Evidence of early circulation of SARS-CoV-2 in France: findings from the population-based "CONSTANCES" cohort

Use of a risk assessment tool to determine the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is contentious. Most studies have focused on a zoonotic origin, but definitive evidence such as an intermediary animal host is lacking. We used an established risk analysis tool for differentiating natural and unnatural epidemics, the modified Grunow-Finke assessment tool (mGFT) to study the origin of SARS-COV-2. The mGFT scores 11 criteria to provide a likelihood of natural or unnatural origin. Using published literature and publicly available sources of information, we applied the mGFT to the origin of SARS-CoV-2. The mGFT scored 41/60 points (68%), with high inter-rater reliability (100%), indicating a greater likelihood of an unnatural than natural origin of SARS-CoV-2. This risk assessment cannot prove the origin of SARS-CoV-2 but shows that the possibility of a laboratory origin cannot be easily dismissed.

Early detection of emerging infectious diseases - implications for vaccine development

Vast quantities of open-source data from news reports, social media and other sources can be harnessed using artificial intelligence and machine learning, and utilised to generate valid early warning signals of emerging epidemics. Early warning signals from open-source data are not a replacement for traditional, validated disease surveillance, but provide a trigger for earlier investigation and diagnostics. This may yield earlier pathogen characterisation and genomic data, which can enable earlier vaccine development or deployment of vaccines. Early warning also provides a more feasible prospect of stamping out epidemics before they spread. There are several of such systems currently, but they are not used widely in public health practice, and only some are publicly available. Routine and widespread use of open-source intelligence, as well as training and capacity building in digital surveillance, will improve pandemic preparedness and early response capability.

Emergence of SARS and COVID-19 and preparedness for the next emerging disease X

Severe acute respiratory syndrome (SARS) and Coronavirus disease 2019 (COVID-19) are two human Coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.

Emergency department CT examinations demonstrate no evidence of early viral circulation at the start of the COVID-19 pandemic-a multicentre epidemiological study

BACKGROUND

Biological studies suggested that the COVID-19 outbreak in France occurred before the first official diagnosis on January 24, 2020. We investigated this controversial topic using a large collection of chest CTs performed throughout French emergency departments within 6 months before the 1st lockdown.

RESULTS

Overall, 49,311 consecutive patients (median age: 60 years, 23,636/49,311 [47.9%] women) with available chest CT images and reports from 61 emergency departments between September 1, 2020, and March 16, 2020 (day before the 1st French lockdown), were retrospectively included in this multicentre study. In the macroscopic analysis of reports automatically (labelled for presence of ground glass opacities [GGOs], reticulations, and bilateral and subpleural abnormalities), we found a significant breakpoint on February 17, 2020, for the weekly time series with 1, 2 and ≥ 3 of these 4 radiological features, with 146/49,311 (0.3%) patients showing bilateral abnormalities and ground glass opacities (GGOs) from that day. According to radiologists, 22/146 (15.1%) CT images showed typical characteristics of COVID-19, including 4/146 (2.7%) before February 2020. According to hospital records, one patient remained without microbial diagnosis, two patients had proven influenza A and one patient had concomitant influenza A and mycoplasma infection.

CONCLUSION

These results suggest that SARS-CoV-2 was not circulating in the areas covered by the 61 emergency departments involved in our study before the official beginning of the COVID-19 outbreak in France. In emergency patients, the strong resemblance among mycoplasma, influenza A and SARS-CoV-2 lung infections on chest CT and the nonspecificity of CT patterns in low prevalence periods is stressed.

CRITICAL RELEVANCE STATEMENT

We proposed here an innovative approach to revisit a controversial 'real' start of the COVID-19 pandemic in France based on (1) a population-level approach combining text mining, time series analysis and an epidemiological dataset and (2) a patient-level approach with careful retrospective reading of chest CT scans complemented by analysis of samples performed contemporarily to the chest CT. We showed no evidence that SARS-CoV-2 was actively circulating in France before February 2020.

Impact of the coronavirus disease 2019 pandemic on sarcoma management in France: a 2019 and 2020 comparison

Background

The coronavirus disease 2019 (COVID-19) pandemic was an unprecedented shock to the healthcare systems, and its consequences on managing rare cancers are unknown. We investigated COVID-19's impact on the activity of sarcoma-labeled networks by comparing key indicators in 2019-2020 (before and during the pandemic, respectively).

Methods

We compared the incidence of limb and trunk soft tissue sarcomas, surgery rate, surgery center, surgery quality, and surgery delays nationally and in various regions, focusing on the three most severely affected regions.

Findings

In this study, sarcoma incidence did not decrease, and the tumor and patient characteristics were similar in both years. The number of patients who underwent surgery in the labeled centers increased significantly (63% versus 57%, p = 0.015), the rate of R0 resection increased (55% versus 47%, p = 0.004), and the rate of re-excision decreased (12% versus 21%, p < 0.0001). In the univariate analysis, the time to surgery was similar in both years. Cox regression analysis revealed that the factors associated with a longer time to surgery were age > 70 years (p = 0.003), retroperitoneal location (p > 0.001), tumor size (p < 0.001), deep tumors (p < 0.001), and regions (p < 0.001). However, we have observed an increase in the time before surgery in the regions most stroked by the COVID-19 pandemic.

Interpretation

The model of the labeled center network for managing rare tumors was resilient. Paradoxically, the quality indicators improved during the pandemic due to the direct referral of patients with sarcomas to the labeled centers.

Summary

This study shows that a nationwide network organization has made it possible to maintain care for these rare tumors during the pandemic.

Delay-differential SEIR modeling for improved modelling of infection dynamics

SEIR (Susceptible-Exposed-Infected-Recovered) approach is a classic modeling method that is frequently used to study infectious diseases. However, in the vast majority of such models transitions from one population group to another are described using the mass-action law. That causes inability to reproduce observable dynamics of an infection such as the incubation period or progression of the disease's symptoms. In this paper, we propose a new approach to simulate the epidemic dynamics based on a system of differential equations with time delays and instant transitions to approximate durations of transition processes more correctly and make model parameters more clear. The suggested approach can be applied not only to Covid-19 but also to the study of other infectious diseases. We utilized it in the development of the delay-based model of the COVID-19 pandemic in Germany and France. The model takes into account testing of different population groups, symptoms progression from mild to critical, vaccination, duration of protective immunity and new virus strains. The stringency index was used as a generalized characteristic of the non-pharmaceutical government interventions in corresponding countries to contain the virus spread. The parameter identifiability analysis demonstrated that the presented modeling approach enables to significantly reduce the number of parameters and make them more identifiable. Both models are publicly available.

A Pictorial Essay Describing the CT Imaging Features of COVID-19 Cases throughout the Pandemic with a Special Focus on Lung Manifestations and Extrapulmonary Vascular Abdominal Complications

With the Omicron wave, SARS-CoV-2 infections improved, with less lung involvement and few cases of severe manifestations. In this pictorial review, there is a summary of the pathogenesis with particular focus on the interaction of the immune system and gut and lung axis in both pulmonary and extrapulmonary manifestations of COVID-19 and the computed tomography (CT) imaging features of COVID-19 pneumonia from the beginning of the pandemic, describing the typical features of COVID-19 pneumonia following the Delta variant and the atypical features appearing during the Omicron wave. There is also an outline of the typical features of COVID-19 pneumonia in cases of breakthrough infection, including secondary lung complications such as acute respiratory distress disease (ARDS), pneumomediastinum, pneumothorax, and lung pulmonary thromboembolism, which were more frequent during the first waves of the pandemic. Finally, there is a description of vascular extrapulmonary complications, including both ischemic and hemorrhagic abdominal complications.

Serological investigation of SARS-CoV-2 infection in patients with suspect measles, 2017-2022

BACKGROUND

Several studies suggested that SARS-CoV-2 was already spreading worldwide during the last months of 2019 before the first outbreak was detected in Wuhan, China. Lombardy (Northern Italy) was the first European region with sustained SARS-CoV-2 transmission and recent investigations detected SARS-CoV-2-RNA-positive patients in Lombardy since late 2019.

METHODS

We tested for anti-SARS-CoV-2 IgG all serum samples available in our laboratory (N = 235, collected between March 2017 and March 2022) that we received within the framework of measles/rubella surveillance from measles and rubella virus-negative patients.

RESULTS

Thirteen of 235 samples (5.5%) were IgG-positive. The positivity rate increased starting in 2019 and was significantly different from the expected false positive rate from 2019 onwards. Additionally, in 2019 the percentage of IgG-positive patients was significantly lower among SARS-CoV-2 RNA-negative patients (3/92) compared to SARS-CoV-2 RNA-positive patients (2/7, p = 0.04). The highest percentage of IgG positivity in the pre-pandemic period was recorded during the second half of 2019. This coincided with an increase in negativity for measles and a widening of the peak of the number of measles discarded cases per 100,000 inhabitants, indicating a higher-than-normal number of measles-negative patients experiencing fever and rash. This also coincided with the first patient positive for SARS-CoV-2 RNA (September 12th, 2019); this patient was also positive for anti-SARS-CoV-2 IgG and IgM.

CONCLUSIONS

Although the number of samples was low and one cannot conclusively establish that the virus started circulating in Lombardy around September 2019, our findings should stimulate similar research investigating the possibility of undetected SARS-CoV-2 pre-pandemic circulation.

The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is regarded as a threat because it spreads quickly across the world without requiring a passport or establishing an identity. This tiny virus has wreaked havoc on people's lives, killed people, and created psychological problems all over the world. The viral spike protein (S) significantly contributes to host cell entry, and mutations associated with it, particularly in the receptor-binding protein (RBD), either facilitate the escape of virus from neutralizing antibodies or enhance its transmission by increasing the affinity for cell entry receptor, angiotensin-converting enzyme 2 (ACE2). The initial variants identified in Brazil, South Africa, and the UK have spread to various countries. On the other hand, new variants are being detected in India and the USA. The viral genome and proteome were applied for molecular detection techniques, and nanotechnology particles and materials were utilized in protection and prevention strategies. Consequently, the SARS-CoV-2 pandemic has resulted in extraordinary scientific community efforts to develop detection methods, diagnosis tools, and effective antiviral drugs and vaccines, where prevailing academic, governmental, and industrial institutions and organizations continue to engage themselves in large-scale screening of existing drugs, both in vitro and in vivo. In addition, COVID-19 pointed on the possible solutions for the environmental pollution globe problem. Therefore, this review aims to address SARS-CoV-2, its transmission, where it can be found, why it is severe in some people, how it can be stopped, its diagnosis and detection techniques, and its relationship with the environment.

Can Some Viral Respiratory Infections Observed Before the Pandemic Announcement Be Related to SARS-CoV-2?

OBJECTIVE

There have been doubts that SARS-CoV-2 has been circulating before the first case was announced. The aim of this study was to evaluate the possibility of COVID-19 in some cases diagnosed to be viral respiratory tract infection in the pre-pandemic period in our center.

MATERIAL AND METHODS

Patients who were admitted to our hospital's pulmonary diseases, infectious diseases, and intensive care clinics with the diagnosis of viral respiratory system infection within a 6-month period between October 2019 and March 12, 2020, were screened. Around 248 archived respiratory samples from these patients were analyzed for SARS-CoV-2 ribonucleic acid by real-timequantitative polymerase chain reaction. The clinical, laboratory, and radiological data of the patients were evaluated.

RESULTS

The mean age of the study group was 47.5 (18-89 years); 103 (41.5%) were female and 145 (58.4%) were male. The most common presenting symptoms were cough in 51.6% (n = 128), fever in 42.7% (n = 106), and sputum in 27.0% (n = 67). Sixty-nine percent (n = 172) of the patients were pre-diagnosed to have upper respiratory tract infection and 22.0% (n = 55) had pneumonia, one-third of the patients (n = 84, 33.8%) were followed in the service. Respiratory viruses other than SARS-CoV-2 were detected in 123 (49.6%) patients. Influenza virus (31.9%), rhinovirus (10.5%), and human metapneumovirus (6.5%) were the most common pathogens, while none of the samples were positive for SARS-CoV-2 RNA. Findings that could be significant for COVID-19 pneumonia were detected in the thorax computed tomography of 7 cases.

CONCLUSION

The negative SARS-CoV-2 real-time-quantitative polymerase chain reaction results in the respiratory samples of the cases followed up in our hospital for viral pneumonia during the pre-pandemic period support that there was no COVID-19 among our cases during the period in question. However, if clinical suspicion arises, both SARS and non-SARS respiratory viral pathogens should be considered for differential diagnosis.

Prospective Metabolomic Studies in Precision Medicine: The AKRIBEA Project

For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship with diabetes), ultimately offering incomplete diagnostic value. Nowadays, precision medicine emerges as an option to improve the prevention and/or treatment of numerous pathologies, focusing on the molecular mechanisms, acting in a patient-specific dimension, and leveraging multiple contributing factors such as genetic, environmental, or lifestyle. Metabolomics grasps the required subcellular complexity while being sensitive to all these factors, which results in a most suitable technique for precision medicine. The aim of this chapter is to describe how NMR-based metabolomics can be integrated in the design of a precision medicine strategy, using the Precision Medicine Initiative of the Basque Country (the AKRIBEA project) as a case study. To that end, we will illustrate the procedures to be followed when conducting an NMR-based metabolomics study with a large cohort of individuals, emphasizing the critical points. The chapter will conclude with the discussion of some relevant biomedical applications.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy

As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.

Tracing the origin of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): A systematic review and narrative synthesis

The aim of the study was to trace and understand the origin of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through various available literatures and accessible databases. Although the world enters the third year of the coronavirus disease 2019 pandemic, health and socioeconomic impacts continue to mount, the origin and mechanisms of spill-over of the SARS-CoV-2 into humans remain elusive. Therefore, a systematic review of the literature was performed that showcased the integrated information obtained through manual searches, digital databases (PubMed, CINAHL, and MEDLINE) searches, and searches from legitimate publications (1966-2022), followed by meta-analysis. Our systematic analysis data proposed three postulated hypotheses concerning the origin of the SARS-CoV-2, which include zoonotic origin (Z), laboratory origin (L), and obscure origin (O). Despite the fact that the zoonotic origin for SARS-CoV-2 has not been conclusively identified to date, our data suggest a zoonotic origin, in contrast to some alternative concepts, including the probability of a laboratory incident or leak. Our data exhibit that zoonotic origin (Z) has higher evidence-based support as compared to laboratory origin (L). Importantly, based on all the studies included, we generated the forest plot with 95% confidence intervals (CIs) of the risk ratio estimates. Our meta-analysis further supports the zoonotic origin of SARS/SARS-CoV-2 in the included studies.

A serological investigation in Southern Italy: was SARS-CoV-2 circulating in late 2019?

In March 2020, the first pandemic caused by a coronavirus was declared by the World Health Organization. Italy was one of the first and most severely affected countries, particularly the northern part of the country. The latest evidence suggests that the virus could have been circulating, at least in Italy, before the first autochthonous SARS-COV-2 case was detected in February 2020. The present study aimed to investigate the presence of antibodies against SARS-CoV-2 in human serum samples collected in the last months of 2019 (September–December) in the Apulia region, Southern Italy. Eight of 455 samples tested proved positive on in-house receptor-binding-domain-based ELISA. Given the month of collection of the positive samples, these findings may indicate early circulation of SARS-CoV-2 in Apulia region in the autumn of 2019. However, it cannot be completely ruled out that the observed sero-reactivity could be an unknown antigen specificity in another virus to which subjects were exposed containing an epitope adventitiously cross-reactive with an epitope of SARS-CoV-2.

The origins of COVID-19 pandemic: A brief overview

The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.

Covid-19: Early Cases and Disease Spread

The emergence and global spread of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is critical to understanding how to prevent or control a future viral pandemic. We review the tools used for this retrospective search, their limits, and results obtained from China, France, Italy and the USA. We examine possible scenarios for the emergence of SARS-CoV-2 in the human population. We consider the Chinese city of Wuhan where the first cases of atypical pneumonia were attributed to SARS-CoV-2 and from where the disease spread worldwide. Possible superspreading events include the Wuhan-based 7^th Military World Games on October 18–27, 2019 and the Chinese New Year holidays from January 25 to February 2, 2020. Several clues point to an early regional circulation of SARS-CoV-2 in northern Italy (Lombardi) as soon as September/October 2019 and in France in November/December 2019, if not before. With the goal of preventing future pandemics, we call for additional retrospective studies designed to trace the origin of SARS-CoV-2.

Association between COVID-19 infection and work exposure assessed by the Mat-O-Covid job exposure matrix in the CONSTANCES cohort

OBJECTIVES

The COVID-19 pandemic has brought to light a new occupational health threat. We aimed to evaluate the association between COVID-19 infection and work exposure to SARS-CoV-2 assessed by a job-exposure matrix (JEM), in a large population cohort. We also estimated the population-attributable fraction among exposed subjects.

METHODS

We used the SAPRIS-SERO sample of the CONSTANCES cohort, limited to subjects actively working, and with a job code available and a questionnaire on extra work activities. The following outcomes were assessed: COVID-19 diagnosis was made by a physician; a seropositivity to the ELISA-S test ('serology strict') and ELISA-S test intermediate with positive ELISA-NP or a positive neutralising antibodies SN ('serology large'). Job exposure was assessed using Mat-O-Covid, an expert-based JEM with an Index used as a continuous variable and a threshold at 13/1000.

RESULTS

The sample included 18 999 subjects with 389 different jobs, 47.7% were men with a mean age of 46.2 years (±9.2 years). The Mat-O-Covid index taken as a continuous variable or with a threshold greater than 13/1000 was associated with all the outcomes in bivariable and multivariable logistic models. ORs were between 1.30 and 1.58, and proportion of COVID-19 attributable to work among exposed participants was between 20% and 40%.

DISCUSSION

Using the Mat-O-Covid JEM applied to a large population, we found a significant association between work exposure to SARS-CoV-2 and COVID-19 infection, though the estimation of attributable fraction among exposed people remained low to moderate. Further studies during other exposed periods and with other methods are necessary.

Wars and sweets: microbes, medicines and other moderns in and beyond the(ir) antibiotic era

Once upon a time, many of us moderns dreamt that our future was bright, squeaky clean, germ-free. Now, we increasingly fear that bacterial resistance movements and hordes of viruses are cancelling our medicated performances, and threatening life as many of us have come to know it. In order for our modern antibiotic theatre of war to go on, we pray for salvation through our intensive surveillance of microbes, crusades for more rational antibiotic wars, increased recruitment of resistance fighters and development of antibiotic armaments through greater investment in our medical-industrial-war complex. But not all of us are in favour of the promise of perpetual antimicrobial wars, no matter how careful or rational their proponents aspire to be. An increasing vocal and diverse opposition has amassed in academic journals, newspapers and other fields of practice denouncing medicalisation and pharamceuticalisation of our daily lives, as well as our modern medicine as overly militaristic. In this paper, rather than simply rehearsing many of these well-made and meaning debates to convert you to yet another cause, I enrol them in redescriptions of our modern medical performances in the hope of awakening you from your aseptic dream. What follows is my invitation for you to re-enact our mythic antibiotic era in all its martial g(l)ory. I promise that it will bring you no physically harm, yet I can't promise it will leave your beliefs unscathed, as you follow its playful redescription of how our objective scientific descriptions, clinical prescriptions, economic strategies, political mandates and military orders, not to mention our warspeak, have always been deeply entangled with triumphs and devastations of The(ir) Great anti-Microbial Wars (aka our antibiotic era).

Evidence of SARS-CoV-2 Antibodies and RNA on Autopsy Cases in the Pre-Pandemic Period in Milan (Italy)

In this study, we analyzed blood samples obtained from 169 cadavers subjected to an autopsy from 1 October 2019 to 27 March 2020. The presence of anti-severe acute respiratory syndrome coronavirus 2 (anti-SARS-CoV-2) antibodies was searched by lateral flow immunochromatographic assay (LFIA) and ELISA tests and the SARS-CoV-2 RNA was tested in blood and available lung tissues by real-time PCR (RT-PCR) and droplet digital PCR (ddPCR). Five cases resulted in positives at the serological screening for anti-SARS-CoV-2. Three results were weakly positive for IgM while only one showed strong reactivity for IgG antibodies. The fifth subject (who died in December 2019) resulted positive for the ELISA test. The detection of SARS-CoV-2 RNA resulted in positive only in the blood and lung tissues of such cases. These data suggest that cadaveric blood may be a suitable substrate for the assessment of SARS-CoV-2 infection; moreover, they extend the observations of sporadic cases of SARS-CoV-2 infection in North Italy prior to the first confirmed cases.

Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?

Two years after the start of the COVID-19 pandemic, key questions about the emergence of its aetiological agent (SARS-CoV-2) remain a matter of considerable debate. Identifying when SARS-CoV-2 began spreading among people is one of those questions. Although the current canonically accepted timeline hypothesises viral emergence in Wuhan, China, in November or December 2019, a growing body of diverse studies provides evidence that the virus may have been spreading worldwide weeks, or even months, prior to that time. However, the hypothesis of earlier SARS-CoV-2 circulation is often dismissed with prejudicial scepticism and experimental studies pointing to early origins are frequently and speculatively attributed to false-positive tests. In this paper, we critically review current evidence that SARS-CoV-2 had been circulating prior to December of 2019, and emphasise how, despite some scientific limitations, this hypothesis should no longer be ignored and considered sufficient to warrant further larger-scale studies to determine its veracity.

Nationwide increases in anti-SARS-CoV-2 IgG antibodies between October 2020 and March 2021 in the unvaccinated Czech population

Background

The aim of the nationwide prospective seroconversion (PROSECO) study was to investigate the dynamics of anti-SARS-CoV-2 IgG antibodies in the Czech population. Here we report on baseline prevalence from that study.

Methods

The study included the first 30,054 persons who provided a blood sample between October 2020 and March 2021. Seroprevalence was compared between calendar periods, previous RT-PCR results and other factors.

Results

The data show a large increase in seropositivity over time, from 28% in October/November 2020 to 43% in December 2020/January 2021 to 51% in February/March 2021. These trends were consistent with government data on cumulative viral antigenic prevalence in the population captured by PCR testing - although the seroprevalence rates established in this study were considerably higher. There were only minor differences in seropositivity between sexes, age groups and BMI categories, and results were similar between test providing laboratories. Seropositivity was substantially higher among persons with history of symptoms (76% vs. 34%). At least one third of all seropositive participants had no history of symptoms, and 28% of participants with antibodies against SARS-CoV-2 never underwent PCR testing.

Conclusions

Our data confirm the rapidly increasing prevalence in the Czech population during the rising pandemic wave prior to the beginning of vaccination. The difference between our results on seroprevalence and PCR testing suggests that antibody response provides a better marker of past infection than the routine testing program.

Early Circulation of SARS-CoV-2, Congo, 2020

To determine when severe acute respiratory syndrome coronavirus 2 arrived in Congo, we retrospectively antibody tested 937 blood samples collected during September 2019–February 2020. Seropositivity significantly increased from 1% in December 2019 to 5.3% in February 2020, before the first officially reported case in March 2020, suggesting unexpected early virus circulation.

Early Evidence of Circulating SARS-CoV-2 in Unvaccinated and Vaccinated Measles Patients, September 2019–February 2020

Background

The global emergence of coronavirus disease 2019 (COVID-19) has challenged healthcare and rapidly spread over the globe. Early detection of new infections is crucial in the control of emerging diseases. Evidence of early recorded COVID-19 cases outside China has been documented in various countries. In this study, we aimed to identify the time of SARS-CoV-2 infection circulation by retrospectively analyzing sera of measles patients, weeks before the reported first COVID-19 cases in Angola.

Materials and Methods

We examined the humoral response against SARS-CoV-2 by using an enzyme-linked immunosorbent assay (ELISA)-based assay on a combined two-step sandwich enzyme immunoassay method. In total, we received 568 study patients with blood specimens collected from 23 September 2019 to 28 February 2020, 442 sera samples that met the criteria of the study were withdrawn and selected from the overall 568 received samples. In this study, we considered seropositives, patients who tested positive for SARS-CoV-2 immunoglobulin G (IgG) and M (IgM) antibodies with the index value >1.

Results

Of the 442 sera samples that met the criteria of the study, 204 were measles seropositive. Forty out of 204 were confirmed reactive to SARS-CoV-2 viral proteins using IgG and IgM more than 2 weeks before the first reported case in Angola. The humoral response analysis showed significant differences (p = 0.01) between the IgG and IgM indexes in the unvaccinated measles patients. Similarly, a significant difference (p = 0.001) was seen between the IgG and IgM indexes in the vaccinated measles patients.

Conclusion

Here, using the humoral response analysis, we report the identification of early circulation SARS-CoV-2 infection weeks before the first recognized cases in the Republic of Angola.

Revisiting Metchnikoff's work in light of the COVID-19 pandemic

Revisiting Metchnikoff's work in light of the COVID-19 pandemic illustrates how much this amazing scientist was a polymath, and one could speculate how much he would have been fascinated and most interested in following the course of the pandemic. Since he coined the word "gerontology", he would have been intrigued by the high mortality among the elderly, and by the concepts of immunosenescence and inflammaging that characterize the SARS-CoV-2 infection. While Metchnikoff's work is mainly associated with the discovery of the phagocytes and the birth of cellular innate immunity, he regularly invited his closest collaborators to investigate humoral immunity, and it was in his laboratory that Jules Bordet made his major discovery of the complement system. While Metchnikoff and his team investigated many infectious diseases, he also contributed to studies linked to vaccination, such as those on typhoid fever performed in chimpanzees, illustrating that non-human primates can provide animal models which are potentially helpful for understanding the pathophysiology of the COVID-19 virus. In the present review, we illustrate how much his own work and the investigations of his trainees were pertinent to this new disease.

Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France)

Introduction: Aside from the reverse transcription-PCR tests for the diagnosis of the COVID-19 in routine clinical care and population-scale screening, there is an urgent need to increase the number and the efficiency for full viral genome sequencing to detect the variants of SARS-CoV-2. SARS-CoV-2 variants assessment should be easily, rapidly, and routinely available in any academic hospital.

Materials and Methods: SARS-CoV-2 full genome sequencing was performed retrospectively in a single laboratory (LPCE, Louis Pasteur Hospital, Nice, France) in 103 SARS-CoV-2 positive individuals. An automated workflow used the Ion Ampliseq SARS-CoV-2 panel on the Genexus Sequencer. The analyses were made from nasopharyngeal swab (NSP) (n = 64) and/or saliva (n = 39) samples. All samples were collected in the metropolitan area of the Nice city (France) from September 2020 to March 2021.

Results: The mean turnaround time between RNA extraction and result reports was 30 h for each run of 15 samples. A strong correlation was noted for the results obtained between NSP and saliva paired samples, regardless of low viral load and high (>28) Ct values. After repeated sequencing runs, complete failure of obtaining a valid sequencing result was observed in 4% of samples. Besides the European strain (B.1.160), various variants were identified, including one variant of concern (B.1.1.7), and different variants under monitoring.

Discussion: Our data highlight the current feasibility of developing the SARS-CoV-2 next-generation sequencing approach in a single hospital center. Moreover, these data showed that using the Ion Ampliseq SARS-CoV-2 Assay, the SARS-CoV-2 genome sequencing is rapid and efficient not only in NSP but also in saliva samples with a low viral load. The advantages and limitations of this setup are discussed.

Nationwide increases in anti-SARS-CoV-2 IgG antibodies between October 2020 and March 2021 in the unvaccinated Czech population

BACKGROUND

The aim of the nationwide prospective seroconversion (PROSECO) study was to investigate the dynamics of anti-SARS-CoV-2 IgG antibodies in the Czech population. Here we report on baseline prevalence from that study.

METHODS

The study included the first 30,054 persons who provided a blood sample between October 2020 and March 2021. Seroprevalence was compared between calendar periods, previous RT-PCR results and other factors.

RESULTS

The data show a large increase in seropositivity over time, from 28% in October/November 2020 to 43% in December 2020/January 2021 to 51% in February/March 2021. These trends were consistent with government data on cumulative viral antigenic prevalence in the population captured by PCR testing - although the seroprevalence rates established in this study were considerably higher. There were only minor differences in seropositivity between sexes, age groups and BMI categories, and results were similar between test providing laboratories. Seropositivity was substantially higher among persons with history of symptoms (76% vs. 34%). At least one third of all seropositive participants had no history of symptoms, and 28% of participants with antibodies against SARS-CoV-2 never underwent PCR testing.

CONCLUSIONS

Our data confirm the rapidly increasing prevalence in the Czech population during the rising pandemic wave prior to the beginning of vaccination. The difference between our results on seroprevalence and PCR testing suggests that antibody response provides a better marker of past infection than the routine testing program.

Outcomes and risk factors with COVID-19 or influenza in hospitalized asthma patients

BACKGROUND

At the time of the SARS-CoV-2 emergence, asthma patients were initially considered vulnerable because respiratory viruses, especially influenza, are associated with asthma exacerbations, increased risk of hospitalization and more severe disease course. We aimed to compare the asthma prevalence in patients hospitalized for COVID-19 or influenza and risk factors associated with poor prognosis with the diseases.

METHODS

This retrospective cohort study used the Paris university hospitals clinical data warehouse to identify adults hospitalized for COVID-19 (January to June 2020) or influenza (November 2017 to March 2018 for the 2017-2018 influenza period and November 2018 to March 2019 for the 2018-2019 period). Asthma patients were identified with J45 and J46 ICD-10 codes. Poor outcomes were defined as admission in intensive care or death.

RESULTS

Asthma prevalence was significantly higher among influenza than COVID-19 patients (n = 283/3 119, 9.1%, 95% CI [8.1-10.1] in 2017-2018 and n = 309/3 266, 9.5%, 95% CI [8.5-10.5] in 2018-2019 versus n = 402/9 009, 4.5%, 95% CI [4.0-4.9]). For asthma patients, 31% with COVID-19 were admitted to an intensive care unit versus 23% and 21% with influenza. Obesity was a risk factor for the 2017-2018 influenza period, smoking and heart failure for the 2018-2019 period. Among COVID-19 patients with asthma, smoking and obesity were risk factors for the severe form.

CONCLUSIONS

In this study, patients with an asthma ICD-10 code were less represented among COVID-19 patients than among influenza-infected ones. However, outcomes were poorer for COVID-19 than influenza patients, both with asthma. These data highlight the importance of protective shields and vaccination against influenza and COVID-19 in this population.

Timeline of SARS-CoV-2 Spread in Italy: Results from an Independent Serological Retesting

The massive emergence of COVID-19 cases in the first phase of pandemic within an extremely short period of time suggest that an undetected earlier circulation of SARS-CoV-2 might have occurred. Given the importance of this evidence, an independent evaluation was recommended by the World Health Organization (WHO) to test a subset of samples selected on the level of positivity in ELISA assays (positive, low positive, negative) detected in our previous study of prepandemic samples collected in Italy. SARS-CoV-2 antibodies were blindly retested by two independent centers in 29 blood samples collected in the prepandemic period in Italy, 29 samples collected one year before and 11 COVID-19 control samples. The methodologies used included IgG-RBD/IgM-RBD ELISA assays, a qualitative micro-neutralization CPE-based assay, a multiplex IgG protein array, an ELISA IgM kit (Wantai), and a plaque-reduction neutralization test. The results suggest the presence of SARS-CoV-2 antibodies in some samples collected in the prepandemic period, with the oldest samples found to be positive for IgM by both laboratories collected on 10 October 2019 (Lombardy), 11 November 2019 (Lombardy) and 5 February 2020 (Lazio), the latter with neutralizing antibodies. The detection of IgM and/or IgG binding and neutralizing antibodies was strongly dependent on the different serological assays and thresholds employed, and they were not detected in control samples collected one year before. These findings, although gathered in a small and selected set of samples, highlight the importance of harmonizing serological assays for testing the spread of the SARS-CoV-2 virus and may contribute to a better understanding of future virus dynamics.

Highlighting the impact of social relationships on the propagation of respiratory viruses using percolation theory

We develop a site-bond percolation model, called PERCOVID, in order to describe the time evolution of all epidemics propagating through respiratory tract or by skin contacts in human populations. This model is based on a network of social relationships representing interconnected households experiencing governmental non-pharmaceutical interventions. As a very first testing ground, we apply our model to the understanding of the dynamics of the COVID-19 pandemic in France from December 2019 up to December 2021. Our model shows the impact of lockdowns and curfews, as well as the influence of the progressive vaccination campaign in order to keep COVID-19 pandemic under the percolation threshold. We illustrate the role played by social interactions by comparing two typical scenarios with low or high strengths of social relationships as compared to France during the first wave in March 2020. We investigate finally the role played by the α and δ variants in the evolution of the epidemic in France till autumn 2021, paying particular attention to the essential role played by the vaccination. Our model predicts that the rise of the epidemic observed in July and August 2021 would not result in a new major epidemic wave in France.

Épidémiologie de la COVID-19, focus sur le pôle de gériatrie des hôpitaux universitaires de Strasbourg

Dans cet article, les auteurs proposent une synthèse concernant l’épidémiologie de la COVID-19, maladie responsable d’une pandémie mondiale depuis son émergence en décembre 2019. L’objectif est d’évoquer les personnes âgées, particulièrement impactées, étant donné que l’âge supérieur à 65 ans et les comorbidités sont des facteurs de risque de formes graves. En France, 90 % des décès ont touché la population âgée. Il s’agit également de faire un focus sur la situation du pôle de gériatrie des hôpitaux universitaires de Strasbourg où, lors de la première vague épidémique, la mortalité a été de 35 % en gériatrie aiguë et de 25 % en USLD. Après la survenue de 100 000 décès en France, l’espoir est grand de contrôler l’épidémie grâce à la stratégie vaccinale.

Phylogenetic reconstruction of the initial stages of the spread of the SARS-CoV-2 virus in the Eurasian and American continents by analyzing genomic data

Samples from complete genomes of SARS-CoV-2 isolated during the first wave (December 2019–July 2020) of the global COVID-19 pandemic from 21 countries (Asia, Europe, Middle East and America) around the world, were analyzed using the phylogenetic method with molecular clock dating. Results showed that the first cases of COVID-19 in the human population appeared in the period between July and November 2019 in China. The spread of the virus into other countries of the world began in the autumn of 2019. In mid-February 2020, the virus appeared in all the countries we analyzed. During this time, the global population of SARS-CoV-2 was characterized by low levels of the genetic polymorphism, making it difficult to accurately assess the pathways of infection. The rate of evolution of the coding region of the SARS-CoV-2 genome equal to 7.3 × 10⁻⁴ (5.95 × 10⁻⁴–8.68 × 10⁻⁴) nucleotide substitutions per site per year is comparable to those of other human RNA viruses (Measles morbillivirus, Rubella virus, Enterovirus C). SARS-CoV-2 was separated from its known close relative, the bat coronavirus RaTG13 of the genus Betacoronavirus, approximately 15–43 years ago (the end of the 20th century).

Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein

Background

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) is pandemic. However, the origins and global transmission pattern of SARS-CoV-2 remain largely unknown. We aimed to characterize the origination and transmission of SARS-CoV-2 based on evolutionary dynamics.

Methods

Using the full-length sequences of SARS-CoV-2 with intact geographic, demographic, and temporal information worldwide from the GISAID database during 26 December 2019 and 30 November 2020, we constructed the transmission tree to depict the evolutionary process by the R package “outbreaker”. The affinity of the mutated receptor-binding region of the spike protein to angiotensin-converting enzyme 2 (ACE2) was predicted using mCSM-PPI2 software. Viral infectivity and antigenicity were tested in ACE2-transfected HEK293T cells by pseudovirus transfection and neutralizing antibody test.

Results

From 26 December 2019 to 8 March 2020, early stage of the COVID-19 pandemic, SARS-CoV-2 strains identified worldwide were mainly composed of three clusters: the Europe-based cluster including two USA-based sub-clusters; the Asia-based cluster including isolates in China, Japan, the USA, Singapore, Australia, Malaysia, and Italy; and the USA-based cluster. The SARS-CoV-2 strains identified in the USA formed four independent clades while those identified in China formed one clade. After 8 March 2020, the clusters of SARS-CoV-2 strains tended to be independent and became “pure” in each of the major countries. Twenty-two of 60 mutations in the receptor-binding domain of the spike protein were predicted to increase the binding affinity of SARS-CoV-2 to ACE2. Of all predicted mutants, the number of E484K was the largest one with 86 585 sequences, followed by S477N with 55 442 sequences worldwide. In more than ten countries, the frequencies of the isolates with E484K and S477N increased significantly. V367F and N354D mutations increased the infectivity of SARS-CoV-2 pseudoviruses (P < 0.001). SARS-CoV-2 with V367F was more sensitive to the S1-targeting neutralizing antibody than the wild-type counterpart (P < 0.001).

Conclusions

SARS-CoV-2 strains might have originated in several countries simultaneously under certain evolutionary pressure. Travel restrictions might cause location-specific SARS-CoV-2 clustering. The SARS-CoV-2 evolution appears to facilitate its transmission via altering the affinity to ACE2 or immune evasion.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-021-00895-4.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients' records and the microbiology laboratory data to identify patients' demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

Bacterial co-infection in patients with SARS-CoV-2 in the Kingdom of Bahrain

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic presents a significant challenge to the medical profession, increasing in the presence of microbial co-infection. Bacterial and Fungal co-infections increase the risk of morbidity and mortality in patients with COVID-19.

AIM

To study the bacterial profile in patients with COVID-19 who needed admission to receive treatment in the main centres concerned with managing COVID-19 disease in the Kingdom of Bahrain.

METHODS

The study was a retrospective observational analysis of the bacterial profile and the bacterial resistance in patients with confirmed COVID-19 disease who needed admission to receive treatment in the main centres assigned to manage patients with COVID-19 disease in the Kingdom of Bahrain from February to October 2020. We used the electronic patients’ records and the microbiology laboratory data to identify patients’ demographics, clinical data, microbial profile, hospital or community-acquired, and the outcomes.

RESULTS

The study included 1380 patients admitted with confirmed COVID-19 disease during the study period. 51% were admitted from February to June, and 49% were admitted from July to October 2020, with a recurrence rate was 0.36%. There was a significant increase in bacterial and fungal co-infection in the second period compared to the first period. The most common isolated organisms were the gram-negative bacteria (mainly Klebsiella pneumoniae, Pseudomonas aeruginosa, multi-drug resistant Acinetobacter baumannii, and Escherichia coli), the gram-positive bacteria (mainly coagulase negative Staphylococci, Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus) and fungaemia (Candida galabrata, Candida tropicalis, Candida albicans, Aspergillus fumigatus, Candida parapsilosis, Aspergillus niger). The hospital-acquired infection formed 73.8%, 61.6%, 100% gram-negative, gram-positive and fungaemia. Most of the hospital-acquired infection occurred in the second period with a higher death rate than community-acquired infections.

CONCLUSION

Bacterial and fungal co-infections in patients admitted with confirmed COVID-19 disease pose higher morbidity and mortality risks than those without co-infections. We should perform every effort to minimize these risks.

COVID-19 and earlier pandemics, sepsis, and vaccines: A historical perspective

Humanity has regularly faced the threat of epidemics and pandemics over the course of history. Successful attempts to protect populations were initially made with the development of new vaccines, such as those against plague and cholera, under the leadership of the bacteriologist Waldemar Haffkine. Vaccines have led to a complete eradication of smallpox and bovine plague and a major reduction in other infectious diseases including diphtheria, typhoid fever, poliomyelitis, and Haemophilus influenzae type B meningitis. While a few coronaviruses have been identified that seasonally infect humans causing mild symptoms, the emergence of a new zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly triggered the ongoing coronavirus disease 2019 (COVID-19) as a global pandemic responsible for widespread mortality. The severe phenotypes of COVID-19 resemble a previous infectious threat that was initially designated as hospital fever and puerperal fever, presently known as sepsis. A SARS-CoV-2 infection has frequently been considered as a form of viral sepsis (owing to common features with bacterial sepsis) but is also associated with an array of specific and unique symptoms. Rapid progress in anti-SARS-CoV-2 vaccine development, in particular, the design of efficient messenger RNA (mRNA) and recombinant adenovirus vaccines, is crucial for curbing the pandemic.

The East-West Divide in Response to COVID-19

Coronavirus disease 2019 (COVID-19) deaths per million population in the countries of the West had often exceeded those in the countries of the East by factor of 100 by May 2021. In this paper, we refer to the West as represented by the United States plus the five most populous countries of Western Europe (France, Germany, Italy, Spain, and the United Kingdom), and the East as the 15 countries in East Asia and Oceania that are members of the Regional Comprehensive Economic Partnership, RCEP (Australia, Brunei, Cambodia, China, Indonesia, Japan, the Republic of Korea, Laos, Malaysia, Myanmar, New Zealand, Philippines, Singapore, Thailand, and Vietnam). This paper argues that currently available information points to the factors most responsible for the East-West divide. Warnings by early January 2020 about an atypical viral pneumonia in Wuhan, China, prompted rapid responses in many jurisdictions in East Asia. Publication of the virus's genome on 10 January 2020 provided essential information for making diagnostic tests and launching vaccine development. China's lockdown of Wuhan on 23 January 2020 provided a final, decisive signal of the danger of the new disease. By late March 2020, China had fully controlled its epidemic, and many other RCEP countries had taken early and decisive measures, including restrictions on travel, that aborted serious outcomes. Inaction during the critical month of February 2020 in the United States and most other Western countries allowed the disease to take hold and spread. In both the East and the West, stringent population-wide non-pharmaceutical interventions were widely implemented at great cost to societies, economies, and school systems. Without these measures, the outcomes could have been even worse. Most countries in the East also implemented tightly focused policies to isolate infectious individuals. Even today, most countries in the West allow infectious individuals to mingle with their families, coworkers, and communities. Much of the East-West divide plausibly results from failure in the West to implement the basic public health policies of early action and the isolation of infectious individuals. Widespread immunization in some RCEP and high-income countries will soon attenuate their outbreaks, while the slow rollout of vaccines in lower income countries is replacing the East-West divide in outcomes with a North-South one. The South is thus replacing the West as the breeding ground for more dangerous variants as exemplified by the highly contagious Delta variant, which may undermine hitherto successful control strategies in many countries.

The real seroprevalence of SARS-CoV-2 in France and its consequences for virus dynamics

The SARS-CoV-2 virus has spread world-wide since December 2019, killing more than 2.9 million of people. We have adapted a statistical model from the SIR epidemiological models to predict the spread of SARS-CoV-2 in France. Our model is based on several parameters and assumed a 4.2% seroprevalence in Occitania after the first lockdown. The recent use of serological tests to measure the effective seroprevalence of SARS-CoV-2 in the population of Occitania has led to a seroprevalence around 2.4%. This implies to review the parameters of our model to conclude at a lower than expected virus transmission rate, which may be due to infectivity varying with the patient’s symptoms or to a constraint due to an uneven population geographical distribution.

Comparative and quantitative analysis of COVID-19 epidemic interventions in Chinese provinces

A mathematical model was developed to evaluate and compare the effects and intensity of the coronavirus disease 2019 prevention and control measures in Chinese provinces. The time course of the disease with government intervention was described using a dynamic model. The estimated government intervention parameters and area difference between with and without intervention were considered as the intervention intensity and effect, respectively. The model of the disease time course without government intervention predicted that by April 30, 2020, about 3.08% of the population would have been diagnosed with coronavirus disease 2019 in China. Guangdong Province averted the most cases. Comprehensive intervention measures, in which social distancing measures may have played a greater role than isolation measures, resulted in reduced infection cases. Shanghai had the highest intervention intensity. In the context of the global coronavirus disease 2019 pandemic, the prevention and control experience of some key areas in China (such as Shanghai and Guangdong) can provide references for outbreak control in many countries.

Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom

In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV-2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea - also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger sample of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.

Analysis of the Genomic Distance Between Bat Coronavirus RaTG13 and SARS-CoV-2 Reveals Multiple Origins of COVID-19

The severe acute respiratory syndrome COVID-19 was discovered on December 31, 2019 in China. Subsequently, many COVID-19 cases were reported in many other countries. However, some positive COVID-19 samples had been reported earlier than those officially accepted by health authorities in other countries, such as France and Italy. Thus, it is of great importance to determine the place where SARS-CoV-2 was first transmitted to human. To this end, we analyze genomes of SARS-CoV-2 using k-mer natural vector method and compare the similarities of global SARS-CoV-2 genomes by a new natural metric. Because it is commonly accepted that SARS-CoV-2 is originated from bat coronavirus RaTG13, we only need to determine which SARS-CoV-2 genome sequence has the closest distance to bat coronavirus RaTG13 under our natural metric. From our analysis, SARS-CoV-2 most likely has already existed in other countries such as France, India, Netherland, England and United States before the outbreak at Wuhan, China.