitis E may not be a common cause of clinically apparent hepatitis that requires hospitalisation

Neutron star parameter constraints for accretion-powered millisecond pulsars from the simulated IXPE data

We have simulated the X-ray polarization data that can be obtained with the Imaging X-ray Polarimetry Explorer, when observing accretion-powered millisecond pulsars. We estimated the necessary exposure times for SAX J1808.4$-$3658 in order to obtain different accuracies in the measured time-dependent Stokes profiles integrated over all energy channels. We found that the measured relative errors depend strongly on the relative configuration of the observer and the emitting hotspot. The improvement in the minimum relative error in Stokes $Q$ and $U$ parameters as a function of observing time $t$ scales as $1/\sqrt{t}$, and spans the range from 30-90% with 200 ks exposure time to 20-60% with 500 ks exposure time (in case of data binned in 19 phase bins). The simulated data were also used to predict how accurate measurements of the geometrical parameters of the neutron star can be made when modelling only $Q$ and $U$ parameters, but not the flux. We found that the observer inclination and the hotspot co-latitude could be determined with better than 10 deg accuracy for most of the cases we considered. These measurements can be used to further constrain neutron star mass and radius when combined with modelling of the X-ray pulse profile.Comment: 12 pages, 11 figures, published in A&

Case Report:False-negative HIV-1 polymerase chain reaction in a 15-month-old boy with HIV-1 subtype C infection

Polymerase chain reaction (PCR) testing is the gold standard for determining the HIV status in children <18 months of age. However, when clinical manifestations are not consistent with laboratory results, additional investigation is required. We report a 15-month-old HIV-exposed boy referred to our hospital after he had been admitted several times for infectious diseases. A rapid antibody test on the child was positive, while routine diagnostic HIV PCRs using the Roche COBAS Ampliprep/COBAS TaqMan HIV Qual Test were negative at 6 weeks, 6 months, 7 months and 15 months. In addition, the same PCR test performed on the HIV-infected mother was also negative. Alternative PCR and viral load assays using different primer sets detected HIV RNA or proviral DNA in both child and mother. Gag sequences from the child and his mother classified both infections as HIV-1 subtype C, with very rare mutations that may have resulted in PCR assay primer/probe mismatch. Consequently, the child was commenced on antiretroviral therapy and made a remarkable recovery. These findings indicate that more reliable PCR assays capable of detecting a wide range of HIV subtypes are desirable to circumvent the clinical problems created by false-negative PCR results

Fulminant hepatitis B virus (HBV) infection in an infant following mother-to-child transmission of an e-minus HBV mutant: Time to relook at HBV prophylaxis in South African infants

The prevalence of hepatitis B virus (HBV) infection in pregnant women is high in South Africa (SA), yet prophylaxis to prevent mother-to-child transmission (MTCT) falls short of international recommendations. We describe a 10-week-old infant who developed fulminant hepatic failure following MTCT. The mother was hepatitis e-antibody positive and had a viral load of only 760 IU/mL. Genetic analysis of virus from mother and infant showed that both had the G1896A mutation in the preC/C gene, which truncates hepatitis e antigen (HBeAg) during translation, causing an HBeAg-negative phenotype. HBeAg attenuates antiviral immune responses, and its absence was probably responsible for the infant’s fulminant hepatitis, due to an uncontrolled immune attack on infected liver cells. Pregnant women are not tested for HBV infection in SA and MTCT rates are unknown. Addition of a birth dose of vaccine, HBV screening of pregnant women and antiviral prophylaxis to positive mothers should be prioritised

Hepatitis E in pig-derived food products in Cape Town, South Africa, 2014

Background. Hepatitis E virus (HEV) genotypes 3 and 4 are zoonoses, with domestic pigs being the most important reservoir. A high anti- HEV IgG seroprevalence of 26 - 28% has been found in humans in Cape Town, South Africa (SA). Studies in industrialised countries have indicated a high prevalence of HEV in pigs and their associated food products.Objectives. To determine whether HEV could be found in pig-derived food products in Cape Town.Methods. Pork-containing food products were purchased from supermarkets and butcheries around the Cape Town metropolitan area. HEV detection by polymerase chain reaction (PCR) was performed, and an amplified viral genome fragment was sequenced from positive samples. Phylogenetic analysis was done on the sequenced fragment.Results. HEV was detected by PCR in 2/144 food samples – both were liver spread samples. One genome fragment sequence was obtained, which was closely related to HEV sequences obtained from humans in Cape Town.Conclusions. HEV can be found in pork-containing meat products available for sale in Cape Town, suggesting that these products could be a potential source of HEV transmission in our geographical area. Meat of pig origin should be thoroughly cooked before being consumed

Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis

BACKGROUND: The extent to which the reduced risk of severe disease seen with SARS-CoV-2 Omicron is due to a decrease in variant virulence, or higher levels of population immunity, is currently not clear. METHODS: RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from 1 November to 14 December 2021 in the Western Cape Province, South Africa, public sector. Vaccination status and prior diagnosed infection, were adjusted for. RESULTS: 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted Hazard Ratio [aHR] of 0.56, 95%CI 0.34-0.91). Complete vaccination was protective of admission with an aHR of 0.45 (95%CI 0.26-0.77). CONCLUSION: Omicron has resulted in a lower risk of hospital admission, compared to contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence

Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study.

Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant’s disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene AllplexTM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting