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and quarantine, physical distancing, decontam- The distribution had a median of 5.0 days ON OUR WEBSITE phones running the app are
ination, and hygiene measures. To implement and standard deviation of 1.9 days. We used Read the full article recorded. Upon an individ-
the right measures at the right time, it is of published parameters for the incubation time at https://dx.doi. ual’s COVID-19 diagnosis,
crucial importance to understand the routes and distribution (median 5.2 days) and the epide- org/10.1126/ contacts are instantly, auto-
timings of transmission. mic doubling time (5.0 days) from the early science.abb6936 matically, and anonymously
..................................................
epidemic data in China. notified of their risk and
RATIONALE: We used key parameters of epi- The model estimated R0 = 2.0 in the early asked to self-isolate. Practical and logistical
demic spread to estimate the contribution of stages of the epidemic in China. The contribu- factors (e.g., uptake, coverage, R0 in a given
different transmission routes with a renewal tions to R0 included 46% from presympto- population) will determine whether an app is
equation formulation, and analytically deter- matic individuals (before showing symptoms), sufficient to control viral spread on its own, or
mined the speed and scale for effective iden- 38% from symptomatic individuals, 10% from whether additional measures to reduce R0 (e.g.,
tification and contact tracing required to stop asymptomatic individuals (who never show symp- physical distancing) are required. The perform-
the epidemic. toms), and 6% from environmentally mediated ance of the app in scenarios with higher values
of R0 can be explored at https://bdi-pathogens.
shinyapps.io/covid-19-transmission-routes/.
Subject A has COVID-19 infection. No symptoms
CONCLUSION: Given the infectiousness of SARS-
CoV-2 and the high proportion of transmissions
Day 1 Home Train Work Home from presymptomatic individuals, control-
A G ling the epidemic by manual contact tracing
A A E F A is infeasible. The use of a contact-tracing app
Close that builds a memory of proximity contacts
B Nearby B and immediately notifies contacts of positive
C D H I cases would be sufficient to stop the epidemic
if used by enough people, in particular when
combined with other measures such as phys-
Day 2 90 Growth ical distancing. An intervention of this kind
rate raises ethical questions regarding access, trans-
quarantined
% contacts
70
A Report symptoms
A
50
0.10
0.05
0.00
parency, the protection and use of personal
Awakes with fever Request home test 30
Positive
0.05
0.10
data, and the sharing of knowledge with other
10 0.15
COVID-19 countries. Careful oversight by an inclusive ad-
▪
10 30 50 70 90
% cases isolated visory body is required.
Instant signal
C
Evidence exists for each of these routes of
oronavirus disease 2019 (COVID-19) is a coming year. The only approaches that we transmission: symptomatic (12), presymptomatic
rapidly spreading infectious disease caused currently have available to stop the epidemic (13), asymptomatic (14), and environmental (12).
by severe acute respiratory syndrome– are those of classical epidemic control, such as For prevention, the crucial information is the
coronavirus 2 (SARS-CoV-2), a betacoro- case isolation, contact tracing and quarantine, relative frequency of different routes of trans-
navirus, which has now established a physical distancing, and hygiene measures. mission so as to allocate finite resources be-
global pandemic. Around half of infected in- The basic reproduction number R0 is the tween different intervention strategies.
dividuals become reported cases, and with typical number of infections caused by an in- Li et al. (12) presented self-reported data on
intensive care support, the case fatality rate is dividual in the absence of widespread immu- exposure for the first 425 cases in Wuhan;
approximately 2% (1). More concerning is nity. Once immunity becomes widespread, the some of these recorded visits to the Huanan
that the proportion of cases requiring inten- effective reproduction number R will become Seafood Wholesale Market. The generalizabil-
sive care support is 5%, and patient manage- lower than R0; once R is less than 1, the pop- ity of transmission in that setting to other set-
ment is complicated by requirements to use ulation has herd immunity and the epidemic tings is highly uncertain, as this large-scale
personal protective equipment and engage in declines. Immunity can only safely be obtained event seeded the epidemic in the absence of
complex decontamination procedures (2). Fa- by vaccination. Here we use the term “sustained any knowledge about the disease. After closure
tality rates are likely to be higher in popula- epidemic suppression” to mean a reduction of of the Huanan Seafood Wholesale Market on
tions older than in Hubei province (such as in R to less than 1 by changing nonimmunological 1 January 2020, of 240 cases with no exposure to
Europe) and in low-income settings where crit- conditions of the population that affect trans- any wet market, 200 individuals (83%) reported
ical care facilities are lacking (3). The public mission, such as social contact patterns. no exposure to an individual with respiratory
health cost of failing to achieve sustained The biological details of transmission of beta- symptoms. Inaccurate recall may explain some
epidemic suppression has been estimated as coronaviruses are known in general terms: responses, including failing to notice symp-
250,000 lives lost in the next few months in These viruses can pass from one individual to toms that were exceptional at a time before
Great Britain, and 1.1 to 1.2 million in the another through exhaled droplets (5), aerosol awareness of the disease began, but it is un-
United States, even with the strongest possible (6), contamination of surfaces (7), and possibly likely to be as much as 83% of them, implying
mitigation action to “flatten the curve” (4). through fecal-oral contamination (8). Here, we that many individuals were infected by non-
Even modest outbreaks will see fatality rates compare different transmission routes that symptomatic individuals.
climb as hospital capacity is overwhelmed, and are more closely aligned to their implications The situation in Singapore at first glance
the indirect effects caused by compromised for prevention. Specifically, we propose four appears different, because unlike in Wuhan,
health care services have yet to be quantified. categories: many individuals were linked to an identified
No treatment is currently available, and vac- 1) Symptomatic transmission: direct trans- symptomatic source. However, the main dif-
cines are not expected to be sufficiently widely mission from a symptomatic individual, through ference is that the linkage was retrospective,
available to control the epidemic within the a contact that can be readily recalled by the such that linkage could be established even if
recipient. transmission occurred before a case was symp-
2) Presymptomatic transmission: direct tomatic. As of 5 March 2020, there were
1
Big Data Institute, Li Ka Shing Centre for Health Information transmission from an individual that occurs 117 cases, of which 25 were imported. By devoting
and Discovery, University of Oxford, Oxford, UK. 2Wellcome
before the source individual experiences no- considerable resources, including police inves-
Centre for Ethics and the Humanities and Ethox Centre,
University of Oxford, Oxford, UK. 3Oxford University NHS ticeable symptoms. (Note that this definition tigation, 75 of the 92 cases of local transmission
Trust, University of Oxford, Oxford, UK. 4Wellcome Centre for may be context-specific—for example, based were traced back to their presumed exposure,
Human Genetics, University of Oxford, Oxford, UK. on whether it is the source or the recipient either to a known case or to a location linked to
*These authors contributed equally to this work. †These authors
contributed equally to this work. who is asked whether the symptoms were spread (15). Linking cases via a location gen-
‡Corresponding author. Email: christophe.fraser@bdi.ox.ac.uk noticeable.) erally includes the possibility of environmentally
10
5
0.10
0
0.0 0.2 0.4 0.6 0.8 1.0
0.05
0 5 10 15 20
Fig. 1. Quantifying transmission timing in 40 transmission pairs. Left: Our inferred generation time distributions, in black; thicker lines denote higher support
for the corresponding functional form, with the Weibull distribution being the best fit. For comparison, we also include the serial interval distributions previously
reported by Li et al. (12) (light blue) and Nishiura et al. (22) (gray) and the incubation period distribution we used here, from Lauer et al. (21) (dashed red line). Right:
Distribution of the posterior probability of presymptomatic transmission for each of the 40 transmission pairs. The red vertical line shows the mean probability.
mediated transmission. Therefore, the large frac- estimates using imperfect data sources. We of 5.5 days, a median of 5.2 days, and a standard
tion of traceable transmission in Singapore does performed a detailed analysis of the timing of deviation of 2.1 days, and is included with our
not contradict the large fraction without symp- events in defined transmission pairs, derived results in Fig. 1.
tomatic exposure in Wuhan. However, it does the generation time distribution, and attributed The generation time is defined for source-
suggest that transmission from asymptomatic, a probability for each pair that transmission recipient transmission pairs as the time be-
rather than presymptomatic, individuals is not was presymptomatic. We also fit a mathe- tween the infection of the source and the
a major driver of spread. Although serological matical model of infectiousness through the infection of the recipient. Because time of in-
surveys are currently lacking, other lines of four routes discussed above over the course of fection is generally not known, the genera-
evidence suggest that the scenario of many infection. This allowed us to calculate R0, es- tion time is often approximated by the serial
asymptomatic infections for each sympto- timate the proportion of transmission from interval, which is defined as the time between
matic one is unlikely. Testing of 1286 close different routes, and make predictions about the onset of symptoms of the source and the
contacts of confirmed cases found that among whether contact tracing and isolation of known onset of symptoms of the recipient. We did
98 individuals testing positive, only 20% did cases would be enough to prevent spread of the not take that approach here; instead, we di-
not have symptoms at first clinical assessment epidemic. rectly estimated the generation time distribu-
(16). Among 634 individuals testing positive tion from 40 source-recipient pairs. These pairs
onboard the Diamond Princess cruise ship, Estimating SARS-CoV-2 transmission were manually selected according to high con-
the proportion of individuals without symp- parameters fidence of direct transmission inferred from
toms was found to be 52%; the proportion We used the exponential growth rate of the publicly available sources at the time of writing
who were asymptomatic (rather than pre- epidemic, r, from the early stages of the epi- (March 2020), and with known time of onset
symptomatic) was estimated as 18% (17). Test- demic in China, such that the effect of control of symptoms for both source and recipient. We
ing of passengers onboard six repatriation measures discussed later will be relative to combined dates of symptom onset with inter-
flights from Wuhan suggests that 40 to 50% of the early stages of an outbreak, exemplified vals of exposure for both source and recipient
infections were not identified as cases (4, 18). by baseline contact patterns and environmental (when available) and the above distribution of
Viral loads of mild cases have been found to be conditions in Hubei during that period. We incubation times, and from these we inferred
less than those of severe cases by a factor of 60 note that this assumption is implicit in many the distribution of generation times. The dis-
(19), and it is likely that the viral loads of estimates of R0. The epidemic doubling time tribution is best described by a Weibull distri-
asymptomatic individuals are lower still, with T2 is equal to loge(2)/r. We used the value r = bution (Akaike information criterion = 148.4,
possible implications for infectiousness and 0.14 per day (20), corresponding to a doubling versus 149.9 for gamma and 152.3 for lognormal
diagnosis. time of 5.0 days. distribution) with mean and median equal to
The most accurate and robust quantifica- The incubation period is defined as the time 5.0 days and standard deviation of 1.9 days,
tion of the relative frequency of routes of between infection and onset of symptoms. It is shown in the left panel of Fig. 1. We also show
transmission would be a well-designed pro- estimated as the time between exposure and the results of a sensitivity analysis to different
spective cohort study with detailed journal report of noticeable symptoms. We used the functional forms, as well as two previously
and phylogenetic investigations. However, incubation period distribution calculated in published serial interval distributions (12, 22).
the current global emergency requires timely (21). The distribution is lognormal with a mean Uncertainty in the fit of the distribution is
shown in fig. S1. Our distribution is robust The value does not depend significantly on the presymptomatic, symptomatic, or environmental—
with respect to the choice of transmission choice of prior (figs. S7 and S8), on the func- which we define to be RA, RP, RS, and RE, re-
events (fig. S2). Correlation in the uncertainty tional form of the distribution of generation spectively. The sum of these is R0.
between the inferred mean and standard times (figs. S9 and S10), or on the choice of The mathematical form for b(t) is
deviation is shown in fig. S3. The distribution transmission events (fig. S11).
of serial intervals for these pairs is shown in bðtÞ ¼ Pa xa bs ðtÞ þ ð1 Pa Þ½1 sðtÞbs ðtÞ þ
fig. S4. The countries from which the trans- A general mathematical model of ︸
asymptomatic ︸
presymptomatic
mission pair data were obtained are shown in SARS-CoV-2 infectiousness t
fig. S5. We used a mathematical formalism (23) that ð1 Pa ÞsðtÞbs ðtÞ þ ∫ bs ðt lÞEðlÞdl
︸
symptomatic l¼0
For each of the 40 transmission pairs, we describes how infectiousness varies as a func- ︸
environmental
estimated the posterior probability that trans- tion of time since infection, t, for a representa-
mission was presymptomatic (i.e., occurred tive cohort of infected individuals. This includes where bs(t) is the infectiousness of an in-
before the onset of symptoms in the infector). heterogeneity between individuals, and aver- dividual currently either symptomatic or pre-
We used a Bayesian approach with an un- ages over those individuals who infect few symptomatic, at age of infection t. Other
informative prior (i.e., transmission before or others and those who infect many. This aver- parameters in this expression, and those feed-
after symptoms equally likely). The 40 prob- age defines the function b(t). Infectiousness ing into it indirectly, are listed in Table 1. A
abilities inferred are shown in the right panel may change with t as a result of changing dis- detailed discussion of this expression, includ-
of Fig. 1; the mean probability is 37% [95% ease biology (notably viral shedding) and/or ing its assumptions, is found in the supple-
confidence interval (CI), 27.5 to 45%], which changing contact with others. The area under mentary materials. The priors chosen for
can be interpreted as the fraction of presymp- the b curve is the reproduction number R0. parameters not directly calculated from data
tomatic transmission events out of presymp- We decomposed b(t) into four contributions are shown in fig. S12. The infectiousness
tomatic plus symptomatic transmission events. that reflect our categorization above, namely model result using central values of all pa-
This mean probability over all pairs is close to asymptomatic transmission, presymptomatic rameters is shown in Fig. 2.
our prior, but the bimodal distribution of transmission, symptomatic transmission, and By drawing input parameter sets from the
individual probabilities in Fig. 1 shows that environmental transmission. The area under uncertainties shown in Table 1, we quantified
these are typically far from the prior (i.e., the the curve of one of these contributions gives the our uncertainty in R0 and its four contributions.
data are strongly informative). Uncertainty in mean total number of transmissions over one The resulting values are shown in Table 2, and
the value of this fraction is shown in fig. S6. full infection, via that route—asymptomatic, their underlying distributions are shown in
fig. S13. Two-dimensional distributions show- to 0.45) from our analysis of the 40 transmission An analytical mathematical framework for
ing correlations in uncertainty are shown in pairs but with overlapping uncertainty. the combined impact of these two interven-
fig. S14. The estimate of RP/(RP + RS) ob- We define q as the fraction of all trans- tions on an epidemic was previously derived
tained by this method is 0.55 (CI, 0.37 to 0.72), missions that do not come from direct contact in (9). In the supplementary materials, we
which is larger than the estimate of 0.37 (CI, 0.28 with a symptomatic individual: 1 – (RS/R0). solve these equations using our infectious-
This corresponds to the q of (9) in the case ness model above—that is, quantifying how
R0 = 2.0: where there is only presymptomatic and the SARS-CoV-2 epidemic is expected to be
Rp = 0.9 from pre−symptomatic symptomatic transmission. From Table 2, controlled (or not) by case isolation and the
Rs = 0.8 from symptomatic this is 0.62 (CI, 0.50 to 0.92). The value of q quarantining of traced contacts. Our results
Re = 0.2 from environmental observed during an exponentially growing are shown in Fig. 3. The black line shows the
Ra = 0.1 from asymptomatic
epidemic will be distorted when the timings threshold for epidemic control: Combined
0.4 of the different contributions to transmission success rates in the region to the upper right
occur at different stages of the infection, as a of the black line are sufficient to reduce R to
β(τ) (transmissions per day)
result of overrepresentation of recently infected less than 1. The x axis is the success rate of
0.3 individuals. This effect can be calculated through case isolation, which can be thought of either
use of the renewal equation, as was recently as the fraction of symptomatic individuals
done to calculate the distribution of time from isolated (assuming perfect prevention of trans-
0.2 onset of COVID-19 symptoms to recovery or mission upon isolation) or the degree to which
death (20) (see supplementary materials). We the infectiousness of symptomatic individuals
calculated the q that would be observed with is reduced (assuming all of them are isolated).
0.1 the early exponential growth seen in China as The y axis is the success rate of contact tracing;
Fig. 3. Quantifying intervention success. Heat map plot shows the exponential growth rate of the epidemic r as a function of the success rate of instant isolation
of symptomatic cases (x axis) and the success rate of instant contact tracing (y axis). Positive values of r (red) imply a growing epidemic; negative values of
r (green) imply a declining epidemic, with greater negative values implying faster decline. The solid black line shows r = 0 (i.e., the threshold for epidemic control).
The dashed lines show uncertainty in the threshold due to uncertainty in R0 (see figs. S15 to S17). The different panels show variation in the delay associated with
the intervention, from initiation of symptoms to case isolation and quarantine of contacts.
Apps with similar aims have been deployed the infected individual. Tests could be requested strong, well-established ethical arguments rec-
in China. Public health policy was implemented by symptomatic individuals through the app. ognizing the importance of achieving health
quarantined
% contacts
70
A Report symptoms
A
50
0.10
0.05
0.00
countries so far appears to be faster, implying
Awakes with fever Request home test 30
Positive
0.05
0.10
either shorter intervals between individuals
10 0.15
COVID-19 10 30 50 70 90 becoming infected and transmitting onward,
% cases isolated or a higher R0. We illustrate the latter effect
Instant signal
in figs. S18 and S19. If this is an accurate pic-
ture of viral spread in Europe and not an arti-
Advise on social distancing Automated test request fact of early growth, epidemic control with
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