Empirical evidence of asymptomatic transmission

Despite its perceived importance, ascertaining evidence for asymptomatic transmission for any disease remains a challenge. This has been especially true with B. pertussis, where identifying individuals asymptomatically infected has historically been difficult [12–14]. Perhaps the most compelling piece of evidence for asymptomatic transmission is the documented failure of cocooning to protect newborns [35, 36], which can only be parsimoniously explained by asymptomatic transmission [9]. Other empirical patterns are expected — in both incidence and genetic data — if asymptomatic transmission is occurring as a result of the aP vaccine preventing symptomatic disease, but failing to block transmission. Here we provide empirical observations, which are both consistent with and in total most parsimoniously accounted for by asymptomatic transmission.

Figure 2 shows a wavelet analysis of B. pertussis incidence in the UK in unvaccinated and under-vaccinated infants (<1 year old), both considered indicators of overall B. pertussis transmission in a population [37]. As wP vaccine coverage increases to greater than 90 % (from the early 1980s to the early 1990s) we see a disruption of the natural approximately 4-year periodicity of B. pertussis cases driven by susceptible turnover [38, 39]. However, the switch from wP to aP in the UK coincides with the return of cyclic patterns, which are similar to the approximately 4-year periodicity seen in the pre-vaccine era.

Fig. 2 Disruption of B. pertussis cycles by vaccination. Panel a shows the square root of B. pertussis cases in infants less than 1 year old in the United Kingdom from 1982 through 2013 (in black) and the percentage vaccine coverage over the same period (in blue). Vertical dashed line indicates the switch to an aP vaccination schedule. Panel b shows the standard wavelet spectrum of the incidence in panel a; panel c shows the Fourier spectrum of the incidence. As vaccination coverage increases (1985 through about 1991) we see a decrease in the power of cycles of approximately 4 years. We begin to see an increase in this power after the introduction of aP vaccination in 2004, suggesting transmission patterns similar to those observed in the pre-transmission-blocking vaccine era Full size image

A second line of evidence comes from changes in age-specific attack rates in the US and UK. Both countries switched to the aP vaccine; however, the US switch occurred seven years before the UK switch. Changes in age-specific attack rates are observed in both countries after switching to the aP vaccine, and appear similar when viewed as time since the switch to aP (Fig. 3). Another important facet of these data is that within both countries the rise in attack rates is synchronous across age groups. These two observations would be an expected consequence of asymptomatic transmission from aP vaccinated individuals as fully aP vaccinated individuals become old enough to attend school and become infected. These observations are challenging to explain with either waning immunity or pathogen evolution alone; for example, waning immunity should most often induce asynchrony in age-specific attack rates [22]. Increases in incidence could be explained by heterogeneous vaccine coverage or changing vaccine effectiveness, which we are assuming in switching from the wP to aP vaccine.

Fig. 3 Increase in B. pertussis incidence after switch to aP vaccination. Figure compares the incidence of B. pertussis after the switch to aP vaccination in the US (panel a) and the UK (panel b). Time since the switch is presented on the x-axis. Note the similarities in the timing of spikes in incidence after the switch to aP vaccination Full size image

Lastly, we find evidence consistent with asymptomatic transmission using the results of a transmission-oriented phylodynamic model [31] fit to 36 US B. pertussis genomes [30]. Asymptomatic transmission is expected to cause a mismatch between incidence estimated from case data and incidence reconstructed from genetic data. Intuitively, this happens because the population genetic variation of the bacteria is a function of the entire infected population size, while case data can only come from symptomatic individuals. This is true even if bacterial sequences are only collected from symptomatic individuals, assuming asymptomatic and symptomatic individuals are mixing with each other. The observed pattern can only be accounted for by asymptomatic transmission or underreporting. Because whooping cough reporting has increased in recent years [40, 41], asymptomatic transmission remains the only plausible explanation for the observed population genomic pattern.

Figure 4 shows the changes in sampling and rates since the mid-1960s for the US. We see an increase in the birth rate after the switch to aP, as expected given the rise in incidence; however, we see a decrease in the sampling rate after the switch to aP. This mismatch between the birth rate and sampling rate indicates that, despite increasing numbers of new B. pertussis cases, the fraction of cases identified decreases. Importantly, the estimated decrease in the sampling rate coincides with the time-window containing the largest number of sampled bacteria and in an era with the greatest accuracy in the laboratory methods used in diagnosing B. pertussis cases [42]. This finding is indicative of an increase in the overall genetic diversity of B. pertussis in the population after the US switched from the wP to the aP vaccine. Natural selection favoring a vaccine escape variant would be expected to reduce the genetic variation and increase the estimated sampling rate, as seen in Australia by Bart et al. [30]. Additionally, waning immunity could result in an increase in the genetic diversity of the bacterial population; however, without systematic underreporting it would not result in a lower estimated sampling rate. Again, we conclude that asymptomatic transmission remains the only parsimonious explanation for the observed phylodynamic patterns.

Fig. 4 Phylodynamic analyses. Figure shows the sampling rate and birth rate derived from the BEAST analysis for the 36 US B. pertussis genomes. Solid white lines with square boxes indicate the posterior median, with the shaded region indicating the 95 % highest posterior density. Darker colors are associated with regions of higher posterior density, with the shape representing the actual posterior density. Despite the birth rate remaining higher after the switch to aP, the sampling rate declines. This pattern would be expected with an increasing rate of asymptomatic transmission Full size image

Consequences of asymptomatic transmission: biased estimates of vaccine effectiveness

Historically, a key indicator of success for vaccination programs is a reduction in pathogen transmission in populations, as measured by the mean proportion of disease-free weeks [24, 43, 44]. Figure 5 presents the proportion of reported B. pertussis-free weeks (fade-outs, panel a) and mean duration of fade-outs (panel b) for the 50 US states in pre-vaccine (1920–1945) and post-vaccine (2006–2013) epochs. The pre-vaccine epoch clearly has fewer weeks with no reported B. pertussis cases than does the modern vaccine epoch. This has been widely interpreted as evidence for decreasing levels of B. pertussis transmission and some degree of herd immunity afforded by the vaccine [7, 15, 44]. However, if situational awareness is impaired by a vaccine that protects against symptomatic disease but does not block transmission, interpreting reported B. pertussis-free weeks can be misleading.

Fig. 5 Comparing disease-free weeks in pre- and post-vaccination scenarios. Panel a shows the proportion of disease-free weeks (fade-outs) per year for the 50 US states in the pre-vaccine (1920–1945, black points and line) and post-vaccine (2006–2013, blue points and line) eras. Lines indicate best-fit exponential curves. Panel b shows the mean duration of consecutive disease-free weeks in both eras Full size image

Figure 6 presents the results of stochastic simulations of the model across various population sizes. Comparing the observed symptomatic cases in the no vaccine and aP vaccine eras, we see results qualitatively similar to empirical data [44]: introduction of aP vaccine leads to a higher proportion of B. pertussis-free weeks across population sizes (Kolmogorov-Smirnov [KS] test, D = 0.46, p =1.2·10−9; panel a). However, examination of the asymptomatic population (the true burden) reveals many fewer weeks with no cases of B. pertussis (KS test, D = 0.53, p =1.2·10−12; panel b), which is in fact not different from the pre-vaccine era (KS test, D = 0.07, p = 0.97; panel c).

Fig. 6 Changes in transmission in pre- and post-vaccination scenarios? Figure shows the proportion of disease-free weeks (fade-outs) for various population sizes from the stochastic formulation of the model. Panel a compares the symptomatic cases in the aP vaccination era with those in the pre-vaccine era; panel b compares the symptomatic to asymptomatic cases in the vaccine era; panel c compares the asymptomatic cases in the post-vaccine era with those in the pre-vaccine era. These results demonstrate no changes in transmission due to vaccination. Parameters: birth rate (μ) = death rate (ν) = 1/75 years −1; recovery rates for symptomatic (γ s ) and asymptomatic (γ a ) = 14 days −1; probability of symptomatic infection (σ) = 0.25; transmissibility (β) is calculated per value of R 0 Full size image

Figure 7 demonstrates the percentage of the true infections observed at steady state ([Observed Incidence/Total Incidence-1]*100) as aP vaccination rate increases and the probability of symptomatic infection (σ) increases. We find that for realistic aP coverage rates (between 85 % and 95 %), the percentage of total cases expected to be observed is low (<15 %), and is highly dependent on the probability of an infection becoming symptomatic (a parameter that is generally not known). These results are likely to be conservative given the low, but unknown, diagnosis rate of asymptomatic infections and known underreporting of symptomatic infections in adults [45].

Fig. 7 How does an inefficient vaccine affect situational awareness? Figure shows the percent difference in observed infections (symptomatic) from true infections (symptomatic + asymptomatic) at steady state as aP vaccination rate increases and the probability of symptomatic infection increases. Shaded area indicates a range of reasonable aP vaccination rates. At current aP vaccination coverage levels, the majority of cases are asymptomatic and therefore undetected. See Additional file 1 for model details. Parameters: birth rate (μ) = death rate (ν) = 1/75 years −1; recovery rates for symptomatic (γ s ) and asymptomatic (γ a ) = 14 days −1; baseline wP vaccination rate = 0.9; transmissibility (β) is calculated such that R 0 =18. Note that previously published values of R 0 for pertussis range from 16–20 [71] to closer to 5 in some populations [72] Full size image

Consequences of asymptomatic transmission: increased B. pertussis incidence

Figure 8 illustrates the fold increase in observed symptomatic and unobserved asymptomatic infections after transitioning from a wP to an aP vaccine at equilibrium. This is calculated by dividing the number of symptomatic or asymptomatic cases with various levels of aP coverage (reported on the x-axis) and 0 % wP coverage by the number of cases with 90 % wP coverage and 0 % aP coverage. This is done to simulate the switch from wP to aP in the US and UK (going from high wP coverage to coverage with aP), and indicates that a change in vaccine could partially account for the rise in cases.

Fig. 8 Can an inefficient vaccine lead to increased transmission? Figure demonstrates the fold increase in observed symptomatic and unobserved asymptomatic infections after transitioning from a wP to an aP vaccine. This is calculated by dividing the number of symptomatic or asymptomatic cases with various levels of aP coverage (reported on the x-axis) and 0 % wP coverage by the number of cases with 90 % wP coverage and 0 % aP coverage. This was designed to simulate the switch from wP to aP in the US and UK (going from high wP coverage to coverage with aP). We see an increase in symptomatic cases across a large range of aP vaccination coverage levels. See Additional file 1 for model details. The gray band indicates the empirical 5.4-fold (95 % bootstrap confidence interval: 0.4–13.3) increase in cases in the US comparing 2012 to the years 1985 through 1995. The model recreates the observed increase in cases. Parameters: birth rate (μ) = death rate (ν) = 1/75 years −1; recovery rates for symptomatic (γ s ) and asymptomatic (γ a ) = 14 days −1; probability of symptomatic infection (σ) = 0.25; baseline wP vaccination rate = 0.9; transmissibility (β) is calculated such that R 0 =18 Full size image

As aP vaccination coverage increases, asymptomatic infections increase up to nearly 30-fold. We see a substantial increase in the observed numbers of symptomatic cases after wP vaccination is replaced by aP vaccination. At low to moderate levels of aP vaccination, there is a 5- to 15-fold increase in symptomatic cases. Only at extremely high levels of aP vaccination (>99 %) is there no change in symptomatic infections. This is in line with the observed rise in B. pertussis incidence: cases in 2012 were 5.4-fold (95 % bootstrap confidence interval: 0.4–13.3) higher than cases in years 1985 through 1995 ([46]). This result is similar to previous findings by van Boven et al. (2005) [47], who found that as wP vaccination coverage increased, primary infections (symptomatic) decreased, while secondary infections (subclinical, or asymptomatic) increased.

Effects of waning immunity to B. pertussis

It is clear that waning immunity plays a role in the epidemiology of B. pertussis, though estimates of the duration of protection to B. pertussis are highly varied [7, 15, 48]. Because the exclusion of waning immunity was a conservative modeling assumption, we focused our analysis on a model where immunity due to vaccination was lifelong. However, as Fig. 9 demonstrates, the inclusion of waning immunity increases symptomatic infections up to 12 % and asymptomatic infections up to 8 %. Importantly, waning immunity would not explain the failure of infant cocooning strategies, the synchrony in age-specific attack rates after the switch to the aP vaccine as presented above, or the observed B. pertussis genomic patterns.