The introduction of VOC and VOI in Colombia changed the dynamics of COVID-19 infection and generated extra burdens in non-clinical measures to control the ongoing pandemic. A major consequence of lineages with an increased reproduction number was an extended wave of infections that lasted for more than 4.5 months. The emergence of these variants might have not been exclusively responsible for this extended wave, as the country also experienced several episodes of civil unrest during this timeframe. As a consequence, standard social distancing measures, quarantines and other non-clinical measures were difficult to implement, however, it motivated the intensity of the vaccination programs, which started mid-February, and was initially concentrated in high-risk groups (advanced age, healthcare workers, and people with comorbidities). With 34.43% of the population fully vaccinated in the Departamento de Antioquia, the lethality of SARS-CoV-2 decreased from 2.2% in non-vaccinated patients to 0.014% in vaccinated patients14. The surveillance of patients with a breakthrough infection offers a mechanism to understand the protective capacity of existing vaccines against emerging variants. A total of 96 patient samples were characterized to provide crucial information and to delineate possible strategies to protect patients at risk. We found that advanced age and comorbidities were highly correlated with fatal and ICU outcomes in patients with breakthrough infections (p < 0.01). Concomitant with the natural course of the disease, PAH and diabetes were dominant in these patients15,16. Other comorbidities, including thyroid disease, cancer, coronary disease, chronic obstructive pulmonary disease (COPD) and chronic kidney disease (CKD) were present in approximately 25% of the patients. Correlated with the advanced age of these patients, around 40% presented neurological or mental disorders. The average age monotonically increased from patients with mild disease, to critical disease with and without comorbidities to deceased patients with and without comorbidities.
The probability of a breakthrough infection after n days post-vaccination was calculated from the distribution of infections from all patients. We found no correlation between the probability of infection and the outcome of disease, indicated by the similarities between the distributions and the cumulative probabilities in patients with fatal outcome and survivors. For instance, the probability to get infected after vaccination within the first 30 days was 60% and 55% for deceased and survivors, respectively. On the other hand, significant differences are observed when the Pfizer-BioNTech and the Sinovac vaccines were compared. We found that the probability of a breakthrough infection with the Pfizer-BioNTech is higher within the first 60 days after vaccination, i.e. 90% of the patients were infected between day 0 and day 60. The Sinovac vaccine, however, resulted in a flatter distribution that persists for 120 days after vaccination. These observations may indicate that the timeline for protection is, on average, faster for the Pfizer-BioNTech biological than for the Sinovac vaccine.
Examination of the SARS-CoV-2 sequences revealed that the mu variant was present in most of the patients with breakthrough infections with fatal and ICU outcomes. The gamma and the B.1.625 variants were also detected in a considerable number of patients. The elevated participation of the mu variant in these patients is not surprising according to recent reports regarding its diminished neutralization capacity in isolates17 and pseudo-virus18. Accounting that we did not observe a dominant emerging variant, some of the breakthrough patients were also infected by persistent non-VOC/VOI variants (mostly of the B.1 group). Some substitutions of therapeutic and immunologic concern were prevalent in the majority of the variants, i.e. the E484K was observed in 90.1%, while the N501Y was present in 79.5%. Other substitutions, like the K417T and the L452R were present in 26.7% and 2.2% of the variants, respectively. Phylogenetic analysis determined the monophyletic nature of the VOC and VOI that circulate in Antioquia and deceased patients and ICU survivors are indicated in the corresponding clade of the variant (Figure 4). It also reinforces the neighboring similarities between the mu and the B.1.625 linage. In fact, in all sequenced mu and B.1.625 strains the substitutions T95I, E484K, D614G and D950N were present in the spike protein. Furthermore, a close relationship between mu and the other VOCs, such as delta, alpha, gamma, and lambda, was not observed. However, all share pivotal mutations in the Spike protein, such as E484K, D614G, P681H and D950N. These substitutions are of great interest because they have been related to higher rates of infection and the potential escape on the immune response19,20,21,22.
Fifteen of the patients with breakthrough infections were suspected of reinfection (Table S4). This classification was made merely on diagnosis, i.e., patients with two positive RT-PCR results with 90 days or more between. Up to September 2021, the OHGL and the PHLA have been unable to corroborate reinfection with sequencing. In most of the cases, one of the samples (either from the first or second infection) did not meet the technical requirements for an acceptable sequence coverage. However, RT-PCR protocols and reagents in Colombia are standardized and the chances are high that the reinfected classification is appropriate. Among these 15 patients, no fatal outcomes were observed and only one patient required an ICU hospitalization. The other patients had mild or asymptomatic disease. The identified viral linages were gamma (7), mu (4), B.1.625 (2) and parental (2).
Our observations empower the importance of the urgent efforts being taken globally to achieve herd immunity and vaccinate most of the global population. They also validate the effectiveness of the vaccines and highlights the need to stay vigilant and monitor viral evolution and its potential impact on vaccine efficacy. As many countries are preparing themselves for re-immunization campaigns, vaccine manufacturers might also consider updating their formulation to provide coverage against emerging variants. In addition, they leverage the necessity of universal vaccines against beta-coronaviruses and highlight the importance of active surveillance as a platform for pathogen discovery. More importantly, our observations show the importance of the ongoing race between immunization and the potential emergence of viral escape mutants. Our analysis similarly supports the need to maintain molecular testing (in symptomatic, asymptomatic, and vaccinated patients) and viral genome surveillance to establish databases for breakthrough infections.