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Rxivist combines biology preprints from bioRxiv and medRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 145,750 papers from 617,050 authors.

Most tweeted biology preprints, last 24 hours

in category epidemiology

*There are gaps in historical Twitter data, most notably in spring 2020. This may result in some preprints appearing with less tweets than they should.

23 results found. For more information, click each entry to expand.

1: Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
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Posted 24 May 2021

Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
39 tweets medRxiv epidemiology

Jamie Lopez Bernal, Nick Andrews, Charlotte Gower, Eileen Gallagher, Ruth Simmons, Simon Thelwall, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Colin Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay

Background: The B.1.617.2 COVID-19 variant has contributed to the surge in cases in India and has now been detected across the globe, including a notable increase in cases in the UK. We estimate the effectiveness of the BNT162b2 and ChAdOx1 COVID-19 vaccines against this variant. Methods: A test negative case control design was used to estimate the effectiveness of vaccination against symptomatic disease with both variants over the period that B.1.617.2 began circulating with cases identified based on sequencing and S-gene target status. Data on all symptomatic sequenced cases of COVID-19 in England was used to estimate the proportion of cases with B.1.617.2 compared to the predominant strain (B.1.1.7) by vaccination status. Results: Effectiveness was notably lower after 1 dose of vaccine with B.1.617.2 cases 33.5% (95%CI: 20.6 to 44.3) compared to B.1.1.7 cases 51.1% (95%CI: 47.3 to 54.7) with similar results for both vaccines. With BNT162b2 2 dose effectiveness reduced from 93.4% (95%CI: 90.4 to 95.5) with B.1.1.7 to 87.9% (95%CI: 78.2 to 93.2) with B.1.617.2. With ChAdOx1 2 dose effectiveness reduced from 66.1% (95% CI: 54.0 to 75.0) with B.1.1.7 to 59.8% (95%CI: 28.9 to 77.3) with B.1.617.2. Sequenced cases detected after 1 or 2 doses of vaccination had a higher odds of infection with B.1.617.2 compared to unvaccinated cases (OR 1.40; 95%CI: 1.13-1.75). Conclusions: After 2 doses of either vaccine there were only modest differences in vaccine effectiveness with the B.1.617.2 variant. Absolute differences in vaccine effectiveness were more marked with dose 1. This would support maximising vaccine uptake with two doses among vulnerable groups.

2: Rapid spread of the SARS-CoV-2 δ variant in the area of Paris (France) in June 2021
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Posted 20 Jun 2021

Rapid spread of the SARS-CoV-2 δ variant in the area of Paris (France) in June 2021
15 tweets medRxiv epidemiology

Samuel Alizon, Stephani Haim-Boukobza, Vincent Foulongne, Laura Verdurme, Sabine Trombert-Paolantoni, Emmanue Lecorche, Benedicte Roquebert, Mircea T. Sofonea

Analysing 5,061 variant-specific tests performed on SARS-CoV-2 positive samples collected in France between 31 May and 8 June 2021 reveals a rapid growth of the {delta} variant in the Ile-de-France region. The next weeks will prove decisive but the magnitude of the estimated transmission advantage (with a 95% confidence interval between 67 and 120\%) could represent a major challenge for public health authorities.

3: Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
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Posted 24 Apr 2021

Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel
11 tweets medRxiv epidemiology

Yair Goldberg, Micha Mandel, Yonatan Woodbridge, Ronen Fluss, Ilya Novikov, Rami Yaari, Arnona Ziv, Laurence Freedman, Amit Huppert

Worldwide shortage of vaccination against SARS-CoV-2 infection while the pandemic is still uncontrolled leads many states to the dilemma whether or not to vaccinate previously infected persons. Understanding the level of protection of previous infection compared to that of vaccination is critical for policy making. We analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with COVID-19, severe disease, and death due to COVID-19. Vaccination was highly effective with overall estimated efficacy for documented infection of 92.8% (CI: [92.6, 93.0]); hospitalization 94.2% (CI: [93.6, 94.7]); severe illness 94.4% (CI: [93.6, 95.0]); and death 93.7% (CI: [92.5, 94.7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection for documented infection is 94.8% (CI: [94.4, 95.1]); hospitalization 94.1% (CI: [91.9, 95.7]); and severe illness 96.4% (CI: [92.5, 98.3]). Our results question the need to vaccinate previously-infected individuals.

4: Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study
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Posted 09 Mar 2021

Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study
8 tweets medRxiv epidemiology

Ida Rask Moustsen-Helms, Hanne-Dorthe Emborg, Jens Nielsen, Katrine Finderup Nielsen, Tyra Krause, Kaare Molbak, Karina Lauenborg Moeller, Ann-Sofie Nicole Berthelsen, Palle Valentiner-Branth

Abstract Background At the end of 2020, Denmark launched an immunization program against SARS-CoV-2. The Danish health authorities prioritized persons currently living in long-term care facilities (LTCF residents) and frontline healthcare workers (HCW) as the first receivers of vaccination. Here we present preliminary population based vaccine effectiveness (VE) estimates in these two target groups. Methods The study was designed as a retrospective registry- and population-based observational cohort study including all LTCF residents and all HWC. The outcome was a polymerase chain reaction confirmed SARS-CoV-2, and VE was estimated for different periods following first and second dose. We used Poisson and Cox regressions to estimate respectively crude and calendar time-adjusted VE for the BNT162b2 mRNA Covid-19 Vaccine from Pfizer/BioNTech with 95% confidence intervals (CI) for vaccinated versus unvaccinated. Results A total of 39,040 LTCF residents (median age at first dose; 84 years, Interquartile range (IQR): 77-90) and 331,039 HCW (median age at first dose; 47 years, IQR: 36-57) were included. Among LTCF residents, 95.2% and 86.0% received first and second dose from 27 December 2020 until 18 February 2021, for HWC the proportion was 27.8% and 24.4%. During a median follow-up of 53 days , there were 488 and 5,663 confirmed SARS-CoV-2 cases in the unvaccinated groups, whereas there were 57 and 52 in LTCF residents and HCW within the first 7 days after the second dose and 27 and 10 cases beyond seven days of second dose. No protective effect was observed for LTCF residents after first dose. In HCW, VE was 17% (95% CI; 4-28) in the > 14 days after first dose (before second dose). Furthermore, the VE in LTCF residents at day 0-7 of second dose was 52% (95% CI; 27-69) and 46% (95% CI; 28-59) in HCW. Beyond seven days of second dose, VE increased to 64% (95% CI; 14-84) and 90% (95% CI; 82-95) in the two groups, respectively. Conclusion The results were promising regarding the VE both within and beyond seven days of second vaccination with the BNT162b2 mRNA Covid-19 Vaccine currently used in many countries to help mitigate the global SARS-CoV-2 pandemic. Impact of the research: So far, observational studies of the real-word effectiveness of the mRNA Vaccine BNT162b2 has been limited to the period after the administration of the first dose. This is the first report to date to present vaccine effectiveness (VE) estimates after the second BNT162b2 mRNA Covid-19 Vaccine. We estimated a VE of 52% and 46% in LTCF residents and HCW within seven days, which increased to 64% and 90% in the two groups respectively beyond seven days of immunization. These findings supports maintaining a two-dose schedule of the BNT162b2 mRNA Covid-19 Vaccine.

5: Evidence for treatment with estradiol for women with SARS-CoV-2 infection
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Posted 24 Aug 2020

Evidence for treatment with estradiol for women with SARS-CoV-2 infection
5 tweets medRxiv epidemiology

Ute Seeland, Flaminia Coluzzi, Maurizio Simmaco, Cameron Mura, Philip E. Bourne, Max Heiland, Robert Preissner, Saskia Preissner

BACKGROUND Given that an individual's age and gender are strongly predictive of COVID-19 outcomes, do such factors imply anything about preferable therapeutic options? METHODS An analysis of electronic health records for a large (68,466-case), international COVID-19 cohort, in five-year age strata, revealed age-dependent sex differences. In particular, we surveyed the effects of systemic hormone administration in women. The primary outcome for estradiol therapy was death. Odds Ratios (ORs) and Kaplan-Meier survival curves were analyzed for 37,086 COVID-19 women in two age groups: pre- (15-49 years) and post-menopausal (>50 years). RESULTS The incidence of SARS-CoV-2 infection is higher in women than men (about +15%) and, in contrast, the fatality rate is higher in men (about +50%). Interestingly, the relationships between these quantities are also linked to age. Pre-adolescent girls had the same risk of infection and fatality rate as boys. Adult premenopausal women had a significantly higher risk of infection than men in the same five-year age stratum (about 16,000 vs. 12,000 cases). This ratio changed again in postmenopausal women, with infection susceptibility converging with men. While fatality rates increased continuously with age for both sexes, at 50 years there was a steeper increase for men. Thus far, these types of intricacies have been largely neglected. Because the hormone 17{beta}-estradiol has a positive effect on expression of the human ACE2 protein--which plays an essential role for SARS-CoV-2 cellular entry--propensity score matching was performed for the women's sub-cohort, comparing users versus non-users of estradiol. This retrospective study of hormone therapy in female COVID-19 patients shows that the fatality risk for women >50 yrs receiving estradiol therapy (user group) is reduced by more than 50%; the OR was 0.33, 95 % CI [0.18, 0.62] and the Hazard Ratio was 0.29, 95% CI [0.11,0.76]. For younger, pre-menopausal women (15-49 yrs), the risk of COVID-19 fatality is the same irrespective of estradiol treatment, probably because of higher endogenous estradiol levels. CONCLUSIONS As of this writing, still no effective drug treatment is available for COVID-19; since estradiol shows such a strong improvement regarding fatality in COVID-19, we suggest prospective studies on the potentially more broadly protective roles of this naturally occurring hormone.

6: SARS-CoV-2 reinfection in a cohort of 43,000 antibody-positive individuals followed for up to 35 weeks
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Posted 15 Jan 2021

SARS-CoV-2 reinfection in a cohort of 43,000 antibody-positive individuals followed for up to 35 weeks
4 tweets medRxiv epidemiology

Laith J Abu-Raddad, Hiam Chemaitelly, Peter J Coyle, Joel A Malek, Ayeda A Ahmed, Yasmin A. Mohamoud, Shameem Younuskunju, Houssein H. Ayoub, Zaina Al Kanaani, Einas Al Kuwari, Adeel A Butt, Andrew Jeremijenko, Anvar Hassan Kaleeckal, Ali Nizar Latif, Riyazuddin Mohammad Shaik, Hanan F. Abdul Rahim, Gheyath K. Nasrallah, HADI M. YASSINE, Mohamed G. Al Kuwari, Hamad Eid Al Romaihi, Mohamed H. Al-Thani, Abdullatif Al Khal, Roberto Bertollini

Background: Reinfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been documented, raising public health concerns. Risk and incidence rate of SARS-CoV-2 reinfection were assessed in a large cohort of antibody-positive persons in Qatar. Methods: All SARS-CoV-2 antibody-positive persons with a PCR-positive swab [≥]14 days after the first-positive antibody test were individually investigated for evidence of reinfection. Viral genome sequencing was conducted for paired viral specimens to confirm reinfection. Incidence of reinfection was compared to incidence of infection in the complement cohort of those antibody-negative. Results: Among 43,044 anti-SARS-CoV-2 positive persons who were followed for a median of 16.3 weeks (range: 0-34.6), 314 individuals (0.7%) had at least one PCR positive swab [≥]14 days after the first-positive antibody test. Of these individuals, 129 (41.1%) had supporting epidemiological evidence for reinfection. Reinfection was next investigated using viral genome sequencing. Applying the viral-genome-sequencing confirmation rate, the risk of reinfection was estimated at 0.10% (95% CI: 0.08-0.11%). The incidence rate of reinfection was estimated at 0.66 per 10,000 person-weeks (95% CI: 0.56-0.78). Incidence rate of reinfection versus month of follow-up did not show any evidence of waning of immunity for over seven months of follow-up. Meanwhile, in the complement cohort of 149,923 antibody-negative persons followed for a median of 17.0 weeks (range: 0-45.6), risk of infection was estimated at 2.15% (95% CI: 2.08-2.22%) and incidence rate of infection was estimated at 13.69 per 10,000 person-weeks (95% CI: 13.22-14.14). Efficacy of natural infection against reinfection was estimated at 95.2% (95% CI: 94.1-96.0%). Reinfections were less severe than primary infections. Only one reinfection was severe, two were moderate, and none were critical or fatal. Most reinfections (66.7%) were diagnosed incidentally through random or routine testing, or through contact tracing. Conclusions: Reinfection is rare. Natural infection appears to elicit strong protection against reinfection with an efficacy ~95% for at least seven months.

7: Viral cultures for COVID-19 infectivity assessment. Systematic review
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Posted 04 Aug 2020

Viral cultures for COVID-19 infectivity assessment. Systematic review
3 tweets medRxiv epidemiology

Tom Jefferson, Elizabeth A Spencer, Jon Brassey, Carl Heneghan

Objective To review the evidence from studies comparing SARS-CoV-2 culture, with the results of reverse transcriptase polymerase chain reaction (RT-PCR). Methods We searched LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for Covid-19 using the terms viral culture or viral replication and associated synonyms up to 10 September 2020. We carried out citation matching and included studies reporting attempts to culture or observe SARS-CoV-2 matching with cutoffs for RT-PCR positivity. One reviewer extracted data for each study and a second reviewer checked end edited the extraction and summarised the narratively by sample: fecal, respiratory, environment, blood or mixed. Where necessary we wrote to corresponding authors of the included or background papers for additional information. We assessed quality using a modified QUADAS 2 risk of bias tool. This is the fourth version of this review that was first published on the 4th of August and updated on the 21t of August, on the 3rd and 10th of September. Results We included 29 studies reporting culturing or observing tissue invasion by SARS-CoV in sputum, naso or oropharyngeal, urine, stool, blood and environmental samples from patients diagnosed with Covid-19. The data are suggestive of a relation between the time from collection of a specimen to test, cycle threshold and symptom severity. The quality of the studies was moderate with lack of standardised reporting. Twelve studies reported that Ct values were significantly lower and log copies higher in samples producing live virus culture. Five studies reported no growth in samples based on a Ct cut-off value. These values ranged from CT > 24 for no growth to Ct > 34 or more. Two studies report a strong relationship between Ct value and ability to recover infectious virus and that the odds of live virus culture reduced by 33% for every one unit increase in Ct. A cut-off RT-PCR Ct > 30 was associated with non-infectious samples. One study that analysed the NSP, N and E gene fragments of the PCR result reported different cut-off thresholds depending on the gene fragment analysed. The duration of RNA shedding detected by PCR was far longer compared to detection of live culture. Six out of eight studies reported RNA shedding for longer than 14 days. Yet, infectivity declines after day 8 even among cases with ongoing high viral loads. A very small proportion of people re-testing positive after hospital discharge or with high Ct are likely to be infectious. Conclusion Prospective routine testing of reference and culture specimens are necessary for each country involved in the pandemic to establish the usefulness and reliability of PCR for Covid-19 and its relation to patient factors. Infectivity is related to the date of onset of symptoms and cycle threshold level. A binary Yes / No approach to the interpretation RT-PCR unvalidated against viral culture will result in false positives with possible segregation of large numbers of people who are no longer infectious and hence not a threat to public health.

8: Longitudinal variability in mortality predicts Covid-19 deaths
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Posted 30 Dec 2020

Longitudinal variability in mortality predicts Covid-19 deaths
1 tweet medRxiv epidemiology

Jon O. Lundberg, Hugo Zeberg

Within Europe, death rates due to covid-19 vary greatly, with some countries being hardly hit while others to date are almost unaffected. It would be of interest to pinpoint the factors that determine a countrys susceptibility to a pandemic such as covid-19. Here we present data demonstrating that mortality due to covid-19 in a given country could have been largely predicted even before the pandemic hit Europe, simply by looking at longitudinal variability of all-cause mortality rates in the years preceding the current outbreak. The variability in death rates during the influenza seasons of 2015-2019 correlate to excess mortality caused by covid-19 in 2020 (R2=0.48, p<0.0001). In contrast, we found no correlation between such excess mortality and age, population density, degree of urbanization, latitude, GNP, governmental health spendings or rates of influenza vaccinations. These data may be of some relevance when discussing the effectiveness of acute measures in order to limit the spread of the disease and ultimately deaths. They suggest that in some European countries there is an intrinsic susceptibility to fatal respiratory viral disease including covid-19; a susceptibility that was evident long before the arrival of the current pandemic.

9: Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern
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Posted 23 Apr 2020

Ongoing outbreak of COVID-19 in Iran: challenges and signs of concern
1 tweet medRxiv epidemiology

Mahan Ghafari, Bardia Hejazi, Arman Karshenas, Stefan Dascalu, Alireza Kadivar, Mohammad Ali Khosravi, Maryam Abbasalipour, Majid Heydari, Sirous Zeinali, Luca Ferretti, Alice Ledda, Aris Katzourakis

Many countries with an early outbreak of SARS-CoV-2 struggled to gauge the size and start date of the epidemic mainly due to limited testing capacities and a large proportion of undetected asymptomatic and mild infections. Iran was among the first countries with a major outbreak outside China. Using all genomic sequences collected from patients with a travel link to Iran, we estimate that the epidemic started on 21/01/2020 (95% HPD: 05/12/2019-14/02/2020) with a doubling time of 3 days (95% HPD: 1.68-16.27). We also show, using air travel data from confirmed exported cases, that from late February to early March the number of active cases across the country were more than a hundred times higher than the reported cases at the time. A detailed province-level analysis of all-cause mortality shows 20,718 (CI 95%: 18,859-22,576) excess deaths during winter and spring 2020 compared to previous years, almost twice the number of reported COVID-19-related deaths at the time. Correcting for under-reporting of prevalence and deaths, we use an SEIR model to reconstruct the outbreak dynamics in Iran. Our model forecasted the second epidemic peak and suggests that by 14/07/2020 a total of 9M (CI 95%: 118K-44M) have recovered from the disease across the country. These findings have profound implications for assessing the stage of the epidemic in Iran and shed light on the dynamics of SARS-CoV-2 transmissions in Iran and central Asia despite significant levels of under-reporting.

10: The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic
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Posted 29 Jan 2021

The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic
1 tweet medRxiv epidemiology

Ariel Karlinsky, Dmitry Kobak

Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported numbers of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the recent average, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no central, frequently-updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 77 countries, openly available as the regularly-updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in the worst-affected countries the annual mortality increased by over 50%, while in several other countries it decreased by over 5%, presumably due to lockdown measures decreasing the non-COVID mortality. Moreover, we found that while some countries have been reporting the COVID-19 deaths very accurately, many countries have been underreporting their COVID-19 deaths by an order of magnitude or more. Averaging across the entire dataset suggests that the world's COVID-19 death toll may be at least 1.6 times higher than the reported number of confirmed deaths.

11: Higher COVID-19 vaccination rates are linked to decreased county-level COVID-19 incidence across USA
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Posted 08 Mar 2021

Higher COVID-19 vaccination rates are linked to decreased county-level COVID-19 incidence across USA
1 tweet medRxiv epidemiology

Arjun Puranik, AJ Venkatakrishnan, Colin Pawlowski, Bharathwaj Raghunathan, Eshwan Ramudu, Patrick Lenehan, Vineet Agarwal, Savita Jayaram, Mayank Choudhary, Venky Soundararajan

Real world evidence studies of mass vaccination across health systems have reaffirmed the safety and efficacy of the FDA-authorized mRNA vaccines for COVID-19. However, the impact of vaccination on community transmission remains to be characterized. Here, we compare the cumulative county-level vaccination rates with the corresponding COVID-19 incidence rates among 87 million individuals from 580 counties in the United States, including 12 million individuals who have received at least one vaccine dose. We find that cumulative county-level vaccination rate through March 1, 2021 is significantly associated with a concomitant decline in COVID-19 incidence (Spearman correlation = -0.22, p-value = 8.3e-8), with stronger negative correlations in the Midwestern counties ( = -0.37, p-value = 1.3e-7) and Southern counties ( = -0.33, p-value = 4.5e-5) studied. Additionally, all examined US regions demonstrate significant negative correlations between cumulative COVID-19 incidence rate prior to the vaccine rollout and the decline in the COVID-19 incidence rate between December 1, 2020 and March 1, 2021, with the US western region being particularly striking ( = -0.66, p-value = 5.3e-37). However, the cumulative vaccination rate and cumulative incidence rate are noted to be statistically independent variables, emphasizing the need to continue the ongoing vaccination roll out at scale. Given confounders such as different coronavirus restrictions and mask mandates, varying population densities, and distinct levels of diagnostic testing and vaccine availabilities across US counties, we are advancing a public health resource to amplify transparency in vaccine efficacy monitoring (https://public.nferx.com/covid-monitor-lab/vaccinationcheck). Application of this resource highlights outliers like Dimmit county (Texas), where infection rates have increased significantly despite higher vaccination rates, ostensibly owing to amplified travel as a vaccination hub; as well as Henry county (Ohio) which encountered shipping delays leading to postponement of the vaccine clinics. This study underscores the importance of tying the ongoing vaccine rollout to a real-time monitor of spatio-temporal vaccine efficacy to help turn the tide of the COVID-19 pandemic.

12: A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
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Posted 25 Feb 2021

A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
1 tweet medRxiv epidemiology

Medini K Annavajhala, Hiroshi Mohri, Pengfei Wang, Jason E. Zucker, Zizhang Sheng, Angela Gomez-Simmonds, Trevor Bedford, David D Ho, Anne-Catrin Uhlemann

Recent months have seen surges of SARS-CoV-2 infection across the globe along with considerable viral evolution1-3. Extensive mutations in the spike protein may threaten efficacy of vaccines and therapeutic monoclonal antibodies4. Two signature mutations of concern are E484K, which plays a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. Here, we report the emergence of a novel variant lineage B.1.526 that contains E484K and its alarming rise to dominance in New York City in recent months. This variant is partially or completely resistant to two therapeutic monoclonal antibodies in clinical use. It is also less susceptible to neutralization by convalescent plasma or vaccinee sera by 4.1-fold or 3.3-3.6-fold, respectively. The B.1.526 lineage has now been reported from at least 32 states in the US and numerous other countries. B.1526 has been outpacing B.1.1.7 in Northern Manhattan, and both variants have been spreading throughout New York with comparable estimated doubling times. Such transmission dynamics, together with its resistance to therapeutic antibodies, would warrant B.1.526 as a SARS-CoV-2 variant of concern.

13: Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals
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Posted 09 Apr 2021

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals
1 tweet medRxiv epidemiology

Talia Kustin, Noam Harel, Uriah Finkel, Shay Perchik, Sheri Harari, Maayan Tahor, Itamar Caspi, Rachel Levy, Michael Leschinsky, Shifra Ken Dror, Galit Bergerzon, Hala Gadban, Faten Gadban, Eti Eliassian, Orit Shimron, Loulou Saleh, Haim Ben-Zvi, Doron Amichay, Anat Ben-Dor, Dana Sagas, Merav Strauss, Yonat Shemer Avni, Amit Huppert, Eldad Kepten, Ran D. Balicer, Doron Nezer, Shay Ben-Shachar, Adi Stern

The SARS-CoV-2 pandemic has been raging for over a year, creating global detrimental impact. The BNT162b2 mRNA vaccine has demonstrated high protection levels, yet apprehension exists that several variants of concerns (VOCs) can surmount the immune defenses generated by the vaccines. Neutralization assays have revealed some reduction in neutralization of VOCs B.1.1.7 and B.1.351, but the relevance of these assays in real life remains unclear. Here, we performed a case-control study that examined whether BNT162b2 vaccinees with documented SARS-CoV-2 infection were more likely to become infected with B.1.1.7 or B.1.351 compared with unvaccinated individuals. Vaccinees infected at least a week after the second dose were disproportionally infected with B.1.351 (odds ratio of 8:1). Those infected between two weeks after the first dose and one week after the second dose, were disproportionally infected by B.1.1.7 (odds ratio of 26:10), suggesting reduced vaccine effectiveness against both VOCs under different dosage/timing conditions. Nevertheless, the B.1.351 incidence in Israel to-date remains low and vaccine effectiveness remains high against B.1.1.7, among those fully vaccinated. These results overall suggest that vaccine breakthrough infection is more frequent with both VOCs, yet a combination of mass-vaccination with two doses coupled with non-pharmaceutical interventions control and contain their spread.

14: Long-term symptoms after SARS-CoV-2 infection in school children: population-based cohort with 6-months follow-up. Short Report
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Posted 18 May 2021

Long-term symptoms after SARS-CoV-2 infection in school children: population-based cohort with 6-months follow-up. Short Report
1 tweet medRxiv epidemiology

Thomas Radtke, Agne Ulyte, Milo Alan Puhan, Susi Kriemler

Although nobody doubts the existence of long COVID in children, it is still unclear to what extent children are affected. The Ciao Corona study is a longitudinal cohort investigating SARS-CoV-2 seroprevalence and clustering of cases among around 2500 children from 55 randomly selected primary and secondary schools in the canton of Zurich in Switzerland. Between June 2020 and April 2021, we completed three testing phases where we collected venous blood for serological analysis (ABCORA 2.0 test) and asked about symptoms with online questionnaires. We compared children who tested positive for SARS-CoV-2 antibodies in October/November 2020 with those who tested negative. Children who were seronegative in October/November 2020 and seroconverted or were not retested by March/April 2021 were excluded from the analysis (n=256). In March-May 2021 we assessed the presence of symptoms occurring since October 2020, lasting for at least 4 weeks, and persisting for either >4 weeks or >12 weeks. Overall, 1355 of 2503 children with a serology result in October/November 2020 and follow up questionnaire in March/April 2021 were included. Among seropositive and seronegative 6-to 16-year-old children and adolescents, 9% versus 10% reported at least one symptom beyond 4 weeks, and 4% versus 2% at least one symptom beyond 12 weeks. None of the seropositive children reported hospitalization after October 2020. Seropositive children, all with a history of pauci-symptomatic SARS-CoV-2 infection, did not report long COVID more frequently than seronegative children. This study suggests a very low prevalence of long COVID in a randomly selected population-based cohort of children followed over 6 months after serological testing.

15: A 2SIR-VD Model for Optimizing Geographical COVID-19 Vaccine Distribution in the Philippines
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Posted 21 May 2021

A 2SIR-VD Model for Optimizing Geographical COVID-19 Vaccine Distribution in the Philippines
1 tweet medRxiv epidemiology

Allan Paolo Almajose, Angus White, Chelsea Diego, Red Lazaro, Nicanor Austriaco

COVID-19 is a novel respiratory disease first identified in Wuhan, China, that is caused by the novel coronavirus, SARS-CoV-2. It has triggered a global pandemic of historic proportions. The government of the Philippines began its national vaccine drive on March 1, 2021, with the goal of vaccinating seventy million of its citizens by the end of the calendar year. To determine the optimum geographical distribution strategy in the Philippines for the limited supply of vaccines that is currently available, we developed and adapted a basic SIR model that allows us to understand the evolution of a pandemic when public health authorities are vaccinating two susceptible populations within a country with different vaccine rates. Our analysis with our 2SIR-VD model revealed that prioritizing vaccine deployment to the National Capital Region (NCR) of the Philippines minimized the number of COVID-19 cases in the country. We therefore recommend deploying 90% of the available vaccine supply to the NCR to mitigate viral transmission there. The remaining 10% would allow the rest of the archipelago to vaccinate all of their senior citizens, thus shielding this vulnerable population against severe disease and death from COVID-19.

16: COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya
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Posted 20 Jun 2021

COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya
1 tweet medRxiv epidemiology

Samuel P C Brand, John Ojal, Rabia Aziza, Vincent Were, Emelda Okiro, Ivy Kombe, Caroline Mburu, Morris Ogero, Ambrose Agweyu, George M Warimwe, James Nyagwange, Henry Karanja, John Gitonga, Daisy Mugo, Sophie Uyoga, Ifedayo M. O Adetifa, J. Anthony G. Scott, Edward Otieno, Nickson Murunga, Mark Otiende, Lynette I Ochola-Oyier, Charles N Agoti, George Githinji, Kadondi Kasera, Patrick Amoth, Mercy Mwangangi, Rashid Aman, Wangari Ng'ang'a, Benjamin Tsofa, Philip Bejon, Matt J Keeling, D James Nokes, Edwine Barasa

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya (~75% June 1st) have implications for a fourth wave and future control strategies.

17: Do antibody positive healthcare workers have lower SARS-CoV-2 infection rates than antibody negative healthcare workers? Large multi-centre prospective cohort study (the SIREN study), England: June to November 2020
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Posted 15 Jan 2021

Do antibody positive healthcare workers have lower SARS-CoV-2 infection rates than antibody negative healthcare workers? Large multi-centre prospective cohort study (the SIREN study), England: June to November 2020
1 tweet medRxiv epidemiology

Victoria Jane Hall, Sarah Foulkes, Andre Charlett, Ana Atti, Edward JM Monk, Ruth Simmons, Edgar Wellington, Michelle J Cole, Ayoub Saei, Blanche Oguti, Katie Munro, Sarah Wallace, Peter D Kirwan, Madhumita Shrotri, Amoolya Vusirikala, Sakib Rokadiya, Meaghan Kall, Maria Zambon, Mary Ramsay, Tim Brooks, SIREN Sudy Group, Colin S. Brown, Meera A Chand, Susan Hopkins

Background: There is an urgent need to better understand whether individuals who have recovered from COVID-19 are protected from future SARS-CoV-2 infection. Methods: A large multi-centre prospective cohort was recruited from publicly funded hospital staff in the UK. Participants attended regular SARS-CoV-2 PCR and antibody testing (every 2-4 weeks) and completed fortnightly questionnaires on symptoms and exposures. At enrolment, participants were assigned to either the positive cohort (antibody positive or prior PCR/antibody test positive) or negative cohort (antibody negative, not previously known to be PCR/antibody positive). Potential reinfections were clinically reviewed and classified according to case definitions (confirmed, probable, possible (subdivided by symptom-status)) depending on hierarchy of evidence. Individuals in the primary infection were excluded from this analysis if infection was confirmed by antibody only. Reinfection rates in the positive cohort were compared against new PCR positives in the negative cohort using a mixed effective multivariable logistic regression analysis. Findings: Between 18 June and 09 November 2020, 44 reinfections (2 probable, 42 possible) were detected in the baseline positive cohort of 6,614 participants, collectively contributing 1,339,078 days of follow-up. This compares with 318 new PCR positive infections and 94 antibody seroconversions in the negative cohort of 14,173 participants, contributing 1,868,646 days of follow-up. The incidence density per 100,000 person days between June and November 2020 was 3.3 reinfections in the positive cohort, compared with 22.4 new PCR confirmed infections in the negative cohort. The adjusted odds ratio was 0.17 for all reinfections (95% CI 0.13-0.24) compared to PCR confirmed primary infections. The median interval between primary infection and reinfection was over 160 days. Interpretation: A prior history of SARS-CoV-2 infection was associated with an 83% lower risk of infection, with median protective effect observed five months following primary infection. This is the minimum likely effect as seroconversions were not included. Funding: Department of Health and Social Care and Public Health England, with contributions from the Scottish, Welsh and Northern Irish governments.

18: Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.
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Posted 01 May 2020

Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.
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Thomas A. J. Meunier

This phenomenological study assesses the impacts of full lockdown strategies applied in Italy, France, Spain and United Kingdom, on the slowdown of the 2020 COVID-19 outbreak. Comparing the trajectory of the epidemic before and after the lockdown, we find no evidence of any discontinuity in the growth rate, doubling time, and reproduction number trends. Extrapolating pre-lockdown growth rate trends, we provide estimates of the death toll in the absence of any lockdown policies, and show that these strategies might not have saved any life in western Europe. We also show that neighboring countries applying less restrictive social distancing measures (as opposed to police-enforced home containment) experience a very similar time evolution of the epidemic.

19: Estimating pre-symptomatic transmission of COVID-19: a secondary analysis using published data
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Posted 11 May 2020

Estimating pre-symptomatic transmission of COVID-19: a secondary analysis using published data
1 tweet medRxiv epidemiology

Miriam Casey, John Griffin, Conor G McAloon, Andrew W Byrne, Jamie M Madden, David McEvoy, Aine B Collins, Kevin Hunt, Ann Barber, Francis Butler, Elizabeth A Lane, Kirsty O Brien, Patrick Wall, Kieran A Walsh, Simon J. More

Objective: To estimate the proportion of pre-symptomatic transmission of SARS-CoV-2 infection that can occur and timing of transmission relative to symptom onset. Setting/design: Secondary analysis of international published data. Data sources: Meta-analysis of COVID-19 incubation period and a rapid systematic review of serial interval and generation time, which are published separately. Participants: Studies were selected for analysis if they had transparent methods and data sources and they provided enough information to simulate full distributions of serial interval or generation time. Twenty-three estimates of serial interval and five of generation time from 17 publications were included. Methods: Simulations were generated of incubation period and of serial interval or generation time. From these, transmission times relative to symptom onset were calculated and the proportion of pre-symptomatic transmission was estimated. Outcome measures: Transmission time of SARS-CoV-2 relative to symptom onset and proportion of pre-symptomatic transmission. Results: Transmission time ranged from a mean of 2.91 (95% CI: 3.18-2.64) days before symptom onset to 1.20 (0.86-1.55) days after symptom onset. Unweighted pooling of estimates of transmission time based on serial interval resulted in a mean of 0.60 days before symptom onset (3.01 days before to 1.81 days after). Proportion of pre-symptomatic transmission ranged from 42.8% (39.8%-45.9%) to 80.6% (78.1%-83.0%). The proportion of pre-symptomatic transmission from pooled estimates was 56.4% (34.9%-78.0%). Conclusions: Whilst contact rates between symptomatic infectious and susceptible people are likely to influence the proportion of pre-symptomatic transmission, there is substantial potential for pre-symptomatic transmission of SARS-CoV-2 in a range of different contexts. Our work suggests that transmission is most likely in the day before symptom onset whereas estimates suggesting most pre-symptomatic transmission highlighted mean transmission times almost three days before symptom onset. This highlights the need for rapid case detection, contact tracing and quarantine.

20: Face masks to prevent transmission of respiratory diseases: Systematic review and meta-analysis of randomized controlled trials
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Posted 04 Aug 2020

Face masks to prevent transmission of respiratory diseases: Systematic review and meta-analysis of randomized controlled trials
1 tweet medRxiv epidemiology

Hanna M Ollila, Markku Partinen, Jukka T Koskela, Riikka Savolainen, Anna Rotkirch, Liisa T Laine

Objectives. To examine the effect of face mask intervention in respiratory infections across different exposure settings and age groups. Design. Systematic review and meta-analysis. Data sources. PubMed, Cochrane Central Register of Controlled Trials, and Web of Science were searched for randomized controlled trials investigating the effect of face masks on respiratory infections published by November 18th 2020. We followed PRISMA guidelines. Eligibility criteria for selecting studies. Randomized controlled trials investigating face masks in respiratory infections across different exposure settings. Two reviewers performed the search, extracted data, and assessed the risk of bias. Random effects meta-analysis with risk ratio, adjusted odds ratios, and number needed to treat were performed. Findings by source control or wearer protection, age groups, exposure settings, and role of non-compliance were evaluated. Results. Seventeen studies were included, (N=11,601 cases and N=10,286 controls, follow-up from 4 days to 19 months). Fourteen trials included adults and children and three trials included children only. Twelve studies showed non-compliance in treatment and eleven in control group. Four studies supported the use of face masks. Meta-analysis across all studies with risk ratios found no association with number of infections (RR=0.957 [0.810 - 1.131], p=0.608). Meta-analysis using odds ratios adjusted for age, sex, and vaccination (when available) showed protective effect of face masks (OR=0.850 [0.736 - 0.982], p=0.027). Subgroup meta-analysis with adjusted odds ratios found a decrease in respiratory infections among adults (14 studies, OR = 0.829 [0.709-0.969], p=0.019) in source control setting (OR = 0.845 [0.7375 - 0.969], p=0.0159) and when face masks were used together with hand hygiene OR = 0.690 [0.568 - 0.838], p=0.0002). Overall between-study heterogeneity was large also in the subgroup analyses. Conclusion. Despite the large between study heterogeneity, compliance bias and differences by environmental settings, the findings support the use of face masks to prevent respiratory infections. PROSPERO registration number CRD42020205523.

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