The world has been facing devastating public health and socioeconomic growth problems 1,2 in the ongoing COVID-19 pandemic. As of 29 September 2021, the pandemic has caused more than 230 million cases and over 4.7 million deaths across the globe 2. The pandemic hit China, Europe, North America first, then to rest part of the world, including the South and Latin America, Africa, and Western Pacific 3–5. Guyana and Suriname are the two countries in South America that have recorded the lowest COVI-19 morbidity and mortality cases. By September 29, 2021, the mortality cases in these two countries were 792 and 893, respectively 6,7. Brazil and Peru are two of the hardest hit countries in terms of either total death cases or death cases per capita in South American region, with the subsequent waves heavily driven by new variants, e.g. P.1 variant 2,8,9. By May 31, 2020, about 75.3% (4,196 of 5,570) of municipalities across all five administrative regions of Brazil reported COVID-19 cases, with 206,555 (40.2%) recovery and 29,314 fatal (17.5%) COVID-19 cases 10. By July 28, 2021, the total death cases in Brazil and Peru were 553,272 and 196,138, respectively. In particular, Peru government updated the reported COVID-19 data and reported that 0.5% of the population died of the disease. This makes Peru and Brazil the first and seventh most affected countries in the world in terms of deaths per capita rate (https://coronavirus.jhu.edu/data/mortality). The situation in the Amazon region was extremely severe with high infection attack rates 10,11.
The rate of COVID-19 vaccination is dramatically increasing worldwide, and the South American countries are scrambling to catch up by creating openings for vaccine diplomacy to reach the target for vaccinating at least 60-70% of the population. The region represents approximately 16% and 24% of the global cases and deaths by October 4, 2021. However, only about 7% of the worldwide vaccine doses have been administered in South America, according to a World Health Organization (WHO) report (2). By October 6, 2021, at least one dose of a COVID-19 vaccine has been administered to over 46% of the world population. And more than 6 billion doses of vaccines have been administered so far globally, with over 23.6 million administered each day (79), see Supplementary Table 1.
Although several effective vaccines are currently available 12, yet, the nonpharmaceutical Interventions (NPIs) measures and other factors 11,13 play significant roles in flattening the epidemic curves and help in reducing the mortality of COVID-19 across the globe. These measures include the changes in human behavior reaction, such as social distancing, usage of face masks11, possible pre-existing serological cross-reactivity against SARS-CoV-2 14, herd immunity 15, availability of medical resources 16, meteorological factors 17,18, reduction in global transportation 19,20, and usage of facemask 21. These factors have resulted in highly geographical heterogeneity for COVID-19 transmission. Moreover, the spatiotemporal variability of COVID-19 epidemics has being studied across different levels through various indices 22–24. Some countries in the South America, such as Chile, has greatly portrayed a positive impact following the NPIs and containment measures of COVID-19 implementation, which include localized lockdowns, banning of large gatherings, night-time curfew, and school and border closures 25. These control measures likely help in suppressing the mortality cases in these countries, as well as preventing the epidemic trend from exponential increase especially during the early epidemic growth phase, as has happened in many countries across the globe 25,26. The dynamic data dashboards (such as the Johns Hopkins data source of the IHME dashboard) of cases and deaths highlighted significant geographical variations in the epidemic patterns of COVID-19 worldwide 2,7,27. Since the beginning of the pandemic, there has been a growing body of modeling studies to estimate the COVID-19 morbidity and mortality (see, for instance 5,13,28−33 and the references therein). The transmissibility and severity of COVID-19 likely increased due to some devastating mutations, such as the D614G amino acid. These evolved mutations may result from natural selection, and the steady increase of the G614 variant at regional stages could designate a fitness gain to this variant 34,35. This mutation could increase the efficiency of the viral cell fusion to the host cell. Therefore, these variants have higher transmission rates 36.
Small changes in the genetic code of viruses occur during the transmission. These changes are called “mutations”. Most of the mutations are transient and some may persist in further transmission. The genetically modified versions of the virus with one or more new mutations from the original version is known as a “variant” 37. According to the COVID-19 Genomic UK Consortium (COG-U.K.) 38, there are thousands of COVID-19 mutations detected, but only few of them are likely to threaten public health 39–41. Studies show that most viruses’ mutations are not harmful and could not cause any severe infection 40,42.
The P.1 variant with N501Y, E484K, and K417T mutations was detected on January 9, 2021, by the Japanese authorities in the airport from four travellers returning from Brazil 43. Health authorities and epidemiologists are currently working to investigate whether this variant is more severe, besides its higher transmission rate, or could be a detriment to current therapies, diagnostics, or vaccines 37,40. The P.1 lineage has been linked with high severity and reinfection scenario 44–46. Previous report on SARS- CoV-2 genomic sequences highlighted that P.1 is more transmissible by up to 1.7 to 2.4- fold and that previous infection by non- P.1 gives about 54 - 79% of the protection against P.1 infection compared with non- P.1 lineages 47. Further information on the frequency and geographic distribution of the P1 lineage can be obtained at the Pango lineages website 43. The mutations of this variant include the N501Y, which has some similarities with the variants identified in South Africa and the United Kingdom (UK) 40. Currently, three COVID-19 variants are considered as the most dangerous variants that have raised public health concerns. These are lineage B.1.1.7 variant identified in the UK with N501Y mutation (which has now evolved to include the E484K mutation in UK) 48; lineage B. 1.351 identified in South Africa; and the lineage P.1 variant identified in Brazil 38,43. These variants are called “variants of concern (VOCs)” 40,49. Since they potentially reduce antibody neutralization and increase affinity for ACE2 receptors, which results in increased severity and could lead to death. They are also linked to higher viral transmissibility, increased disease severity, and possible evasion of immunity, potentially impacting reinfection and vaccine effectiveness 9,42,50.
The P.1 variant has been detected in over 70 countries 43, including the United States, Canada, Belgium, Turkey, India, Brazil and Peru as of September 29, 2021. It is currently storming across the South American region, giving rise to more severe cases and deaths even in places with high vaccination coverages. The resurgence of a second wave in the South America would be an important lesson for the rest of the world to tighten and improve the current control measures. Peru, a country of around 30 million people, is currently one of the world’s hardest-hit countries with a COVID-19 mortality rate of about 200,000 (which makes the death per capita the highest globally by June 1, 2021) 7,51,52, and a resurgence observed in April 2021 that can be declared as the most deadly month for Peru since the pandemic began 51,53,54. The flooded variant (P.1) were likely the cause of over 40% of infections in Lima 54. Health authorities are also currently investigating another strain called C.37, which first emerged in Peru in August 2020, and has raised public health concerns, especially among the neighbouring countries such as Argentina, Chile, and Ecuador 55. Colombia also experienced a similar scenario, where occupancy in intensive-care units hit 90% in the capital, Bogotá, and hospitals in other cities nearly overwhelmed 54. A number of cross-sectional studies suggest that P.1 variant is up to 2.2 times more contagious and as much as 61% more capable of reinfecting people than the original SARS-CoV-2 virus 40,54,56,57.
Many countries in South America that experienced sharp rise in cases and deaths have, for the most part, not done extensive genomic sequencing to determine how many people have been infected by P.1 9. Some reports show that the P.1 variant is the primary driver of the pandemic in the region 9. Furthermore, according to Buss et al., the basic reproduction number (\({R}_{0}\)) for Amazonas was estimated at 2.5-3.0 10,11, which shows the high transmission potential of the virus to spread and cause large outbreaks. Moreover, the expected infection attack rate (IAR, i.e., proportion of the total population being infected) in a homogeneously mixed population during an unmitigated epidemic was estimated at 89-94% 58. When the percentage of infected individuals exceeds the herd immunity threshold of 60-67% (which can be calculated using the relation
each infection generates less than one secondary case, thus incidence declines 59. Estimation of vital epidemiological quantities, such as the infection fatality rate and reproduction numbers, are essential measures to understand the epidemics' spread to guide public health practitioners and policymakers in planning an effective and sustainable policy for disease prevention and control.
This study aimed to investigate spatiotemporal variability and similarity of the COVID-19 epidemic, as well as estimate IAR, IFR and reproduction number in the 12 most-affected countries in South America (i.e., Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Guyana, Paraguay, Peru, Suriname, Uruguay, and Venezuela). Epidemiologically, the higher number of these parameters represents that the epidemic continues to spread. We also aimed to explore the transmission trends and identify the epidemic main drivers in the region (e.g., human behavioral changes, social distancing, and minimal or partial compliance of other NPIs measures by the general public). Further, we will compare the results of each scenario to reveal possible reasons for the current fluctuations (rise and fall) in mortality that would help to assess mitigation strategies, and inform public health responses and policymakers for effective control of the outbreak.