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Charles M’Poca Charles, Nafissa Bique Osman, Domingos Arijama, Benjamim Matingane, Tomás Sitoé, Darlene Kenga, Cesaltina Lorenzoni, Elvira Luís, Rodolfo De Carvalho Pacagnella, Jahit Sacarlal, et al.
Reproductive Health, Volume 19, pp 1-11;

Background: Although there is a significant increase of evidence regarding the prevalence and impact of COVID-19 on maternal and perinatal outcomes, data on the effects of the pandemic on the obstetric population in sub-Saharan African countries are still scarce. Therefore, the study aims were to assess the prevalence and impact of COVID-19 on maternal and neonatal outcomes in the obstetric population at Central Hospital of Maputo (HCM), Mozambique. Methods: Prospective cohort study conducted at teaching and referral maternity, HCM, from 20 October 2020 to 22 July 2021. We collected maternal and perinatal outcomes up to 6 weeks postpartum of eligible women (pregnant and postpartum women—up to the 14th day postpartum) screened for COVID-19 (individual test for symptomatic participants and pool testing for asymptomatic). The primary outcome was maternal death, Severe Acute Respiratory Syndrome (SARS) and Intensive Care Unit (ICU) admission. We estimated the COVID-19 prevalence and the unadjusted RR (95% CI) for maternal and perinatal outcomes. We used the chi-square or Fisher's exact test to compare categorical variables (two-sided p-value < 0.05 for statistical significance). Results: We included 239 participants. The overall prevalence of COVID-19 was 9.2% (22/239) and in the symptomatic group was 32.4% (11/34). About 50% of the participants with COVID-19 were symptomatic. Moreover, the most frequent symptoms were dyspnoea (33.3%), cough (28.6%), anosmia (23.8%), and fever (19%). Not having a partner, being pregnant, and alcohol consumption were vulnerability factors for SARS-CoV-2 infection. The risk of adverse maternal and neonatal outcomes (abortion, foetal death, preterm birth, Apgar, and NICU admission) was not significantly increased with COVID-19. Moreover, we did not observe a significant difference in the primary outcomes (SARS, ICU admission and maternal death) between COVID-19 positive and COVID-19 negative groups. Conclusion: The prevalence of COVID-19 in the obstetric population is higher than in the general population, and fifty percent of pregnant and postpartum women with COVID-19 infection are asymptomatic. Not having a partner and alcohol consumption were factors of greatest vulnerability to SARS-COV-2 infection. Moreover, being pregnant versus postpartum was associated with increased vulnerability to COVID-19. Data suggest that pregnant women with COVID-19 may have a higher frequency of COVID-19 infection, reinforcing the need for universal testing, adequate follow-up for this population, and increasing COVID-19 therapy facilities in Mozambique. Moreover, provide counselling during Antenatal care for COVID-19 preventive measures. However, more prospective and robust studies are needed to assess these findings.
, , , Zaidat A. Musa, , Elsie Ilori, Natalia Blanco, Andrew Mitchell, , Mirna Moloney, et al.
Published: 17 June 2022
PLOS Global Public Health, Volume 2;

The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Europe and the United States, with much lower reported incidence. Population-based studies are needed to estimate true cumulative incidence of SARS-CoV-2 to inform public health interventions. This study estimated SARS-CoV-2 seroprevalence in four selected states in Nigeria in October 2020. We implemented a two-stage cluster sample household survey in four Nigerian states (Enugu, Gombe, Lagos, and Nasarawa) to estimate age-stratified prevalence of SARS-CoV-2 antibodies. All individuals in sampled households were eligible for interview, blood draw, and nasal/oropharyngeal swab collection. We additionally tested participants for current/recent malaria infection. Seroprevalence estimates were calculated accounting for the complex survey design. Across all four states, 10,629 (96·5%) of 11,015 interviewed individuals provided blood samples. The seroprevalence of SARS-CoV-2 antibodies was 25·2% (95% CI 21·8–28·6) in Enugu State, 9·3% (95% CI 7·0–11·5) in Gombe State, 23·3% (95% CI 20·5–26·4) in Lagos State, and 18·0% (95% CI 14·4–21·6) in Nasarawa State. Prevalence of current/recent malaria infection ranged from 2·8% in Lagos to 45·8% in Gombe and was not significantly related to SARS-CoV-2 seroprevalence. The prevalence of active SARS-CoV-2 infection in the four states during the survey period was 0·2% (95% CI 0·1–0·4). Approximately eight months after the first reported COVID-19 case in Nigeria, seroprevalence indicated infection levels 194 times higher than the 24,198 officially reported COVID-19 cases across the four states; however, most of the population remained susceptible to COVID-19 in October 2020.
International Journal of Environmental Research and Public Health, Volume 19;

Exposure to atmospheric particulate matter and nitrogen dioxide has been linked to SARS-CoV-2 infection and death. We hypothesized that long-term exposure to farming-related air pollutants might predispose to an increased risk of COVID-19-related death. To test this hypothesis, we performed an ecological study of five Italian Regions (Piedmont, Lombardy, Veneto, Emilia-Romagna and Sicily), linking all-cause mortality by province (administrative entities within regions) to data on atmospheric concentrations of particulate matter (PM2.5 and PM10) and ammonia (NH3), which are mainly produced by agricultural activities. The study outcome was change in all-cause mortality during March–April 2020 compared with March–April 2015–2019 (period). We estimated all-cause mortality rate ratios (MRRs) by multivariate negative binomial regression models adjusting for air temperature, humidity, international import-export, gross domestic product and population density. We documented a 6.9% excess in MRR (proxy for COVID-19 mortality) for each tonne/km2 increase in NH3 emissions, explained by the interaction of the period variable with NH3 exposure, considering all pollutants together. Despite the limitations of the ecological design of the study, following the precautionary principle, we recommend the implementation of public health measures to limit environmental NH3 exposure, particularly while the COVID-19 pandemic continues. Future studies are needed to investigate any causal link between COVID-19 and farming-related pollution.
Published: 8 June 2021
Journal: Vaccines
The routine detection, surveillance, and reporting of novel SARS-CoV-2 variants is crucial, as these threaten to hinder global vaccination efforts. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. This local Israeli variant was not associated with a higher infection rate or higher prevalence. Furthermore, the local variant was successfully neutralized by sera from fully vaccinated individuals at a comparable level to the B.1.1.7 variant and an Israel wild-type strain. While it is not a variant of concern, routine monitoring by sequencing is still required.
, M. Asso-Bonnet, M. Vasse, Emilie Catherinot, Colas Tcherakian, Antoine Magnan, Simon Chauveau, Sylvie Colin de Verdière, Hélène Salvatore, Antoine Roux, et al.
European Journal of Clinical Microbiology & Infectious Diseases, Volume 40, pp 2041-2045;

The publisher has not yet granted permission to display this abstract.
The SARS-CoV-2 variant with lineage B.1.351 clusters investigation team
Two cases of confirmed SARS-CoV-2 infection with the B.1.351 variant were reported in France in mid-January, 2020. These cases attended a gathering in Mozambique in mid-December 2020. Investigations led to the identification of five imported cases responsible for 14 transmission chains and a total 36 cases. Epidemiological characteristics seemed comparable to those described before the emergence of the South African variant B.1.351. The lack of tertiary transmission outside of the personal sphere suggests that distancing and barrier measures were effective.
Published: 12 January 2021
BACKGROUND The COVID-19 pandemic has affected the response capacity of the health care workforce, and health care professionals have been experiencing acute stress reactions since the beginning of the pandemic. In Spain, the first wave was particularly severe among the population and health care professionals, many of whom were infected. These professionals required initial psychological supports that were gradual and in line with their conditions. OBJECTIVE In the early days of the pandemic in Spain (March 2020), this study aimed to design and validate a scale to measure acute stress experienced by the health care workforce during the care of patients with COVID-19: the Self-applied Acute Stress Scale (EASE). METHODS Item development, scale development, and scale evaluation were considered. Qualitative research was conducted to produce the initial pool of items, assure their legibility, and assess the validity of the content. Internal consistency was calculated using Cronbach α and McDonald ω. Confirmatory factor analysis and the Mann-Whitney-Wilcoxon test were used to assess construct validity. Linear regression was applied to assess criterion validity. Back-translation methodology was used to translate the scale into Portuguese and English. RESULTS A total of 228 health professionals from the Spanish public health system responded to the 10 items of the EASE scale. Internal consistency was .87 (McDonald ω). Goodness-of-fit indices confirmed a two-factor structure, explaining 55% of the variance. As expected, the highest level of stress was found among professionals working in health services where a higher number of deaths from COVID-19 occurred (P<.05). CONCLUSIONS The EASE scale was shown to have adequate metric properties regarding consistency and construct validity. The EASE scale could be used to determine the levels of acute stress among the health care workforce in order to give them proportional support according to their needs during emergency conditions, such as the COVID-19 pandemic.
Pascal Mertens, Nathalie De Vos, Delphine Martiny, Christian Jassoy, Ali Mirazimi, Lize Cuypers, Sigi Van Den Wijngaert, , Pierrette Melin, Karolien Stoffels, et al.
Published: 8 May 2020
Frontiers in Medicine, Volume 7;

Introduction: COVID-19 Ag Respi-Strip, an immunochromatographic (ICT) assay for the rapid detection of SARS-CoV-2 antigen on nasopharyngeal specimen, has been developed to identify positive COVID-19 patients allowing prompt clinical and quarantine decisions. In this original research article, we describe the conception, the analytical and clinical performances as well as the risk management of implementing the COVID-19 Ag Respi-Strip in a diagnostic decision algorithm. Materials and Methods: Development of the COVID-19 Ag Respi-Strip resulted in a ready-to-use ICT assay based on a membrane technology with colloidal gold nanoparticles using monoclonal antibodies directed against the SARS-CoV and SARS-CoV-2 highly conserved nucleoprotein antigen. Four hundred observations were recorded for the analytical performance study and thirty tests were analyzed for the cross-reactivity study. The clinical performance study was performed in a retrospective multi-centric evaluation on aliquots of 328 nasopharyngeal samples. COVID-19 Ag Respi-Strip results were compared with qRT-PCR as golden standard for COVID-19 diagnostics. Results: In the analytical performance study, the reproducibility showed a between-observer disagreement of 1.7%, a robustness of 98%, an overall satisfying user friendliness and no cross-reactivity with other virus-infected nasopharyngeal samples. In the clinical performance study performed in three different clinical laboratories during the ascendant phase of the epidemiological curve, we found an overall sensitivity and specificity of 57.6 and 99.5%, respectively with an accuracy of 82.6%. The cut-off of the ICT was found at CT <22. User-friendliness analysis and risk management assessment through Ishikawa diagram demonstrate that COVID-19 Ag Respi-Strip may be implemented in clinical laboratories according to biosafety recommendations. Conclusion: The COVID-19 Ag Respi-Strip represents a promising rapid SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 in 15 min at the peak of the pandemic. Its role in the proposed diagnostic algorithm is complementary to the currently-used molecular techniques.
Haley du Bois, Taylor A. Heim, Sheikh Abdul Rahman, Bhrugu Yagnik, , Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, , et al.
Science Immunology, Volume 6;

Autoantibodies neutralizing type I IFNs increase in prevalence over 60 years of age and underlie about 20% of all fatal COVID-19 cases.
Yun-Yun Wang, for the Zhongnan Hospital of Wuhan University Novel Coronavirus Management and Research Team, Ying-Hui Jin, Xue-Qun Ren, Yi-Rong Li, Xiao-Chun Zhang, ,
Military Medical Research, Volume 7, pp 1-3;

On 6 February 2020, our team had published a rapid advice guideline for diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infection, and this guideline provided our experience and make well reference for fighting against this pandemic worldwide. However, the coronavirus disease 2019 (COVID-19) is a new disease, our awareness and knowledge are gradually increasing based on the ongoing research findings and clinical practice experience; hence, the strategies of diagnosis and treatment are also continually updated. In this letter, we answered one comment on our guideline and provided the newest diagnostic criteria of “suspected case” and “confirmed case” according to the latest Diagnosis and Treatment Guidelines for COVID-19 (seventh version) that issued by the National Health Committee of the People’s Republic of China.
Published: 15 January 2023
Journal: Viruses
Viruses, Volume 15;

In human beings, there are five reported variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). However, in contrast to human beings, descriptions of infections of animals with specific variants are still rare. The aim of this study is to systematically investigate SARS-CoV-2 infections in companion animals in close contact with SARS-CoV-2-positive owners (“COVID-19 households”) with a focus on the Delta variant. Samples, obtained from companion animals and their owners were analyzed using a real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and next-generation sequencing (NGS). Animals were also tested for antibodies and neutralizing activity against SARS-CoV-2. Eleven cats and three dogs in nine COVID-19-positive households were RT-qPCR and/or serologically positive for the SARS-CoV-2 Delta variant. For seven animals, the genetic sequence could be determined. The animals were infected by one of the pangolin lineages B.1.617.2, AY.4, AY.43 and AY.129 and between zero and three single-nucleotide polymorphisms (SNPs) were detected between the viral genomes of animals and their owners, indicating within-household transmission between animal and owner and in multi-pet households also between the animals. NGS data identified SNPs that occur at a higher frequency in the viral sequences of companion animals than in viral sequences of humans, as well as SNPs, which were exclusively found in the animals investigated in the current study and not in their owners. In conclusion, our study is the first to describe the SARS-CoV-2 Delta variant transmission to animals in Switzerland and provides the first-ever description of Delta-variant pangolin lineages AY.129 and AY.4 in animals. Our results reinforce the need of a One Health approach in the monitoring of SARS-CoV-2 in animals.
, Innovative Genomics Institute SARS-CoV-2 Testing Consortium, Dirk Hockemeyer, Fyodor Urnov, Ralph Green
Published: 12 April 2020
The appearance and spread of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) led to the official declaration of a global pandemic, with states in the US implementing shelter-in-place orders at an unprecedented scale. SARS-CoV-2 has a robust person-to-person transmission rate and an asymptomatic period of two weeks or more, leading to widespread infection that has overwhelmed healthcare infrastructures around the globe. Effective public health measures require extensive, accurate, and rapid testing to determine infection rates. Here we describe the strategy we used to establish a CLIA-licensed clinical laboratory to perform a validated Laboratory-Developed Test (LDT) for SARS-CoV-2 in Berkeley, California and the surrounding Bay Area community. Our procedures for implementing the technical, regulatory, and data management workstreams necessary for clinical sample processing provide a roadmap to aid others in setting up similar testing centers.Note on Nomenclature: in accordance with established virology and infectious disease nomenclature, throughout this document we use “SARS-CoV-2” to refer to the viral agent causing infection and “COVID-19” to refer to the human infectious disease caused by that viral agent.
, Maria Grazia Cusi, Mauro Pistello, Luisa Galli, Alessandro Bartoloni, Gabriele Anichini, Chiara Azzari, Michele Emdin, Claudia Gandolfo, Fabrizio Maggi, et al.
Published: 4 August 2020
Objective: To evaluate the performance of two available rapid immunological tests for identification of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) antibodies and their subsequent application to a regional screening of health care workers (HCW) in Tuscany (Italy).Design: measures of accuracy and HCW serological surveillanceSetting: 6 major health facilities in Tuscany, Italy.Participants: 17,098 HCW of the Tuscany Region. Measures of accuracy were estimated to assess sensitivity in 176 hospitalized Covid-19 clinical subjects at least 14 days after a diagnostic PCR-positive assay result. Specificity was assessed in 295 sera biobanked in the pre-Covid-19 era in winter or summer 2013-14Main outcome measures: Sensitivity and specificity, and 95% confidence intervals, were measured using two serological tests, named T-1 and T-2. Positive and Negative predictive values were estimated at different levels of prevalence. HCW of the health centers were tested using the serological tests, with a follow-up nasopharyngeal PCR-test swab in positive tested cases.Results: Sensitivity was estimated as 99% (95%CI: 95%-100%) and 97% (95% CI: 90%-100%), whereas specificity was the 95% and 92%, for Test T-1 and T-2 respectively. In the historical samples IgM cross-reactions were detected in sera collected during the winter period, probably linked to other human coronaviruses. Out of the 17,098 tested, 3.1% have shown the presence of SARS-CoV-2 IgG antibodies, among them 6.8% were positive at PCR follow-up test on nasopharyngeal swabs.Conclusion: Based on the low prevalence estimate observed in this survey, the use of serological test as a stand-alone test is not justified to assess the individual immunity status. Serological tests showed good performance and might be useful in an integrated surveillance, for identification of infected subjects and their contacts as required by the policy of contact tracing, with the aim to reduce the risk of dissemination, especially in health service facilities.
, Sarah Louise Murphy, Jan Cato Holter, , Annika E Michelsen, Tøri Vigeland Lerum, Mari Kaarbø, Lars Heggelund, Aleksander Rygh Holten, Ane Kristine Finbråten, et al.
The Journal of Infectious Diseases, Volume 226, pp 2150-2160;

Immune dysregulation is a major factor in the development of severe Covid-19. The homeostatic chemokines CCL19 and CCL21 have been implicated as mediators of tissue inflammation, but data on their regulation in SARS-CoV-2 infection is limited. We thus investigated the levels of these chemokines in Covid-19 patients. Serial blood samples were obtained from patients hospitalized with Covid-19 (n = 414). Circulating CCL19 and CCL21 levels during hospitalization and three-month follow-up were analyzed. In vitro assays and analysis of RNAseq data from public repositories were performed to further explore possible regulatory mechanisms. A consistent increase in circulating levels of CCL19 and CCL21 was observed, with high levels correlating with disease severity measures, including respiratory failure, need for intensive care, and 60-day all-cause mortality. High levels of CCL21 at admission were associated with persisting impairment of pulmonary function at the three-month follow-up. Our findings highlight CCL19 and CCL21 as markers of immune dysregulation in Covid-19. This may reflect aberrant regulation triggered by tissue inflammation, as observed in other chronic inflammatory and autoimmune conditions. Determination of the source and regulation of these chemokines and their effects on lung tissue is warranted to further clarify their role in Covid-19.
, Lise Estcourt, Heli Harvala, David Roberts, David K. Menon, On behalf of the United Kingdom SARS-CoV-2 Convalescent Plasma Evaluation (SCoPE) Consortium
Published: 20 July 2020
Journal: Critical Care
Critical Care, Volume 24, pp 1-5;

Miriam Lisci, Philippa R. Barton, Jonathan Lezmy, I. Lorena Arancibia-Cárcamo, Mardo Kõivomägi, Matthew P. Swaffer, , Robin Marwal, Radhakrishnan Vs, Kalaiarasan Ponnusamy, et al.
Science, Volume 374, pp 995-999;

Deadly surge in Delhi: In the spring of 2021, Delhi, India experienced a wave of coronavirus cases that overwhelmed healthcare services despite the population showing a high level of immune positivity. Dhar et al . collated a mixture of serosurveillance, quantitative polymerase chain reaction, and genomic data, finding that waves of variants had passed through the Delhi population during 2020 and 2021. The alpha (B.1.1.7) variant dominated in March 2021 and was rapidly replaced by the delta (B.1.617.2) variant in April and May 2021. The delta variant outcompeted its predecessors by mutations that enhanced replication, immune evasion, and host receptor avidity, thus increasing transmissibility, reinfection, and vaccination breakthrough. —CA
Gabriela Gonzalez‐Aleman, Hernan P. Zamponi, Leonardo Juarez‐Aguaysol, Gabriela Kukoc, Maria Eugenia Dominguez, Belén Pini, Eduardo G Padilla, Maria Calvó, Silvia Beatriz Molina‐Rangeon, Gonzalo Guerrero, et al.
Published: 20 December 2022
by Wiley
Alzheimer's & Dementia, Volume 18;

, Audrey Duval, Jean Ralph Zahar, Lulla Opatowski, Laura Temime, Niels Hendrickx, Kévin Jean, Sofía Jijón, Ajmal Oodally, George Shirreff, et al.
Published: 11 January 2022
Nature Communications, Volume 13, pp 1-10;

Healthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive response to local surges in outbreak risk are unclear. We simulate SARS-CoV-2 transmission in a long-term care hospital with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). Across scenarios, nosocomial incidence is reduced by up to 40-47% (range of means) with routine symptomatic RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4-5 days between the two screening rounds is optimal for transmission prevention. Screening efficacy varies depending on test sensitivity, test type, subpopulations targeted, and community incidence. Efficiency, however, varies primarily depending on underlying outbreak risk, with health-economic benefits scaling by orders of magnitude depending on the COVID-19 containment measures in place.
Oscar F. Chacón-Camacho, Rocío Arce-González,
Boletin Medico Del Hospital Infantil de Mexico, Volume 77, pp 252-261;

Since the emergence of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China at the end of 2019, when its characteristics were practically unknown, one aspect was evident: its high contagion rate. This high infection rate resulted in the spread of the virus in China, Europe, and, eventually, the rest of the world, including Mexico. At present, around 9 million people are infected, and around 470,000 have died worldwide. In this context, the need to generate protective immunity, and especially the generation of a vaccine that can protect the world population against infection in the shortest possible time, is a challenge that is being addressed in different countries using different strategies in multiple clinical trials. This opinion article will present the evidence of the induction of immune response in some of the viruses of the coronavirus family before COVID-19, such as SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus). The information collected about the induction of an immune response by SARS-CoV-2 will be presented, as well as a description of the vaccine candidates reported to date in the various ongoing clinical trials. Finally, an opinion based on the evidence presented will be issued on the potential success of developing vaccine prototypes.
, Shay Fleishon, Talia Kustin, Michal Mandelboim, Oran Erster, Israel Consortium of SARS-CoV-2 sequencing, Ella Mendelson, Orna Mor, Neta S. Zuckerman
Published: 7 August 2021
The SARS-Coronavirus-2 (SARS-CoV-2) driven pandemic was first recognized in late 2019, and the first few months of its evolution were relatively clock-like, dominated mostly by neutral substitutions. In contrast, the second year of the pandemic was punctuated by the emergence of several variants that bore evidence of dramatic evolution. Here, we compare and contrast evolutionary patterns of various variants, with a focus on the recent Delta variant. Most variants are characterized by long branches leading to their emergence, with an excess of non-synonymous substitutions occurring particularly in the Spike and Nucleocapsid proteins. In contrast, the Delta variant that is now becoming globally dominant, lacks the signature long branch, and is characterized by a step-wise evolutionary process that is ongoing. Contrary to the “star-like” topologies of other variants, we note the formation of several distinct clades within Delta that we denote as clades A-E. We find that sequences from the Delta D clade are dramatically increasing in frequency across different regions of the globe. Delta D is characterized by an excess of non-synonymous mutations, mostly occurring in ORF1a/b, some of which occurred in parallel in other notable variants. We conclude that the Delta surge these days is composed almost exclusively of Delta D, and discuss whether selection or random genetic drift has driven the emergence of Delta D.
, Tuva B. Dahl, Jan C. Holter, Anders B. Kildal, Sarah L. Murphy, Kuan Yang, Ana Quiles‐Jiménez, Lars Heggelund, Karl Erik Müller, Anders Tveita, et al.
Published: 18 August 2022
by Wiley
Journal of Internal Medicine, Volume 292, pp 816-828;

, Joana Isidro, , Sílvia Duarte, Helena Cortes-Martins, , , , Luís Vieira, Raquel Guiomar, et al.
Communications Medicine, Volume 2, pp 1-11;

Background: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods: By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. Results: We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions: Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.
, Alessandro Zulli, Isabel M. Ott, , , , , , Mallery I. Breban, , et al.
Published: 2 September 2021
Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2 RNA has proven an effective and efficient technique to approximate COVID-19 case rates in the population. Predicting variant abundances from wastewater, however, is technically challenging. Here we show that by sequencing SARS-CoV-2 RNA in wastewater and applying computational techniques initially used for RNA-Seq quantification, we can estimate the abundance of variants in wastewater samples. We show by sequencing samples from wastewater and clinical isolates in Connecticut U.S.A. between January and April 2021 that the temporal dynamics of variant strains broadly correspond. We further show that this technique can be used with other wastewater sequencing techniques by expanding to samples taken across the United States in a similar timeframe. We find high variability in signal among individual samples, and limited ability to detect the presence of variants with clinical frequencies <10%; nevertheless, the overall trends match what we observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in variant prevalence in situations where clinical sequencing is unavailable or impractical.
, , Nathan D. Grubaugh, Tara Alpert, Isabel M. Ott, Mallery I. Breban, Richard A. Martinello, Cindy Smith, Matthew W. Davis, Dayna Mcmanus, et al.
Published: 30 December 2021
by Wiley
Transplant Infectious Disease, Volume 24;

The publisher has not yet granted permission to display this abstract.
Patricia González-Donapetry, Paloma García-Clemente, Iván Bloise, Consuelo García-Sánchez, Miguel Ángel Sánchez Castellano, María Pilar Romero, Almudena Gutiérrez Arroyo, Jesús Mingorance, María De Ceano-Vivas La Calle, Julio García-Rodriguez, et al.
Published: 17 February 2021
Real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the reference laboratory method to diagnose SARS-CoV-2 infection then requires equipment and is time-consuming. There is a crucial demand for rapid techniques such as antigen detection test. Considering the different diagnostic accuracy of tests with other respiratory viruses in adults and children, SARS-CoV-2 antigen test must be evaluated specifically in children. The purpose of this study was to evaluate the performance of Panbio COVID-19 Ag Rapid Test Device (Abbott) as a point-of-care test for diagnosis of SARS-CoV-2 in comparison to RT-qPCR in a pediatric population. Four hundred forty nasopharyngeal swabs were tested. Amongst the 18 positive RT-qPCR samples, 14 were detected by the rapid antigen test, given an overall sensitivity of 77.7%. All the samples detected positive with the antigen rapid test were also positive with RT-qPCR. The sensitivity of Panbio COVID-19 Ag Rapid Test Device is lower in children than in adults. Nevertheless, considering the good values of specificity, negative and positive predictive values this test could be used as a frontline test to obtain quick results, although the negative values with COVID-19 high clinical suspicion should be confirmed using RT-qPCR.
, , , Yamrot M. Amha, Mitchel Bartolo, Richard Danielson, Yeggie Dearborn, George Di Giovanni, Christobel Ferguson, Stephanie Fevig, et al.
Environmental Science: Water Research & Technology, Volume 7, pp 504-520;

In response to COVID-19, the international water community rapidly developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. Wastewater surveillance using such methods has the potential to complement clinical testing in assessing community health. This interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), divided into eight method groups based on sample concentration approach and whether solids were removed. Two raw wastewater samples were collected in August 2020, amended with a matrix spike (betacoronavirus OC43), and distributed to 32 laboratories across the U.S. Replicate samples analyzed in accordance with the project's quality assurance plan showed high reproducibility across the 36 SOPs: 80% of the recovery-corrected results fell within a band of ±1.15 log10 genome copies per L with higher reproducibility observed within a single SOP (standard deviation of 0.13 log10). The inclusion of a solids removal step and the selection of a concentration method did not show a clear, systematic impact on the recovery-corrected results. Other methodological variations (e.g., pasteurization, primer set selection, and use of RT-qPCR or RT-dPCR platforms) generally resulted in small differences compared to other sources of variability. These findings suggest that a variety of methods are capable of producing reproducible results, though the same SOP or laboratory should be selected to track SARS-CoV-2 trends at a given facility. The methods showed a 7 log10 range of recovery efficiency and limit of detection highlighting the importance of recovery correction and the need to consider method sensitivity when selecting methods for wastewater surveillance.
, , , , , EMEA-MESuRS working group on the nosocomial modelling of SARS-CoV-2
Published: 29 September 2021
Covid-19 poses significant risk of nosocomial transmission, and preventing this requires good estimates of the basic reproduction number R0 in hospitals and care facilities, but these are currently lacking. Such estimates are challenging due to small population sizes in these facilities and inconsistent testing practices. We estimate the patient-to-patient R0 and daily transmission rate of SARS-CoV-2 using data from a closely monitored hospital outbreak in Paris 2020 during the first wave. We use a realistic epidemic model which accounts for progressive stages of infection, stochastic effects and a large proportion of asymptomatic infections. Innovatively, we explicitly include changes in testing capacity over time, as well as the evolving sensitivity of PCR testing at different stages of infection. We conduct rigorous statistical inference using iterative particle filtering to fit the model to the observed patient data and validate this methodology using simulation. We provide estimates for R0 across the entire hospital (2.6) and in individual wards (from 3 to 15), possibly reflecting heterogeneity in contact patterns or control measures. An obligatory mask-wearing policy introduced during the outbreak is likely to have changed the R0, and we estimate values before (8.7) and after (1.3) its introduction, corresponding to a policy efficacy of 85%.
Paolo Boffetta, Francesco Violante, Paolo Durando, Giuseppe De Palma, Enrico Pira, Luigi Vimercati, Alfonso Cristaudo, Giancarlo Icardi, Emma Sala, Maurizio Coggiola, et al.
Published: 11 March 2021
Scientific Reports, Volume 11, pp 1-8;

Healthcare workers (HCWs) are at increased risk of being infected with SARS-CoV-2, yet limited information is available on risk factors of infection. We pooled data on occupational surveillance of 10,654 HCW who were tested for SARS-CoV-2 infection in six Italian centers. Information was available on demographics, job title, department of employment, source of exposure, use of personal protective equipment (PPEs), and COVID-19-related symptoms. We fitted multivariable logistic regression models to calculate odds ratios and 95% confidence intervals of infection. The prevalence of infection ranged from 3.0 to 22.0%, and was correlated with that of the respective areas. Women were at lower risk of infection compared to men. Fever, cough, dyspnea and malaise were the symptoms most strongly associated with infection, together with anosmia and ageusia. No differences in the risk of infection were detected according to job title, or working in a COVID-19 designated department. Reported contact with a patient inside or outside the workplace was a risk factor. Use of a mask was strongly protective against risk of infection as was use of gloves. The use of a mask by the source of exposure (patient or colleague) had an independent effect in reducing infection risk.
, Francesco Violante, Paolo Durando, Giuseppe De Palma, Enrico Pira, Luigi Vimercati, Alfonso Cristaudo, Giancarlo Icardi, Emma Sala, Maurizio Coggiola, et al.
Published: 30 July 2020
Healthcare workers (HCW) are at increased risk of being infected with SARS-CoV-2, yet limited information is available on risk factors of infection. We pooled data on occupational surveillance of 10,654 HCW who were tested for SARS-CoV-2 infection in six Italian centers. Information was available on demographics, job title, department of employment, source of exposure, use of personal protective equipment (PPE), and COVID-19-related symptoms. We fitted multivariable logistic regression models to calculate odds ratios (OR) and 95% confidence intervals (CI). The prevalence of infection varied across centers and ranged from 3.0% to 22.0%, being strongly correlated with that of the respective areas. Women were at lower risk of infection compared to men. Fever, cough, dyspnea and malaise were the symptoms most strongly associated with infection, together with anosmia and ageusia. No differences in the risk of infection were detected between job titles, or working in a COVID-19 designated department. Reported contact with a patient inside or outside the workplace was a risk factor. Use of a mask was strongly protective against risk of infection as was use of gloves. The use of a mask by the source of exposure (patient or colleague) had an independent effect in reducing infection risk.
, Ahmad Al Shafie, Essam Hassan, Laura Temime, Kévin Jean, Mohamed El-Kassas, Audrey Duval, Kenza Hamzi, Niels Hendrickx, Ajmal Oodally, et al.
Published: 17 November 2022
Scientific Reports, Volume 12, pp 1-8;

In response to the COVID-19 epidemic, Egypt established a unique care model based on quarantine hospitals where only externally-referred confirmed COVID-19 patients were admitted, and healthcare workers resided continuously over 1- to 2-week working shifts. Using a mathematical model accounting for the false-negative rates of RT-PCR tests, we computed the incidence rate of SARS-CoV-2 infection among HCWs, while unveiling the proportion of infections remaining undiagnosed despite routine testing. We relied on longitudinal data, including results of routine RT-PCR tests, collected within three Egyptian quarantine hospitals. We estimated an incidence rate (per 100 person-day, PD) of 1.05 (95% CrI 0.58–1.65) at Hospital 1, 1.92 (95% CrI 0.93–3.28) at Hospital 2 and 7.62 (95% CrI 3.47–13.70) at Hospital 3. We found that the risk for an HCW to be infected during a working shift lay within the range of risk levels previously documented in standard healthcare settings for Hospitals 1–2, whereas it was > threefold higher for Hospital 3. This large variation suggests that HCWs from quarantine hospitals may face a high occupational risk of infection, but that, with sufficient infection control measures, this risk can be brought down to levels similar to those observed in standard healthcare settings.
, Estela Cordero-Laurent, Adriana Godínez, Melany Calderón-Osorno, Hebleen Brenes, Claudio Soto-Garita, Cristian Pérez-Corrales, Jan Felix Drexler, Andres Moreira-Soto, Eugenia Corrales-Aguilar, et al.
Published: 22 December 2020
Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. Costa Rica was first exemplary for the region in its pandemic control, declaring a swift state of emergency on March 16th that led to a low quantity of cases, until measures were lifted in early May. From the first detected case in March 6th to December 31st almost 170 000 cases have been reported in Costa Rica, 99.5% of them from May onwards. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave.Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) are predominant, with phylogenetic relationships that are in line with the results of other Latin American countries, suggesting introduction and multiple re-introductions from other regions of the world. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants. These correspond mostly to non-synonymous mutations (51.6%, 146) but 45.6% (129) corresponded to synonymous mutations. The 283 variants showed an expected power-law distribution: 190 single nucleotide mutations were identified in single sequences, only 16 single nucleotide mutations were found in >5% sequences, and only two mutations in >50% genomes. These mutations were distributed through the whole genome. However, 63.6% were present in ORF1ab, 11.7% in Spike gene and 10.6% in the Nucleocapsid gene. Additionally, the prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in all the 2020. Structural modeling of the Spike protein with the T1117I mutation suggest a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. Nevertheless, in-vitro experiments are required to support these in-silico findings. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of COVID-19 pandemic in Costa Rica suggest introduction of lineages from other countries as travel bans and measures were lifted, similar to results found in other studies, as well as an increase in the Spike-T1117I variant that needs to be monitored and studied in further analyses as part of the surveillance program during the pandemic.
, , Ns Trovão, S Duarte, H Cortes-Martins, H Martiniano, I Gordo, R Leite, L Vieira, Portuguese network for SARS-CoV-2 genomics (Consortium), et al.
Published: 23 February 2021
Background Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. This unprecedented collaborative effort culminated in the generation of 1275 SARS-CoV-2 genome sequences, which represent 15.5% of all confirmed cases in March 2020, making Portugal one of the countries generating the highest volumes of SARS-CoV-2 genomic data during early COVID-19 pandemic. Methods We reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal using recent phylodynamic models that allow integration of individual-based travel history, in order to obtain a more realistic reconstruction of the viral dynamics. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy and Switzerland), which was broadly consistent with the available travel history data, as well as with the countries with most frequent connectivity and/or with the highest number of Portuguese immigrants. Although most introductions were estimated to have occurred during the last week of February and the first week of March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal several weeks before the first confirmed local cases on March 2, 2020. Discussion and Conclusion While the implemented preventive and early control measures seem to have been successful in mitigating community transmission from most independent introductions, our results suggest that their earlier implementation could have largely minimized the number of introductions and subsequent virus expansion. Here we lay the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlight the need for systematic, continuous and geographically-representative genomic surveillance to guide national and international public health authorities toward the characterization and control of SARS-CoV-2 circulating diversity.
, Isabelle Malet, Valentin Leducq, Karen Zafilaza, Delphine Sterlin, Delphine Planas, Adélie Gothland, , , , et al.
Published: 8 February 2021
Nature Communications, Volume 12, pp 1-7;

There are only few data concerning persistence of neutralizing antibodies (NAbs) among SARS-CoV-2-infected healthcare workers (HCW). These individuals are particularly exposed to SARS-CoV-2 infection and at potential risk of reinfection. We followed 26 HCW with mild COVID-19 three weeks (D21), two months (M2) and three months (M3) after the onset of symptoms. All the HCW had anti-receptor binding domain (RBD) IgA at D21, decreasing to 38.5% at M3 (p < 0.0001). Concomitantly a significant decrease in NAb titers was observed between D21 and M2 (p = 0.03) and between D21 and M3 (p < 0.0001). Here, we report that SARS-CoV-2 can elicit a NAb response correlated with anti-RBD antibody levels. However, this neutralizing activity declines, and may even be lost, in association with a decrease in systemic IgA antibody levels, from two months after disease onset. This short-lasting humoral protection supports strong recommendations to maintain infection prevention and control measures in HCW, and suggests that periodic boosts of SARS-CoV-2 vaccination may be required.
Published: 1 July 2021
Journal: Qeios
Importance: SARS coronavirus 2 (SARS­­­-CoV-2) is spread mainly through airborne transmission and colonizes the human upper respiratory tract. It causes coronavirus disease 2019 (COVID-19), which has major therapeutic challenges as there are no treatments to prevent the infection from spreading or the development of the disease in a severe form. Objective: COVID-19 is diagnosed through identification of viral genetic material from nasopharyngeal swabs using PCR. The quantification of viral RNA using the cycle threshold (Ct) values is of great diagnostic importance. Nasal wash with saline or hypertonic saline is very important for the hygiene of the nose and sinuses. The aim of this research was to investigate the effect of an intense nasal wash on the viral load in patients with a SARS-CoV-2 infection. Design: A case-control study investigating the association of a nasopharyngeal wash and viral load in adult patients who tested positive for COVID-19 and were hospitalized was performed. All patients were treated with the standard protocol of care for COVID-19. Group A (n = 20) patients were each provided with a 25 mL bottle of hypertonic solution for a nasopharyngeal wash to be performed for 20–30 s, thrice within 6 h. Group B (n = 5) patients served as negative controls (no intervention). Nasal swabs were taken before and after the 6-h period by the same doctor and RT-PCR followed. Results: There was a 23.6% (median value) and 17.3% (mean value) reduction in the viral load after nasopharyngeal washing. On the other hand, Ct values remained practically stable for the negative control patients within the same 6-h period. Conclusion: To the best of our knowledge, this is the first study which demonstrates the potential effect of hypertonic water on the reduction of SARS-CoV-2 viral load in hospitalized patients with COVID-19. Further randomized, controlled studies are needed to confirm the effects of hypertonic water on the prevention and clinical outcome of SARS-CoV-2-infected patients.
, Anne M. Hahn, Mary E. Petrone, Shuntai Zhou, David Ferguson, Mallery I. Breban, Kien Pham, Mario A. Peña-Hernández, Christopher Castaldi, Verity Hill, et al.
Published: 2 July 2022
Summary: The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
Andrea Lo Vecchio, Silvia Garazzino, Andrea Smarrazzo, Elisabetta Venturini, Marco Poeta, Paola Berlese, Marco Denina, Antonella Meini, Samantha Bosis, Luisa Galli, et al.
Published: 1 December 2021
The gastrointestinal (GI) tract is one of the target organs affected by SARS-CoV-2. The colocalization of angiotensin-converting enzyme 2 and the proteaselike transmembrane serine protease 2, essential receptors for SARS-CoV-2 cell binding and internalization, has been noted in the human GI tract.1,2 The presence of isolated GI symptoms in some patients with SARS-CoV-2 infection, as well as the prolonged fecal shedding reported in neonates and children, supports the hypothesis of a fecal-oral transmission of SARS-CoV-2.3
, Chantal B. F. Vogels, Inci Yildirim, Jessica E. Rothman, , Valter Monteiro, Jeff R. Gehlhausen, Melissa Campbell, , Alexandra Tabachnikova, et al.
Published: 11 October 2021
Journal: Nature
Nature, Volume 600, pp 523-529;

The publisher has not yet granted permission to display this abstract.
Orna Mor, Michal Mandelboim, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Yaniv Lustig, Israel National Consortium for SARS-CoV-2 sequencing, Ella Mendelson,
Published: 7 July 2021
Emerging SARS-CoV-2 variants may threaten global vaccination efforts and awaited reduction in outbreak burden. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. The variant infected 270 individuals in Israel between December 2020 and March 2021, until diminishing due to the gain in dominance of the Alpha variant in February 2021. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread.
Petra Mlcochova, Steven Kemp, Mahesh Shanker Dhar, Guido Papa, Bo Meng, Swapnil Mishra, Charlie Whittaker, Thomas Mellan, Isabella Ferreira, Rawlings Datir, et al.
Published: 22 June 2021
The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and has spread throughout India, displacing the B.1.1.7 (Alpha) variant and other pre-existing lineages. Mathematical modelling indicates that the growth advantage is most likely explained by a combination of increased transmissibility and immune evasion. Indeed in vitro, the delta variant is less sensitive to neutralising antibodies in sera from recovered individuals, with higher replication efficiency as compared to the Alpha variant. In an analysis of vaccine breakthrough in over 100 healthcare workers across three centres in India, the Delta variant not only dominates vaccine-breakthrough infections with higher respiratory viral loads compared to non-delta infections (Ct value of 16.5 versus 19), but also generates greater transmission between HCW as compared to B.1.1.7 or B.1.617.1 (p=0.02). In vitro, the Delta variant shows 8 fold approximately reduced sensitivity to vaccine-elicited antibodies compared to wild type Wuhan-1 bearing D614G. Serum neutralising titres against the SARS-CoV-2 Delta variant were significantly lower in participants vaccinated with ChadOx-1 as compared to BNT162b2 (GMT 3372 versus 654, p<0001). These combined epidemiological and in vitro data indicate that the dominance of the Delta variant in India has been most likely driven by a combination of evasion of neutralising antibodies in previously infected individuals and increased virus infectivity. Whilst severe disease in fully vaccinated HCW was rare, breakthrough transmission clusters in hospitals associated with the Delta variant are concerning and indicate that infection control measures need continue in the post-vaccination era.
, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil, Israel National Consortium for SARS-CoV-2 sequencing, Ella Mendelson, et al.
Published: 28 March 2021
Routine detection, surveillance and reporting of SARS-CoV-2 novel variants is important, as these threaten to hinder vaccination efforts. Herein we report a local novel strain that includes a non-synonymous mutation in the spike (S) protein - P681H and additional synonymous mutations. The P681H Israeli strain has not been associated with higher infection rates and was neutralized by sera from vaccinated individuals in comparable levels to the B.1.1.7 strain and a non-P681H strain from Israel.
, , David Roca Pascual, María Slöcker Barrio, Juan Carlos De Carlos Vicente, Amaya Bustinza Arriortua, , Maite Cuervas-Mons Tejedor, Pedro Pablo Oyágüez Ugidos, Iolanda Jordan, et al.
Intensive Care Medicine, Volume 46, pp 1774-1776;

, Emilie Jolly, Tiffany Pascreau, Marianne Asso-Bonnet, Laurence Mazaux, Marc Vasse, on behalf of the SARS-CoV-2 Foch Hospital study group
Published: 25 May 2020
Infectious Diseases, Volume 52, pp 583-584;

Steven A. Kemp, Mark T. K. Cheng, William L. Hamilton, Kimia Kamelian, Sujit Singh, Partha Rakshit, Anurag Agrawal, , , Himanshu Chauhan, et al.
Published: 21 June 2022
Scientific Reports, Volume 12, pp 1-11;

Breakthrough infections with SARS-CoV-2 Delta variant have been reported in doubly-vaccinated recipients and as re-infections. Studies of viral spread within hospital settings have highlighted the potential for transmission between doubly-vaccinated patients and health care workers and have highlighted the benefits of high-grade respiratory protection for health care workers. However the extent to which vaccination is preventative of viral spread in health care settings is less well studied. Here, we analysed data from 118 vaccinated health care workers (HCW) across two hospitals in India, constructing two probable transmission networks involving six HCWs in Hospital A and eight HCWs in Hospital B from epidemiological and virus genome sequence data, using a suite of computational approaches. A maximum likelihood reconstruction of transmission involving known cases of infection suggests a high probability that doubly vaccinated HCWs transmitted SARS-CoV-2 between each other and highlights potential cases of virus transmission between individuals who had received two doses of vaccine. Our findings show firstly that vaccination may reduce rates of transmission, supporting the need for ongoing infection control measures even in highly vaccinated populations, and secondly we have described a novel approach to identifying transmissions that is scalable and rapid, without the need for an infection control infrastructure.
, , , , Andrew Marques, Hriju Adhikari, Zheng Jin Tu, Rebecca Marrero Rolon, Lars F. Westblade, , et al.
Journal of Clinical Microbiology, Volume 60;

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection.
, David R. Peaper, Brendan J. Kelly, , Andrew Marques, Hriju Adhikari, Zheng Jin Tu, Rebecca Marrero Rolon, Lars F. Westblade, Daniel A. Green, et al.
Published: 28 April 2022
Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
Mario A. Peña-Hernández, Jon Klein, Amyn A. Malik, Andreas Coppi, , Chantal B. F. Vogels, , David R. Peaper, Marie-Louise Landry, Craig Wilen, et al.
Published: 4 January 2022
The frequency of SARS-CoV-2 breakthrough infections in fully vaccinated individuals increased with the emergence of the Delta variant, particularly with longer time from vaccine completion. However, whether breakthrough infections lead to onward transmission remains unclear. Here, we conducted a study involving 125 patients comprised of 72 vaccinated and 53 unvaccinated individuals, to assess the levels of infectious virus in vaccinated and unvaccinated individuals. Quantitative plaque assays showed no significant differences in the titers of virus between these cohorts. However, the proportion of nasopharyngeal samples with culturable virus was lower in the vaccinated patients relative to unvaccinated patients (21% vs. 40%). Finally, time-to-event analysis with Kaplan-Myer curves revealed that protection from culturable infectious virus waned significantly starting at 5 months after completing a 2-dose regimen of mRNA vaccines. These results have important implications in timing of booster dose to prevent onward transmission from breakthrough cases.
Yongliang Zhao, Wenjia Ni, Simeng Liang, Lianghui Dong, Min Xiang, Zeng Cai, Danping Niu, Qiuhan Zhang, Dehe Wang, Yucheng Zheng, et al.
Published: 23 December 2021
SARS-CoV-2 continued to spread globally along with different variants. Here, we systemically analyzed viral infectivity and immune-resistance of SARS-CoV-2 variants to explore the underlying rationale of viral mutagenesis. We found that the Beta variant harbors both high infectivity and strong immune resistance, while the Delta variant is the most infectious with only a mild immune-escape ability. Remarkably, the Omicron variant is even more immune-resistant than the Beta variant, but its infectivity increases only in Vero E6 cells implying a probable preference for the endocytic pathway. A comprehensive analysis revealed that SARS-CoV-2 spike protein evolved into distinct evolutionary paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance, resulting in a narrow spectrum of the current single-strain vaccine. In light of these findings and the phylogenetic analysis of 2674 SARS-CoV-2 S-protein sequences, we generated a consensus antigen (S6) taking the most frequent mutations as a pan-vaccine against heterogeneous variants. As compared to the ancestry SWT vaccine with significantly declined neutralizations to emerging variants, the S6 vaccine elicits broadly neutralizing antibodies and full protections to a wide range of variants. Our work highlights the importance and feasibility of a universal vaccine strategy to fight against antigen drift of SARS-CoV-2.
The Victorian SARS‐CoV‐2 Reinfection Study Group, Corinna Minko, Filimon Haile, Jessica Gu, Daniel Kidd, Michael Cross, Mohana Baptista, Simon Crouch, Anna B Pierce, Rhonda L Stuart, et al.
Published: 22 November 2021
by Wiley
The Medical Journal of Australia, Volume 216, pp 199-201;

Sabrina Jungnick, Bernhard Hobmaier, Lena Mautner, Mona Hoyos, Maren Haase, Armin Baiker, Heidi Lahne, Ute Eberle, Clara Wimmer, Sabrina Hepner, et al.
SARS-CoV-2 variants of concern (VOC) should not escape molecular surveillance. We investigated if SARS-CoV-2 rapid antigen tests (RATs) could detect B.1.1.7 and B.1.351 VOCs in certain laboratory conditions. Infectious cell culture supernatants containing B.1.1.7, B.1.351 or non-VOC SARS-CoV-2 were respectively diluted both in DMEM and saliva. Dilutions were analysed with Roche, Siemens, Abbott, nal von minden and RapiGEN RATs. While further studies with appropriate real-life clinical samples are warranted, all RATs detected B.1.1.7 and B.1.351, generally comparable to non-VOC strain.
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