+++ Epidemiology +++

* * * Next update: 24 November. In the meantime, find the global updates at 7 Days. * * *

19 November

Xing Y, Wong GWK, Ni W, Hu X, Xing Q. Rapid Response to an Outbreak in Qingdao, China. N Engl J Med 2020, published 18 November. Full-text: https://doi.org/10.1056/NEJMc2032361

Three COVID-19 cases in Qingdao in October: a taxi driver who was admitted to Qingdao Central Hospital for a transient ischemic attack on October 10; his wife who had been working part-time as a nursing assistant at Qingdao Chest Hospital; and a man with pulmonary tuberculosis who was treated at the same hospital. These were the first cases after a 2-month period without local SARS-CoV-2 transmission in China. What would you have done during the next 7 days? The Chinese authorities tested 10.9 million people and identified another 9 cases related to the initial cluster. The outbreak was controlled without a lockdown.


18 November

Denny TN, Andrews L, Bonsignori M, et al. Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus — Duke University, Durham, North Carolina, August 2–October 11, 2020. MMWR Morb Mortal Wkly Rep. ePub: 17 November 2020. Full-text: http://dx.doi.org/10.15585/mmwr.mm6946e1

Test them all? In fall 2020, Duke University’s COVID-19 prevention strategy included risk reduction behaviors, but also frequent testing using pooled SARS-CoV-2 PCR testing, and contact tracing. Of 10,265 students who received testing 68,913 times, 84 had positive results. Of these, 51% were asymptomatic, and some had high viral loads. This plan allowed campus to remain open for 10 weeks of classes without substantial outbreaks among residential or off-campus populations. Importantly, no evidence from contact tracing linked transmission with in-person classes. Pooled testing permitted a nearly 80% savings in use of reagents and laboratory resources compared with testing each individual specimen.

17 November

Mahale P, Rothfuss C, Bly S, et al. Multiple COVID-19 Outbreaks Linked to a Wedding Reception in Rural Maine — August 7–September 14, 2020. MMWR Morb Mortal Wkly Rep 2020;69:1686–1690. Full-text: http://dx.doi.org/10.15585/mmwr.mm6945a5

Do you have a niece who, despite all the warnings, is unwaveringly sticking to her plans to get married in January? Who says that only 50 guests (ok, 55) will come and that temperature checks for all guests will be conducted at the facility entrance? That there will be enough space, with 10 tables, with 4–6 guests seated around each table? That signs posted at the entrance will instruct visitors to wear masks? Then give her this paper to read. A wedding reception in a small rural town in Maine was the likely source of COVID-19 outbreaks in the local community, a long-term care facility, and a correctional facility. Outcome: 177 cases, seven hospitalizations, and seven deaths. Read here why people should avoid large gatherings, practice physical distancing, wear masks, stay home when ill, and self-quarantine after exposure to a person with confirmed SARS-CoV-2 infection.

(If your niece doesn’t want to read a scientific paper, provide her with “15 Benefits of A Summer Wedding”: https://www.nichemarket.co.za/blog/extravaganza/benefits-summer-wedding. Benefit No. 16 is found probably below, in the vaccine section.)


Ali H, Kondapally K, Pordell P, et al. COVID-19 Outbreak in an Amish Community — Ohio, May 2020. MMWR Morb Mortal Wkly Rep 2020;69:1671–1674. Full-text:  http://dx.doi.org/10.15585/mmwr.mm6945a2

How social gatherings likely contributed to rapid transmission of SARS-CoV-2 in an Amish community. In May, after a cluster of seven COVID-19 cases was identified, 23/30 (77%) additional residents tested by RT-PCR received positive test results. Rapid and sustained transmission of SARS-CoV-2 was associated with multiple social gatherings. Although Amish communities might be experiencing challenges with preventing and mitigating SARS-CoV-2 transmission, the authors conclude that leveraging Amish cultural beliefs of communal responsibility could help limit the spread of SARS-CoV-2.


Wang EA, Western B, Berwick DM. COVID-19, Decarceration, and the Role of Clinicians, Health Systems, and Payers. A Report From the National Academy of Sciences, Engineering, and Medicine. JAMA November 16, 2020. Full-text: https://doi.org/10.1001/jama.2020.22109

By August 2020, 90 of the largest 100 cluster outbreaks in the United States had occurred in prisons and jails. Reducing the incarcerated population (“decarceration”) is an important and urgent strategy for mitigating viral transmission in prisons and jails. In their courageous viewpoint, Emily Wang and colleagues argue that decarceration in the service of both public health and safer communities will require sustained engagement from clinicians, health systems, and Medicaid authorities.


15 September

Brotons P, Launes C, Buetas E, et al. Susceptibility to Sars-COV-2 Infection Among Children And Adults: A Seroprevalence Study of Family Households in the Barcelona Metropolitan Region, Spain. Clinical Infectious Diseases, November 12, 2020. Full-text: https://doi.org/10.1093/cid/ciaa1721

Children have similar probability as adults to become infected by SARS-CoV-2 in quarantined family households. Pedro Brotons and colleagues from Barcelona performed a large cross-sectional seroprevalence study, enrolling 381 family households including 381 first-reported PCR-positive adult cases and 1084 contacts (672 children, 412 adults). SARS-CoV-2 infection seroprevalence rates were 18% (118/672) in children and 19% (77/335) in adult contacts. Nearly all positive pediatric contacts were asymptomatic or had mild symptoms.


Ebrahim SH, Ahmed Y, Algahtani SA, et al. The Hajj pilgrimage during the COVID-19 pandemic in 2020: event hosting without the mass gathering. Journal of Travel Medicine November 13, 2020. Full-text:  https://academic.oup.com/jtm/advance-article/doi/10.1093/jtm/taaa194/5979518

Examples of religious congregations that resulted in seeding or surging of domestic and international COVID-19 outbreaks include events in Daegu, South Korea; Qom, Iran; Albany, Georgia; Arkansas + Maine, USA; and Mulhouse, France. Read how the science-driven steering of the 2020 Hajj with vastly reduced pilgrim numbers allowing for full compliance of the mitigation strategies avoided the cancellation of the event.


14 November

Malani A, Shah D, Kang G, et al. Seroprevalence of SARS-CoV-2 in slums versus non-slums in Mumbai, India. Lancet Global Health 2020, published 13 November. Full-text: https://doi.org/10.1016/S2214-109X(20)30467-8

This is the final article of a pre-print study we presented on August 4: Kolthur-Seetharam U, Shah D, Shastri J, Juneja S, Kang G, Malani A, Mohanan M, Lobo GN, Velhal G, Gomare M. SARS-CoV2 Serological Survey in Mumbai by NITI-BMC-TIFR. Tata Institute of Fundamental Research (TIFR) 2020, published 29 June. Full-text: https://www.tifr.res.in/TSN/article/Mumbai-Serosurvey%20Technical%20report-NITI.pdf

“We usually prefer peer-reviewed studies and seldom present pre-published papers. We are even less readily inclined to present a PDF with just the technical details of an unpublished study. Today we make an exception. In a cross-sectional survey in Mumbai, India, Ullas Kolthur-Seetharam and colleagues estimated the prevalence of SARS-CoV-2 infection in three Mumbai areas (called ‘wards’) in July 2020. The authors found, on average, a prevalence of around 57% in the slum areas of Chembur, Matunga and Dahisar, and 16% in neighboring non-slums. If these data are confirmed, some Mumbai areas would soon reach herd immunity and could return to a pre-COVID way of life.”


See also a short comment in The Economist. Anonymous. A minority of people with covid-19 account for the bulk of transmission. The Economist 2020, published 7 November. Full-text: https://www.economist.com/graphic-detail/2020/11/07/a-minority-of-people-with-covid-19-account-for-the-bulk-of-transmission


13 November

Uyoga S, Adetifa IMO, Karanja HK, et al. Seroprevalence of anti–SARS-CoV-2 IgG antibodies in Kenyan blood donors. Science 2020, published 11 November. Full-text: https://doi.org/10.1126/science.abe1916

In April-June 2020, the crude prevalence of anti–SARS-CoV-2 IgG among blood donors in Kenya was 5,6% (174/3098). It was highest in urban counties, Mombasa (8,0%), Nairobi (7,3%) and Kisumu (5,5%). Of note, Kenya reported only 341 deaths by the end of that period. The authors conclude that the sharp contrast between the reported COVID-19 cases and deaths suggests that the disease might be attenuated in Africa.


Waterfield T, Watson C, Moore R, et al. Seroprevalence of SARS-CoV-2 antibodies in children: a prospective multicentre cohort study. Arch Dis Child. 2020 Nov 10:archdischild-2020-320558. PubMed: https://pubmed.gov/33172887. Full-text: https://doi.org/10.1136/archdischild-2020-320558

Fatigue, gastrointestinal symptoms and changes in sense of smell or taste were the symptoms most strongly associated with SARS-CoV-1 antibody positivity in children. Thomas Waterfield et al. report 68/992 (6,9%) children aged 2-15 years with positive SARS-CoV-2 antibody tests. Of these, 34/68 (50%) reported no symptoms prior to testing. Four independent variables were identified as significantly associated with SARS-CoV-2 seropositivity: known infected household contact OR=10,9; fatigue OR=16,8; gastrointestinal symptoms OR=6,6; and changes in sense of smell or taste OR=10,0.


Slot E, Hogema BM, Reusken CBEM, et al. Low SARS-CoV-2 seroprevalence in blood donors in the early COVID-19 epidemic in the Netherlands. Nat Commun 11, 5744 (2020). Full-text: https://doi.org/10.1038/s41467-020-19481-7

One month into the outbreak and more than 2 weeks after social distancing and lockdown interventions were implemented, the proportion of SARS-CoV-2 antibody-positive individuals in the Dutch population tested was 2,7%. Hans Zaaijer, Ed Slot and colleagues also demonstrate that the hardest-hit areas had a seroprevalence of up to 9,5%; the seroprevalence was sex-independent throughout age groups (18–72 years); and antibodies were significantly more often present in young people aged 18–30 years.


11 November

Kurian SJ, Bhatti AUR, Alvi MA, et al. Correlations Between COVID-19 Cases and Google Trends Data in the United States: A State-by-State Analysis. Mayo Clin Proc. 2020 Nov;95(11):2370-2381. PubMed: https://pubmed.gov/33164756. Full-text: https://doi.org/10.1016/j.mayocp.2020.08.022

Google might see a nascent epidemic two weeks before the first reported cases. This is the result of a study by Mohamad Bydon, Shyam J. Kurian and colleagues from Mayo Clinic, Rochester after developing a digital surveillance model using Google Trends. The authors searched the following keywords: COVID symptoms, coronavirus symptoms, sore throat+shortness of breath+fatigue+cough, coronavirus testing center, loss of smell, Lysol (sanitizer), antibody, face mask, coronavirus vaccine, and COVID stimulus check. Find out which one did best. The authors suggest that this information could enable better preparation and planning for health care systems.


10 November

Brown KA, Jones A, Daneman N, et al. Association Between Nursing Home Crowding and COVID-19 Infection and Mortality in Ontario, Canada. JAMA Intern Med. November 9, 2020. Full-text: https://doi.org/10.1001/jamainternmed.2020.6466

In this cohort study that included 78,607 residents of 618 nursing homes in Ontario, Canada, 5218 (6.6%) developed COVID-19 infection and 1452 (1.8%) died of COVID-19 infection as of May 20, 2020. The case fatality rate was 27.8% (1452/5218). Of note, COVID-19 mortality in homes with low crowding (number of occupants per room and bathroom across an entire home) was less than half (1.3%) than that of homes with high crowding (2.7%).


9 November

Siegenfeld AF, Bar-Yam Y. The impact of travel and timing in eliminating COVID-19. Commun Phys 3, 204 (2020). Full-text: https://doi.org/10.1038/s42005-020-00470-7

Mathematical models, showing that these are no good times for travel. When a reduction in travel is coupled with other control measures, the travel reduction will not only delay the spread of the outbreak but in some cases will also be the determining factor in whether or not the outbreak is eliminated.


Kanu FA, Smith EE, Offutt-Powell T, et al. Declines in SARS-CoV-2 Transmission, Hospitalizations, and Mortality After Implementation of Mitigation Measures— Delaware, March–June 2020. MMWR Morb Mortal Wkly Rep. ePub: 6 November 2020. Full-text: http://dx.doi.org/10.15585/mmwr.mm6945

No single mitigation strategy is likely to be effective alone: State-mandated stay-at-home orders and public mask mandates coupled with case investigations and contact tracing contributed to an 82% reduction in COVID-19 incidence, 88% reduction in hospitalizations, and 100% reduction in mortality in Delaware during late April–June.

5 November

Pozzer A, Dominici F, Haines A, et al. Regional and global contributions of air pollution to risk of death from COVID-19. Cardiovasc Res 2020, published 26 October. Full-text: https://doi.org/10.1093/cvr/cvaa288

Air pollution might be an important cofactor increasing the risk of mortality from COVID-19. Jos Lelieveld, Andrea Pozzer and colleagues characterized global exposure to fine particulates based on satellite data and estimate that particulate air pollution contributed around 15% to COVID-19 mortality worldwide (East Asia, 27%; Europe, 19%; North America, 17%).


4 November

O’Driscoll M, Dos Santos GR, Wang L, et al. Age-specific mortality and immunity patterns of SARS-CoV-2. Nature (2020). Full-text: https://doi.org/10.1038/s41586-020-2918-0

The age distribution of deaths in younger age groups (<65 years) is consistent across different settings. This is the result of a study by Henrik Salje, Megan O’Driscoll and colleagues who used age-specific COVID-19 death data from 45 countries and the results of 22 seroprevalence studies to investigate the fatality patterns across multiple countries. The authors also demonstrate how outbreaks in nursing homes can drive overall population IFRs infection-to-fatality ratio), through both increased attack rates and increased vulnerability. They estimate that around 5% of the populations had been infected by the 1st of September 2020, with much higher transmission likely to have occurred in a number of Latin American countries.


Vijayan T, Shin M, Adamson PC, et al. Beyond the 405 and the 5: Geographic variations and factors associated with SARS-CoV-2 positivity rates in Los Angeles County. Clin Infect Dis 2020, published 3 November. Full-text: https://doi.org/10.1093/cid/ciaa1692

SARS-CoV-2 infection was more frequent in communities with high proportions of Latino/a residents, those living below the federal poverty line and with high household densities. This is the conclusion of a study by Tara Vijayan et al. in Los Angeles County (LAC) after analyzing more than 800,000 SARS-CoV-2 tests. The overall positivity rate was 10.2%.


30 October

Bassi F, Arbia G, Falorsi PD. Observed and estimated prevalence of Covid-19 in Italy: How to estimate the total cases from medical swabs data. Sci Total Environ. 2020 Oct 8:142799. PubMed: https://pubmed.gov/33066965. Full-text: https://doi.org/10.1016/j.scitotenv.2020.142799

A national survey in Italy from May to July 2020 found a nationwide seropositivity rate of 2.5% (Sabbadini 2020). Insiders never believed these figures and favored a seropositivity rate of 5-10% like in Spain or in France. Now we have a new estimate of COVID-19 prevalence in Italy by Francesca Bassi and colleagues: 9%, corresponding to almost 6 million Italians.


27 October

Bedford J, Enria D, Giesecke J, et al. Living with the COVID-19 pandemic: act now with the tools we have. Lancet 2020, published 24 October. Full-text: https://doi.org/10.1016/S0140-6736(20)32117-6

Let’s face reality: at the beginning of the second pandemic wave, we have some steroids which have been shown to reduce mortality in patients with severe COVID-19 (see Corticosteroids); and then we have a drug (remdesivir, Veklury®), which had a marginal benefit in a company-sponsored trial. That’s the COVID-19 treatment armamentarium as of October 2020 (see COVID Reference: Treatment). David Heymann, Juliet Bedford and colleagues summarize how to get through the 2020/2021 winter with what we have.


25 October

Mallapaty S. Why COVID outbreaks look set to worsen this winter. Nature News, October 23, 2020. Full-text: https://doi.org/10.1038/d41586-020-02972-4

It’s too soon to say whether COVID is seasonal like the flu — but where clusters aren’t under control, infections will continue to swell. Smriti Mallapaty explains how a small seasonal effect will probably contribute to bigger outbreaks in winter. Difficult months ahead.


Rafiei Y, Mello MM. The Missing Piece — SARS-CoV-2 Testing and School Reopening. October 21, 2020. Full-text: https://doi.org/10.1056/NEJMp2028209

Many health authorities (including the CDC) still recommend against screening testing in schools, citing constraints on testing capacity and the unavailability of real-world studies of its effectiveness. They focus on screening for COVID-19 symptoms. In this important viewpoint, Yasmin Rafiei and Michelle M. Mello explain why this will not work. They believe that increasing routine screening using rapid tests in schools should rank among the most urgent national priorities. Nevertheless, the testing-related challenges are immense (financial, logistics etc.). See above.


24 October

Guzzetta G, Riccardo F, Marziano V, Poletti P, Trentini F, Bella A, et al. Impact of a nationwide lockdown on SARS-CoV-2 transmissibility, Italy. Emerg Infect Dis. 2021 Jan. Full-text: https://doi.org/10.3201/eid2701.202114

While preparing for the next lockdown, let’s keep in mind that it worked during the first wave. The national lockdown put in place as of March 11 in Italy brought the net (Rt) reproduction numbers below 1 in most regions and provinces within 2 weeks. Although Rt had been declining steeply even before the national lockdown in regions with intense interventions, Giorgio Guzzetta and colleagues estimate that the epidemic was brought under control only after the implementation of the lockdown. In addition, lockdown was fundamental to prevent an explosion in the number of cases in other regions in which transmission had started weeks later compared with the outbreak epicenters in Lombardy, Veneto and Emilia Romagna.


23 October

Aschwanden C. The false promise of herd immunity for COVID-19. Nature News Feature October 21. Full-text: https://doi.org/10.1038/d41586-020-02948-4

Herd immunity has recently been discussed as a desirable result of wide-scale vaccination programs. (High levels of vaccination-induced immunity in the population benefits those who can’t receive or sufficiently respond to a vaccine, such as people with compromised immune systems.) However, discussing herd immunity as a tool in the absence of vaccines has never been heard of before the SARS-CoV-2 pandemic. If you are tired and frustrated with distancing, lockdown and curfews and tempted by the notion of herd immunity (better: ‘herd protection’), read this brilliant article by Nature’s leading science writer Christie Aschwanden. Find out why proposals to largely let the virus run its course — embraced by Donald Trump’s administration and others — could bring untold death and suffering. Seasonal coronaviruses that cause common colds provoke a waning immunity that seems to last approximately a year. Until proof of the contrary, we should assume immunity to SARS-CoV-2 to be comparable. Without vaccines there will be no herd immunity in the foreseeable future.


Adlhoch C, Pebody R. What to expect for the influenza season 2020/21 with the ongoing COVID-19 pandemic in the World Health Organization European Region. Euro Surveill. 2020;25(42):pii=2001816. Full-text: https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001816

Less flu cases in this season? The positivity rate of 0.2% in the 2020 inter-seasonal period was lower than the average (1.1%) observed over the previous five inter-seasonal periods. However, although COVID-19 prevention and control measures will also support influenza prevention, influenza remains a threat to human health and a potential burden on the healthcare system.


22 October

Smith GD, Blastland M, Munafò M. Covid-19’s known unknowns. BMJ 2020;371:m3979. Full-text: https://www.bmj.com/content/371/bmj.m3979

Do we know exactly what’s going on with SARS-CoV-2 and exactly what to do about it? Over the past months, we have seen strongly contrasting but apparently equally authoritative statements about almost any topic. Stop the nonsense, write Georges Davey-Smith and his colleagues. Acknowledging uncertainty a little more might improve not only the atmosphere of the debate and the science, but also public trust. In any case, the more certain someone is about COVID-19, the less you should trust them.


19 October

Moozhipurath RK, Kraft L, Skiera B. Evidence of protective role of Ultraviolet-B (UVB) radiation in reducing COVID-19 deaths. Sci Rep 10, 17705 (2020). Full-text: https://doi.org/10.1038/s41598-020-74825-z

Serious? The authors applied a fixed-effect log-linear regression model to a panel dataset of 152 countries over 108 days (n = 6524). They used the cumulative number of COVID-19 deaths and case-fatality rate (CFR) as the main dependent variables and isolated the ultraviolet index (UVI) effect from potential confounding factors. After controlling for time-constant and time-varying factors, the authors found a significant negative association between UVI and COVID-19 deaths, indicating evidence of the protective role of Ultraviolet-B (UVB) in mitigating COVID-19 deaths. If confirmed via clinical studies, then the possibility of mitigating COVID-19 deaths via sensible sunlight exposure or vitamin D intervention would be highly attractive.


15 October

Alwan NA, Burgess RA, Ashworth S, et al. Scientific consensus on the COVID-19 pandemic: we need to act now. Lancet 2020, published 15 October. Full-text: https://doi.org/10.1016/S0140-6736(20)32153-X

Herd immunity against SARS-CoV-2? Allowing large uncontrolled outbreaks in the low-risk population while protecting the vulnerable? Developing population immunity in the low-risk population, which will eventually protect the vulnerable? The authors don’t beat about the bush: “Dangerous fallacy unsupported by scientific evidence.” Their conclusion: “Japan, Vietnam, and New Zealand, to name a few countries, have shown that robust public health responses can control transmission, allowing life to return to near-normal, and there are many such success stories. The evidence is very clear: controlling community spread of COVID-19 is the best way to protect our societies and economies until safe and effective vaccines and therapeutics arrive within the coming months. We cannot afford distractions that undermine an effective response; it is essential that we act urgently based on the evidence.”


Poirier C, Luo W, Majumder MS, et al. The role of environmental factors on transmission rates of the COVID-19 outbreak: an initial assessment in two spatial scales. Sci Rep 10, 17002 (2020). Full-text: https://doi.org/10.1038/s41598-020-74089-7

Bad news for CCOs (‘Coronavirus Climate Optimists’): changes in weather (i.e., increase of temperature and humidity as spring and summer months arrive in the Northern Hemisphere) may not necessarily lead to declines in case counts without the implementation of drastic public health interventions. Only absolute humidity might play a role.


14 October

Jefferies S, French N, Gilkison G, et al. COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study. The Lancet 2020, published 13 October. Full-text: https://doi.org/10.1016/S2468-2667(20)30225-5

New Zealand’s government response resulted in low burden of disease, low levels of population disease disparities, and the initial achievement of COVID-19 elimination (Jefferies 2020, Robert 2020). Here, Sarah Jefferies et al. describe 1503 COVID-19 cases from Feb 2 to May 13, after which time community transmission ceased in New Zeeland, including 95 (6.3%) hospital admissions and 22 (1.5%) COVID-19 deaths. 1034 (69%) cases were imported or import related, tending to be younger adults, of European ethnicity, and of higher socioeconomic status. 702 (47%) cases were linked to 34 outbreaks.

See also the comment by Robert A. Lessons from New Zealand’s COVID-19 outbreak response. The Lancet 2020, published 13 October. Full-text:  https://doi.org/10.1016/S2468-2667(20)30237-1


13 October

Soper GA. The lessons of the pandemic. Science 1919, published 30 May. Full-text: https://science.sciencemag.org/content/49/1274/501

Do some time travel.


10 October

Rader B, Scarpino SV, Nande A, et al. Crowding and the shape of COVID-19 epidemics. Nat Med 2020, published 5 October. Full-text: https://doi.org/10.1038/s41591-020-1104-0

The dynamic of the current SARS epidemics in the Greater Paris and Madrid are reason for concern. In this article, Moritz Kraemer, Benjamin Rader and colleagues predict that crowded cities worldwide could experience more prolonged epidemics. The 2020/2021 autumn and winter season will be a hard time.


Oster AM, Caruso E, DeVies J, Hartnett KP, Boehmer TK. Transmission Dynamics by Age Group in COVID-19 Hotspot Counties — United States, April–September 2020. MMWR Morb Mortal Wkly Rep. ePub: 9 October 2020. Fulltext: http://dx.doi.org/10.15585/mmwr.mm6941e1

Understanding whether increasing incidence is predominantly occurring in specific age groups is important for identifying opportunities to prevent or reduce transmission. Here the authors analyze hotspot counties, particularly those in the US South and West. The positivity rate increased earliest in younger persons (18-24 years), followed by several weeks of increasing percent positivity among older age groups.




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