Viral Loads
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2021 ◽  
Anna Denzler ◽  
Max L. Jacobs ◽  
Viktoria Witte ◽  
Paul Schnitzler ◽  
Claudia M. Denkinger ◽  

Background: Currently, more than 500 different AgPOCTs for SARS-CoV-2 diagnostics are on sale, for many of which no data about sensitivity other than self-acclaimed values by the manufacturers are available. In many cases these do not reflect real-life diagnostic sensitivities. Therefore, manufacturer-independent quality checks of available AgPOCTs are needed, given the potential implications of false-negative results. Objective: The objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) in order to rapidly identify poor performing products. Methods: We present a methodology for quick assessment of the sensitivity of SARS-CoV-2 lateral flow test stripes suitable for quality evaluation of many different products. We established reference samples with high, medium and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison. Results: Among 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (~7.0*10⁸ to ~1.7*10⁵ SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (~1.4*10⁶ copies/ ml), while only five tests detected the Ct28 test sample (~1.7*10⁵ copies/ ml). In the low range of analytical sensitivity we found three saliva spit tests only delivering positive results for the Ct21 sample (~2.2*10⁷ copies/ ml). Comparison with published data support our AgPOCT ranking. Importantly, we identified an AgPOCT offered in many local drugstores and supermarkets, which did not reliably recognize the sample with highest viral load (Ct16 test sample with ~7.0*10⁸ copies/ ml) leading to serious doubts in its usefulness in SARS-CoV-2 diagnostics. Conclusion: The rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1510
Francisco R. Carvallo ◽  
Mathias Martins ◽  
Lok R. Joshi ◽  
Leonardo C. Caserta ◽  
Patrick K. Mitchell ◽  

Coronavirus disease 19 (COVID-19), has claimed millions of human lives worldwide since the emergence of the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019. Notably, most severe and fatal SARS-CoV-2 infections in humans have been associated with underlying clinical conditions, including diabetes, hypertension and heart diseases. Here, we describe a case of severe SARS-CoV-2 infection in a domestic cat (Felis catus) that presented with hypertrophic cardiomyopathy (HCM), a chronic heart condition that has been described as a comorbidity of COVID-19 in humans and that is prevalent in domestic cats. The lung and heart of the affected cat presented clear evidence of SARS-CoV-2 replication, with histological lesions similar to those observed in humans with COVID-19 with high infectious viral loads being recovered from these organs. The study highlights the potential impact of comorbidities on the outcome of SARS-CoV-2 infection in animals and provides important information that may contribute to the development of a feline model with the potential to recapitulate the clinical outcomes of severe COVID-19 in humans.

2021 ◽  
Kasen K Riemersma ◽  
Brittany E Grogan ◽  
Amanda Kita-Yarbro ◽  
Gunnar E Jeppson ◽  
David H O'Connor ◽  

SARS-CoV-2 variant B.1.617.2 (delta) is associated with higher viral loads [1] and increased transmissibility relative to other variants, as well as partial escape from polyclonal and monoclonal antibodies [2]. The emergence of the delta variant has been associated with increasing case counts and test-positivity rates, indicative of rapid community spread. Since early July 2021, SARS-CoV-2 cases in the United States have increased coincident with delta SARS-CoV-2 becoming the predominant lineage nationwide [3]. Understanding how and why the virus is spreading in settings where there is high vaccine coverage has important public health implications. It is particularly important to assess whether vaccinated individuals who become infected can transmit SARS-CoV-2 to others. In Wisconsin, a large local contract laboratory provides SARS-CoV-2 testing for multiple local health departments, providing a single standard source of data using the same assay to measure virus burdens in test-positive cases. This includes providing high-volume testing in Dane County, a county with extremely high vaccine coverage. These PCR-based tests provide semi-quantitative information about the viral load, or amount of SARS-CoV-2 RNA, in respiratory specimens. Here we use this viral load data to compare the amount of SARS-CoV-2 present in test-positive specimens from people who self-report their vaccine status and date of final immunization, during a period in which the delta variant became the predominant circulating variant in Wisconsin. We find no difference in viral loads when comparing unvaccinated individuals to those who have vaccine "breakthrough" infections. Furthermore, individuals with vaccine breakthrough infections frequently test positive with viral loads consistent with the ability to shed infectious viruses. Our results, while preliminary, suggest that if vaccinated individuals become infected with the delta variant, they may be sources of SARS-CoV-2 transmission to others.

2021 ◽  
James A Hay ◽  
Lee Kennedy-Shaffer ◽  
Michael J Mina

A plausible mechanism for the increased transmissibility of SARS-CoV-2 variants of concern (VOCs) results from VOC infections causing higher viral loads in infected hosts. However, investigating this hypothesis using routine RT-qPCR testing data is challenging because the population-distribution of viral loads changes depending on the epidemic growth rate; lower cycle threshold (Ct) values for a VOC lineage may simply reflect increasing incidence relative to preexisting lineages. To understand the extent to which viral loads observed under routine surveillance systems reflect viral kinetics or population dynamics, we used a mathematical model of competing strain dynamics and simulated Ct values for variants with different viral kinetics. We found that comparisons of Ct values obtained under random cross-sectional surveillance were highly biased unless samples were obtained at times when the variants had comparable growth rates. Conversely, comparing Ct values from symptom-based testing was largely unaffected by epidemic dynamics, and accounting for the time between symptom onset and sample collection date further reduced the risk of statistical errors. Finally, we show how a single cross-sectional sample of Ct values can be used to jointly estimate differences in viral kinetics and epidemic growth rates between variants. Epidemic dynamics should be accounted for when investigating strain-specific viral kinetics using virologic surveillance data, and findings should be corroborated with longitudinal viral kinetics studies.

2021 ◽  
Vol 21 (1) ◽  
Zhenyan Han ◽  
Yuan Zhang ◽  
Jin Zhou ◽  
Qingqing Wang ◽  
Yonghua Huang ◽  

Abstract Background Hepatitis B virus (HBV) remains a major global public health problem worldwide; in endemic areas, mother-to-child transmission (MTCT) of HBV is the most common transmission route. Previous studies have shown that amniocentesis for prenatal diagnosis increases the risk of MTCT of HBV among highly viraemic mothers. However, no data is available on MTCT related fetal blood sampling (FBS) because of the paucity of cases or lack of attention. We present a case series of HBV-infected women who underwent FBS with or without antiviral therapy during pregnancy and discuss the risk of MTCT after FBS. Case presentation Six hepatitis B surface antigen (HBsAg)-positive pregnant women who underwent FBS for prenatal diagnosis were retrospectively reviewed. Their infants were followed up with HBV serology parameters until at least 12 months of age. Among 6 cases, two hepatitis B e-antigen (HBeAg)-positive mothers had high viral loads > 7.0 log10 IU/mL, and one of them received antiviral therapy at 26+ 3 gestational weeks and achieved an anticipated level of 4.52 log10 IU/mL before FBS, while the other one did not receive any antiviral treatment. The other 4 cases were HBeAg-negative with low viral loads. Only a child born to the HBeAg-positive mother, who had no antiviral therapy with a viral load of 7.48 log10 IU/mL before FBS, was found to have MTCT with HBsAg persistently positive from birth to 12 months of age. The other 5 children were both HBsAg-negative and HBsAb-positive at the end of follow-up. Conclusions FBS may increase the risk of MTCT of HBV in women with HBeAg-positive and high viral loads; therefore, FBS should be avoided in this high-risk population. Maternal HBV serologic testing and awareness of the potential risk of MTCT should be recommended before FBS. Antiviral therapy may be effective to decrease the risk of MTCT after FBS in highly viraemic women.

2021 ◽  
Vol 21 (1) ◽  
Danxiao Wu ◽  
Xiaojuan Wang ◽  
Fangjun Feng ◽  
Dairong Wang ◽  
Yiqin Hu ◽  

Abstract Background Nucleic acid amplification testing (NAT) for blood screening has been previously performed in some countries to determine NAT yields. The current study sought to explore the non-discriminating reactive NAT yields using individual-NAT (ID-NAT) and characteristics of HBV NAT yields through a 10-year retrospective analysis in Zhejiang, China. Methods Blood donations were analyzed using individual-NAT mode by the transcription-mediated amplification (TMA) method. Supplementary HBV serological tests were performed using chemiluminescent immunoassay, and HBV viral load assay was performed by real-time polymerase chain reaction. Follow-up studies were performed in partial donors with low HBV viral loads. Results Non-discriminating reactive NAT yields and HBV NAT yields varied in different years. The yields ranged from 853.73 per million to 2018.68 per million and 624.60 per million to 1669.50 per million, respectively. In the 476 NAT yields, 19 were probable window periods (WP), 33 probable occult hepatitis B virus infections (OBIs), 409 were confirmed OBIs and 15 were chronic HBV infections. ID-NAT results were categorized in four groups, and the findings showed that the levels of HBV DNA viral loads were different in the four different groups (χ2 = 275.02, p < 0.01). HBV viral load distribution was significantly different between anti-HBs positive and anti-HBc positive samples (χ2 = 49.429, p < 0.01). Notably, only 42.03% donors were NAT repeated positive in the 138 repeat donors’ follow up tests. Conclusion NAT screening of blood donations can reduce the risk of transfusion-transmitted HBV infections. Positive proportions of anti-HBs and anti-HBc are correlated with the HBV viral load level. However, low level of viral load donors pose risks in HBV NAT assays, and show fluctuating state for HBV viral load and leads to non-repeated NAT results during follow up studies.

2021 ◽  
Yazan Ibrahim

Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. This study reports SARS-CoV-2 viral load in wastewater influents and treated effluents of 11 wastewater treatment plants (WWTPs), as well as untreated wastewater from 38 various locations, in the United Arab Emirates (UAE) in May and June 2020. Composite samples collected over twenty-four hours were thermally deactivated for safety, followed by viral concentration using ultrafiltration, RNA extraction using commercially available kits, and viral quantification using RT-qPCR. Furthermore, estimates of the prevalence of SARS-CoV-2 infection in different regions were simulated using Monte Carlo. Results showed that the viral load in wastewater influents from these WWTPs ranged from 7.50E+02 to over 3.40E+04 viral gene copies/L with some plants having no detectable viral RNA by RT-qPCR. The virus was also detected in 85% of untreated wastewater samples taken from different locations across the country, with viral loads in positive samples ranging between 2.86E+02 and over 2.90E+04 gene copies/L. It was also observed that the precautionary measures implemented by the UAE government correlated with a drop in the measured viral load in wastewater samples, which were in line with the reduction of COVID-19 cases reported in the population. Importantly, none of the 11 WWTPs' effluents tested positive during the entire sampling period, indicating that the treatment technologies used in the UAE are efficient in degrading SARS-CoV-2, and confirming the safety of treated re-used water in the country. SARS-CoV-2 wastewater testing has the potential to aid in monitoring or predicting an outbreak location and can shed light on the extent viral spread at the community level.

Theresa Awortu Jeremiah ◽  
Ransom Baribefii Jacob ◽  
Zaccheaus Awortu Jeremiah ◽  
Osaro Mgbere ◽  
Chris Anyamene ◽  

Aims: Burden of infectious diseases in correctional institutions constitutes a public health concern due to the confined nature and congestion of the prisons. This study aimed at surveying Burden of HIV, Tuberculosis Infection and Risk factors amongst inmates of Correctional Institutions in Port Harcourt Nigeria Study Design: The study was descriptive, comprising both males and females. A total of 178 inmates constituted the study population Place and Duration of Study: Port Harcourt Maximum Prisons, Creek Road and the Juvenile Remand Home, Borokiri, Port Harcourt, Nigeria, between the months of May to December 2019. Methodology: Two millilitres of blood was collected from each participant after receiving their informed consent. The blood was dispensed into EDTA anti-coagulant bottles and used for serological investigations of HIV 1&2, and TB.  Samples positive for TB was confirmed using the GeneXpert Molecular technique while HIV 1&2 were confirmed using Real-Time PCR and their Viral Loads determined. Results: The overall prevalence of HIV and MTB in the study population were: HIV 1 & 2 (3.9%) and Tuberculosis (0.6%) The Mean Viral Loads of positive samples were HIV 1&2 (479.3 copies/ml); and High MTB was detected. The most significant risk factors identified are as follows:, inmates with tattoos on their bodies (c2=83.6, p<0.0001), took part in blood initiation ceremonies (c2=110.1, p<0.0001), have exchanged needles/sharp objects (c2=2.2, p>0.0001), have tribal marks (c2=58.4, p<0.0001), received blood (c2=151.1, p<0.0001). Majority of the inmates have had sex before, 159(89.3%) [89(56.0%) had multiple sex partners up to 3 and above, 32(20.1%) had 2 partners while 38(23.9%) said they were single sex partners (c2=37.1, p<0.0001)]. On condom use, 90(50.6%) of the inmates do not use condom while 88(49.4%) admitted they use condoms. 7(3.9%) of the inmates have indulged in anal sex (c2=151.1, p<0.0001). 6(3.4%) had history of family drug use while 23(12.9%) have used drugs prior to imprisonment Conclusion: The prevalence of HIV among inmates in this study is quite high and remains a public health problem while that of Mycobacterium tuberculosis (MTB) though appearing relatively low still remains a public health risk. The risk factors amongst inmates of Correctional Institutions in Port Harcourt Nigeria have been identified in this study. The high HIV 1 & 2 prevalence with MTB prevalence with high viral load results indicates poor health conditions which if not contained can spread to other inmates. This requires prompt interventions and treatment among the correctional inmates.

2021 ◽  
pp. eabh0755
Neeltje van Doremalen ◽  
Jyothi N. Purushotham ◽  
Jonathan E. Schulz ◽  
Myndi G. Holbrook ◽  
Trenton Bushmaker ◽  

ChAdOx1 nCoV-19/AZD1222 is an approved adenovirus-based vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) currently being deployed globally. Previous studies in rhesus macaques revealed that intramuscular vaccination with ChAdOx1 nCoV-19/AZD1222 provided protection against pneumonia but did not reduce shedding of SARS-CoV-2 from the upper respiratory tract. Here, we investigated whether intranasally administered ChAdOx1 nCoV-19 reduces detection of virus in nasal swabs after challenging vaccinated macaques and hamsters with SARS-CoV-2 carrying a D614G mutation in the spike protein. Viral loads in swabs obtained from intranasally vaccinated hamsters were decreased compared to control hamsters, and no viral RNA or infectious virus was found in lung tissue after a direct challenge or after direct contact with infected hamsters. Intranasal vaccination of rhesus macaques resulted in reduced virus concentrations in nasal swabs and a reduction in viral loads in bronchoalveolar lavage and lower respiratory tract tissue. Intranasal vaccination with ChAdOx1 nCoV-19/AZD1222 reduced virus concentrations in nasal swabs in two different SARS-CoV-2 animal models, warranting further investigation as a potential vaccination route for COVID-19 vaccines.

2021 ◽  
Ellen C. Carbo ◽  
Anne Russcher ◽  
Margriet E.M. Kraakman ◽  
Caroline S. de Brouwer ◽  
Igor A. Sidorov ◽  

Introduction Immunocompromised patients are prone to reactivations of multiple latent DNA viruses. Viral load monitoring by single-target quantitative PCRs (qPCR) is the current cornerstone for virus quantification. In this study, a metagenomic next-generation sequencing (mNGS) approach was used for identification and load monitoring of transplantation-related DNA viruses. Methods Longitudinal plasma samples from six patients that were qPCR-positive for cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyoma virus (BKV, adenovirus (ADV), parvovirus B19 (B19V), and torque teno-virus (TTV) were sequenced using the quantitative metagenomic Galileo Viral Panel Solution (Arc Bio, LLC) reagents and bioinformatics pipeline combination. Qualitative and quantitative performance was analysed with focus on viral load ranges relevant for clinical decision-making. Results All pathogens identified by qPCR were also identified by mNGS. In addition, BKV, CMV, and HHV6B were detected by mNGS which were not ordered initially but could be confirmed by qPCR. Viral loads determined by mNGS correlated with the qPCR results, with inter-method differences in viral load per virus ranging from 0.19 log10 IU/ml for EBV to 0.90 log10 copies/ml for ADV. TTV, analysed by mNGS in a semi-quantitative way, showed a mean difference of 3.0 log10 copies/ml. Trends over time in viral load determined by mNGS and qPCR were comparable, and clinical thresholds for initiation of treatment were equally indicated by mNGS. Conclusion The Galileo Viral Panel for quantitative mNGS performed comparable to qPCR with regard to detection and viral load determination, within clinically relevant ranges of patient management algorithms.

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