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During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.

We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life. IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.